Skip to content

Standards

data_standardortools_collection

collection concerns_data_topic has_relevant_organization purpose_detail is_open requires_registration url publication formal_specification id category name description subclass_of contributor_name contributor_github_name contributor_orcid contribution_date
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 The ACE file format is a specification for storing data about genomic contigs. The original ACE format was developed for use with Consed, a program for viewing, editing, and finishing DNA sequence assemblies. ACE files are generated by various assembly programs, including Phrap, CAP3, Newbler, Arachne, AMOS (sequence assembly) (more specifically Minimo) and Tigr Assembler v2. True False https://en.wikipedia.org/wiki/ACE_(genomic_file_format) https://web.archive.org/web/20100609072313/http://bcr.musc.edu/manuals/CONSED.txt B2AI_STANDARD:1 BiomedicalStandard .ACE format .ACE format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
policy B2AI_ORG:67 NIH has issued the Data Management and Sharing (DMS) policy (effective January 25, 2023) to promote the sharing of scientific data. Sharing scientific data accelerates biomedical research discovery, in part, by enabling validation of research results, providing accessibility to high-value datasets, and promoting data reuse for future research studies. Under the DMS policy, NIH expects that investigators and institutions do the following. Plan and budget for the managing and sharing of data, Submit a DMS plan for review when applying for funding, Comply with the approved DMS plan. True False https://sharing.nih.gov/data-management-and-sharing-policy/about-data-management-and-sharing-policy/data-management-and-sharing-policy-overview B2AI_STANDARD:2 BiomedicalStandard DMS 2023 NIH Data Management and Sharing Policy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:1 B2AI_ORG:93 The Access to Biological Collections Data (ABCD) Schema is an evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data). The ABCD Schema attempts to be comprehensive and highly structured, supporting data from a wide variety of databases. It is compatible with several existing data standards. Parallel structures exist so that either (or both) atomised data and free-text can be accommodated. Version 1.2 is currently in use with the GBIF (Global Biodiversity Information Facility) and BioCASE (Biological Collection Access Service for Europe) networks. Apart from the GBIF and BioCASE networks, the potential for the application of ABCD extends to internal networks, or in-house legacy data access (e.g. datasets from external sources that shall not be converted and integrated into an institution's own data, but be kept separately, though easily accessible). By defining relations between terms, ABCD is a step towards an ontology for biological collections. True False https://abcd.tdwg.org/ B2AI_STANDARD:3 BiomedicalStandard ABCD Access to Biological Collections Data Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 AGP format describes the assembly of a larger sequence object from smaller objects. The large object can be a contig, a scaffold (supercontig), or a chromosome. Each line (row) of the AGP file describes a different piece of the object, and has the column entries defined below. Extended comments follow. It does not serve for either a description of how sequence reads were assembled, or a description of the alignments between components used to construct a larger object. Not all of the information in proprietary assembly files can be represented in the AGP format. It is also not for recording the spans of features like repeats or genes. True False https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/ B2AI_STANDARD:4 BiomedicalStandard AGP AGP format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:3 B2AI_ORG:8 The Analytical Information Markup Language (AnIML) is the emerging ASTM XML standard for analytical chemistry data. It is currently in pre-release form. It is a combination of a highly flexible core schema that defines XML tagging for any kind of analytical information; A set of technique definition documents. These XML files, one per analytical technique, apply tight constraints to the flexible core and in turn are defined by the Technique Schema; Extensions to Technique Definitions are possible to accommodate vendor- and institution-specific data fields. Mission Statement Our goal is to serve as the open-source development platform for a new XML standard for Analytical Chemistry Information. The project is a collaborative effort between many groups and individuals and is sanctioned by the ASTM subcommittee E13.15. http://animl.cvs.sourceforge.net/viewvc/animl/schema/animl-core.xsd True False https://www.animl.org/ B2AI_STANDARD:5 BiomedicalStandard AnIML Analytical Information Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines Guidelines intended to improve the reporting of animal experiments. True False https://arriveguidelines.org/ doi:10.1371/journal.pbio.3000411 B2AI_STANDARD:6 BiomedicalStandard ARRIVE Animal Research Reporting In Vivo Experiments Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:37 B2AI_ORG:40 Provides a common means of electronically storing both the ECG wave form and associated annotations. True False https://www.hl7.org/implement/standards/product_brief.cfm?product_id=70 B2AI_STANDARD:7 BiomedicalStandard aECG Annotated ECG standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_TOPIC:15 B2AI_ORG:71 The Annotation and Image Markup project provides a standardized schema for capturing the results of medical imaging exams, primarily radiology, using controlled terminologies/ontologies. AIM captures results in terms of the region within an image in which areas of interest are located, the semantic descriptions of those regions, inferences about them, calculations on them, and quantitative features derived by computer programs run on them. AIM is interoperable with DICOM-SR and HL7-CDA, other standards for image metadata, but it provides unique advantages by providing an explicit semantic model of imaging results. True False https://github.com/NCIP/annotation-and-image-markup B2AI_STANDARD:8 BiomedicalStandard AIM Annotation and Image Markup schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_ORG:4 AI in healthcare; three major expressions of how trust is created and maintained - Human Trust, Technical Trust, and Regulatory Trust. False False https://shop.cta.tech/collections/standards/products/the-use-of-artificial-intelligence-in-healthcare-trustworthiness-cta-2090 B2AI_STANDARD:9 BiomedicalStandard ANSI/CTA-2090 ANSI/CTA Standard - The Use of Artificial Intelligence in Health Care Trustworthiness Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 A binary version of raw DNA sequence reads from Applied Biosystems sequencing analysis software. Also known as ABIF. False False https://projects.nfstc.org/workshops/resources/articles/ABIF_File_Format.pdf B2AI_STANDARD:10 BiomedicalStandard AB1 Applied Biosystems sequence read binary format file Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 A binary version of raw DNA sequence reads from Applied Biosystems sequencing analysis software. False False https://tools.thermofisher.com/content/sfs/manuals/4346366_DNA_Sequenc_Analysis_5_1_UG.pdf B2AI_STANDARD:11 BiomedicalStandard ABI Applied Biosystems sequence read binary format file Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 A binary alignment format used by the ARB package. True False http://www.arb-home.de/documentation.html doi:10.1093/nar/gkh293 B2AI_STANDARD:12 BiomedicalStandard ARB ARB software binary alignment format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:79 ADL is designed as an abstract human-readable and computer-processible syntax. ADL archetypes can be hand-edited using a normal text editor. The intended audience includes standards bodies producing health informatics standards; Academic groups using openEHR; The open source healthcare community; Solution vendors; Medical informaticians and clinicians interested in health information. True False https://specifications.openehr.org/releases/AM/latest/ADL1.4.html B2AI_STANDARD:13 BiomedicalStandard ADL Archetype Definition Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:4 B2AI_ORG:40 Specifications for sharing single sets of patient care plans. Based on FHIR R2. True False http://www.fhir.org/guides/argonaut/r2/StructureDefinition-argo-careplan.html B2AI_STANDARD:14 BiomedicalStandard StructureDefinition-argo-careplan Argonaut Data Query Implementation Guide Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema B2AI_TOPIC:16 The curation process is significantly slowed down by missing information in the articles analyzed. The identity of the clones used to generate ISH probes and the precise sequences tested in reporter assays constituted the most frequent omissions. To help authors ensure in the future that necessary information is present in their article, the Article Minimum Information Standard (AMIS) guidelines have been defined. The guideline describes the mandatory (and useful) information that should be mentioned in literature articles to facilitate the curation process. These guidelines extend the minimal information defined by the MISFISHIE format (Deutsch at al. 2008, Nature Biotechnology). True False doi:10.1038/npre.2010.5054.1 B2AI_STANDARD:15 BiomedicalStandard AMIS Article Minimum Information Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 A format for sequence alignments. True False https://genome.ucsc.edu/goldenPath/help/axt.html B2AI_STANDARD:16 BiomedicalStandard Axt Axt Alignment Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 A file containing the index for a Binary Alignment Map (BAM) file. True False https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/ B2AI_STANDARD:17 BiomedicalStandard BAI BAM indexing format file Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 The bedGraph format allows display of continuous-valued data in track format. True False http://genome.ucsc.edu/goldenPath/help/bedgraph.html B2AI_STANDARD:18 BiomedicalStandard BEDgraph BEDgraph format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 The bigBed format stores annotation items that can be either a simple or a linked collection of exons, much as BED files do. True False https://genome.ucsc.edu/goldenPath/help/bigBed.html B2AI_STANDARD:19 BiomedicalStandard bigBED Big Browser Extensible Data Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. True False https://genome.ucsc.edu/goldenPath/help/bigWig.html B2AI_STANDARD:20 BiomedicalStandard bigWig Big Wiggle Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 sequencing alignment True False https://samtools.github.io/hts-specs/ B2AI_STANDARD:21 BiomedicalStandard BAM/CRAM Binary Alignment Map / Compressed Reference-oriented Alignment Map Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 A BAM file (.bam) is the binary version of a SAM file. True False https://en.wikipedia.org/wiki/Binary_Alignment_Map https://samtools.github.io/hts-specs/SAMv1.pdf B2AI_STANDARD:22 BiomedicalStandard BAM Binary Alignment Map format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 A .2bit file stores multiple DNA sequences (up to 4 Gb total) in a compact randomly-accessible format. The file contains masking information as well as the DNA itself. True False http://genome.ucsc.edu/FAQ/FAQformat.html#format7 B2AI_STANDARD:23 BiomedicalStandard 2bit Binary sequence information Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 A binary version of the variant call format (VCF). True False https://samtools.github.io/bcftools/bcftools.html B2AI_STANDARD:24 BiomedicalStandard BCF Binary variant call format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:1 B2AI_ORG:44 Because of the many different ways to organize data, a major goal of the BioCompute project is to build and maintain a formal standard through recognized, accredited standards setting organizations like the Institute for Electrical and Electronics Engineers (IEEE) and the International Standards Organization (ISO). A formal, consensus-based standard builds predictability and even more stability into the way in which bioinformatic methods are communicated. The standard, officially known as 2791-2020, has two parts, the standards document and the schema, which is maintained in an open source repository. True False https://docs.biocomputeobject.org/user_guide/ doi:10.5731/pdajpst.2016.006734 B2AI_STANDARD:25 BiomedicalStandard BioCompute BioCompute Object standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:20 B2AI_ORG:70 A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. True False https://biolink.github.io/biolink-model/ doi:10.1111/cts.13302 B2AI_STANDARD:26 BiomedicalStandard Biolink Biolink Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage A language for representing scientific findings in the life sciences in a computable form. True False https://bel.bio/ https://language.bel.bio/ B2AI_STANDARD:27 BiomedicalStandard BEL Biological Expression Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:15 B2AI_ORG:31 B2AI_ORG:40 B2AI_ORG:71 The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 BRIDG Work Group, the US National Cancer Institute (NCI), and the US Food and Drug Administration (FDA). The goal of the BRIDG Model is to produce a shared view of the dynamic and static semantics for the domain of basic, pre-clinical, clinical, and translational research and its associated regulatory artifacts. True False https://bridgmodel.nci.nih.gov/ doi:10.1093/jamia/ocx004 https://github.com/CBIIT/bridg-model/ B2AI_STANDARD:28 BiomedicalStandard BRIDG Model Biomedical Research Integrated Domain Group Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:21 BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap. True False http://www.biopax.org/ doi:10.1038/nbt.1666 B2AI_STANDARD:29 BiomedicalStandard BioPAX BioPAX standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:1 B2AI_ORG:28 Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. True False https://bioschemas.org/ https://github.com/BioSchemas/specifications B2AI_STANDARD:30 BiomedicalStandard Bioschemas Bioschemas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:1 B2AI_ORG:72 Human biospecimens are subject to a number of different collection, processing, and storage factors that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research utilizing human tissues, it is critical that information regarding the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications around biospecimen-related research and help reassure patient contributors and the advocacy community that the contributions are valued and respected True False doi:10.1002/cncy.20147 B2AI_STANDARD:31 BiomedicalStandard BRISQ Biospecimen Reporting for Improved Study Quality Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:20 B2AI_ORG:28 Data model and exchange formats for basic bioinformatics types of data - sequences, alignments, feature records with associated data and metadata. True False http://bioxsd.org/ doi:10.1093/bioinformatics/btq391 https://github.com/bioxsd/bioxsd B2AI_STANDARD:32 BiomedicalStandard BioXSD BioXSD Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:22 The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to organize and describe data. This document defines the BIDS specification, which provides many details to help implement the standard. It includes the core specification as well as many extensions to specific brain imaging modalities, and increasingly also to other kinds of data. True False https://bids-specification.readthedocs.io/en/stable/ doi:10.1038/sdata.2016.44 https://github.com/bids-standard/bids-specification B2AI_STANDARD:33 BiomedicalStandard BIDS Brain Imaging Data Structure Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 The Brief Fatigue Inventory (BFI) is used to rapidly assess the severity and impact of cancer-related fatigue. An increasing focus on cancer-related fatigue emphasized the need for sensitive tools to assess this most frequently reported symptom. The six interference items correlate with standard quality-of-life measures. True False https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/symptom-research/symptom-assessment-tools/brief-fatigue-inventory.html doi:10.1002/(sici)1097-0142(19990301)85:5<1186::aid-cncr24>3.0.co;2-n http://www.npcrc.org/files/news/brief_fatigue_inventory.pdf B2AI_STANDARD:34 BiomedicalStandard BFI Brief Fatigue Inventory Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 The Brief Pain Inventory (BPI) rapidly assesses the severity of pain and its impact on functioning. The BPI has been translated into dozens of languages, and it is widely used in both research and clinical settings. True False https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/symptom-research/symptom-assessment-tools/brief-pain-inventory.html http://www.npcrc.org/files/news/briefpain_short.pdf B2AI_STANDARD:35 BiomedicalStandard BPI Brief Pain Inventory Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 BED (Browser Extensible Data) format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding. Lower-numbered fields must always be populated if higher-numbered fields are used. True False https://genome.ucsc.edu/FAQ/FAQformat.html#format1 https://github.com/samtools/hts-specs/blob/master/BEDv1.pdf B2AI_STANDARD:36 BiomedicalStandard BED Browser Extensible Data Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:10 A graphical notation that depicts the steps in a business process. BPMN depicts the end-to-end flow of a business process. The notation has been specifically designed to coordinate the sequence of processes and the messages that flow between different process participants in a related set of activities. True False https://www.omg.org/bpmn/index.htm B2AI_STANDARD:37 BiomedicalStandard BPMN Business Process Modeling Notation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:10 A common meta- model and notation for modeling and graphically expressing a case as well as an interchange format for exchanging case models among different tools. True False https://www.omg.org/cmmn/ B2AI_STANDARD:38 BiomedicalStandard CMMN Case Management Model and Notation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:4 The CARE guidelines provide a framework that supports transparency and accuracy in the publication of case reports and the reporting of information from patient encounters. True False https://www.care-statement.org/ B2AI_STANDARD:39 BiomedicalStandard CARE Case Report guidelines Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:15 The CDISC Case Report Tabulation Data Definition Specification (define.xml) Version 1.0 reflects changes from a comment period through the Health Level 7 (HL7) Regulated Clinical Research Information Management Technical Committee (RCRIM) in December 2003 (www.hl7.org) and CDISC's website in September 2004 as well as the work done by the define.xml team in conjunction with the CDISC ODM team to add functionality, features, and additional documentation. This document specifies the standard for providing Case Report Tabulations Data Definitions in an XML format for submission to regulatory authorities (e.g., FDA). The XML schema used to define the expected structure for these XML files is based on an extension to the CDISC Operational Data Model (ODM). The 1999 FDA electronic submission (eSub) guidance and the electronic Common Technical Document (eCTD) documents specify that a document describing the content and structure of the included data should be provided within a submission. This document is known as the Data Definition Document (e.g., define.pdf in the 1999 guidance). The Data Definition Document provides a list of the datasets included in the submission along with a detailed description of the contents of each dataset. To increase the level of automation and improve the efficiency of the Regulatory Review process, define.xml can be used to provide the Data Definition Document in a machine-readable format. True True https://www.cdisc.org/standards/data-exchange/define-xml B2AI_STANDARD:40 BiomedicalStandard Define CDISC Case Report Tabulation Data Definition Specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:15 Controlled terminology for data analysis and assessments. True False https://evs.nci.nih.gov/ftp1/CDISC/ADaM/ADaM%20Terminology.html https://evs.nci.nih.gov/ftp1/CDISC/ADaM/ B2AI_STANDARD:41 BiomedicalStandard CDISC ADaM CDISC Controlled Terminology for Analysis Dataset Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:15 Controlled terminology for biomedical protocols. True False https://evs.nci.nih.gov/ftp1/CDISC/Protocol/Protocol%20Terminology.html https://evs.nci.nih.gov/ftp1/CDISC/Protocol/ B2AI_STANDARD:42 BiomedicalStandard CDISC Protocol CDISC Controlled Terminology for Data Collection for Protocol Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_TOPIC:7 B2AI_ORG:15 Disease-specific metadata, examples and guidance on implementing CDISC standards. True False https://www.cdisc.org/standards/therapeutic-areas B2AI_STANDARD:43 BiomedicalStandard CDISC TAUGs CDISC Controlled Terminology for Therapeutic Area Standards Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:15 A standard for organizing and formatting data to streamline processes in collection, management, analysis and reporting. True False https://www.cdisc.org/standards/foundational/sdtm https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ B2AI_STANDARD:44 BiomedicalStandard SDTM CDISC Controlled Terminology Standards for Data Aggregation through Study Data Tabulation Model (including QRS, Medical Device and Pharmacogenomics Data) Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:15 A standard way to collect data consistently across studies and sponsors so that data collection formats and structures provide clear traceability of submission data into the Study Data Tabulation Model (SDTM). True False https://www.cdisc.org/standards/foundational/cdash https://evs.nci.nih.gov/ftp1/CDISC/SDTM/ B2AI_STANDARD:45 BiomedicalStandard CDASH CDISC Controlled Terminology Standards for Data Collection through Clinical Data Acquisition Standards Harmonization Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_ORG:15 CDISC Dataset-XML, which was released for comment under the name “StudyDataSet-XML” but was renamed to avoid confusion with the CDISC SDS team, is a new standard used to exchange study datasets in an XML format. The purpose of Dataset-XML is to support the interchange of tabular data for clinical research applications using ODM-based XML technologies. The Dataset-XML model is based on the CDISC Operational Data Model (ODM) standard and should follow the metadata structure defined in the CDISC Define-XML standard. Dataset-XML can represent any tabular dataset including SDTM, ADaM, SEND, or non-standard legacy datasets. Some noteworthy items relating to Dataset-XML v1.0 include alternative to SAS Version 5 Transport (XPT) format for datasets ODM-based model for representation of SEND, SDTM, ADaM or legacy datasets Capable of supporting CDISC regulatory data submissions Based on Define-XML v2 or v1 metadata, easy to reference Dataset-XML supports all language encodings supported by XML. True True https://www.cdisc.org/standards/data-exchange/dataset-xml B2AI_STANDARD:46 BiomedicalStandard CDISC Dataset CDISC Dataset-XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:4 B2AI_ORG:15 LAB provides a standard model for the acquisition and exchange of laboratory data, primarily between labs and sponsors or CROs. The LAB standard was specifically designed for the interchange of lab data acquired in clinical trials. True True https://www.cdisc.org/standards/data-exchange/lab B2AI_STANDARD:47 BiomedicalStandard CDISC LAB CDISC Laboratory Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:4 B2AI_ORG:15 standard for exchanging biomedical data True False https://www.cdisc.org/standards/data-exchange/odm B2AI_STANDARD:48 BiomedicalStandard CDISC ODM CDISC Operational Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:15 The CDISC Protocol Representation Model Version 1.0 (PRM V1.0) is intended for those involved in the planning and design of a research protocol. The model focuses on the characteristics of a study and the definition and association of activities within the protocols, including arms and epochs. PRM V1.0 also includes the definitions of the roles that participate in those activities. The scope of this model includes protocol content including Study Design, Eligibility Criteria, and the requirements from the ClinicalTrials.gov and World Health Organization (WHO) registries. The majority of business requirements were provided by subject matter experts in clinical trial protocols. PRM V1.0 is based on the BRIDG Release 3.0 Protocol Representation sub-domain. It includes all classes in the BRIDG Protocol Representation sub-domain plus some classes from other BRIDG sub-domains, generally classes required for ClinicalTrials.gov and the WHO registries. True True https://www.cdisc.org/standards/foundational/protocol B2AI_STANDARD:49 BiomedicalStandard CDISC PRM CDISC Protocol Representation Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:15 The CDISC SEND is intended to guide the organization, structure, and format of standard nonclinical tabulation datasets for interchange between organizations such as sponsors and CROs and for submission to the US Food and Drug Administration (FDA) True True https://www.cdisc.org/standards/foundational/send B2AI_STANDARD:50 BiomedicalStandard SEND CDISC Standard for the Exchange of Nonclinical Data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:15 The CDISC Study Design Model in XML (SDM-XML) version 1.0 allows organizations to provide rigorous, machine-readable, interchangeable descriptions of the designs of their clinical studies, including treatment plans, eligibility and times and events. As an extension to the existing CDISC Operational Data Model (ODM) specification, SDM-XML affords implementers the ease of leveraging existing ODM concepts and re-using existing ODM definitions. SDM-XML defines three key sub-modules – Structure, Workflow, and Timing – permitting various levels of detail in any representation of a clinical study’s design, while allowing a high degree of authoring flexibility. The specification document is available for download as a PDF file. A ZIP file containing the XML Schemas, several examples, and an SDM-XML element and attribute reference also is available. True True https://www.cdisc.org/standards/data-exchange/sdm-xml B2AI_STANDARD:51 BiomedicalStandard CDISC SDM CDISC Study Design Model in XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat Chado is a modular schema covering many aspects of biology, not just sequence data. Chado-XML has exactly the same scope as the Chado schema. True False doi:10.1093/bioinformatics/btm189 https://github.com/GMOD/Chado B2AI_STANDARD:52 BiomedicalStandard CHADO CHADO XML interchange Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. True False http://genome.ucsc.edu/goldenPath/help/chain.html B2AI_STANDARD:53 BiomedicalStandard chain Chain Format for pairwise alignment Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:27 The CARD file format is the standard means in CHARMM for providing a human readable and writable coordinate file. True False https://charmm-gui.org/charmmdoc/io.html B2AI_STANDARD:54 BiomedicalStandard CARD CHARMM Card File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:3 CML (Chemical Markup Language) is an XML language designed to hold most of the central concepts in chemistry. It was the first language to be developed and plays the same role for chemistry as MathML for mathematics and GML for geographical systems. CML covers most mainstream chemistry and especially molecules, reactions, solid-state, computation and spectroscopy. Since it has a special flexible approach to numeric science it also covers a very wide range of chemical properties, parameters and experimental observation. It is particularly concerned with the communication between machines and humans, and machines to machines. It has been heavily informed by the current chemical scholarly literature and chemical databases. XML is a mainstream approach providing semantics for science, such as MathML, SBML/BIOPAX (biology), GML and KML (geo) SVG (graphics) and NLM-DTD, ODT and OOXML (documents). CML provides support for most chemistry, especially molecules, compounds, reactions, spectra, crystals and computational chemistry (compchem). CML has been developed by Peter Murray-Rust and Henry Rzepa since 1995. It is the de facto XML for chemistry, accepted by publishers and with more than 1 million lines of Open Source code supporting it. CML can be validated and built into authoring tools (for example the Chemistry Add-in for Microsoft Word). A list of CML-compliant and CML-aware software can be found on the software page. The infrastructure includes legacy converters, dictionaries and conventions, Semantic Web and Linked Open Data. There are several versions of the CML schema. The most recent schema is schema 3. This essentially relaxes many of the constraints imposed in the previous stable release (schema 2.4), allowing users to put together the elements and attributes in a more flexible manner to fit the data that they want to represent more easily. True False https://www.xml-cml.org/ B2AI_STANDARD:55 BiomedicalStandard CML Chemical Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:4 B2AI_TOPIC:35 Provides a structure and format for exchanging information about the clinical effect of genetic variants, which retains the contextual and supporting information related to the interpretation of the variant. True False https://dataexchange.clinicalgenome.org/interpretation/ https://github.com/clingen-data-model/clingen-interpretation B2AI_STANDARD:56 BiomedicalStandard ClinGen Interpretation ClinGen Interpretation Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:16 Exchange of data about and produced by in vitro diagnostic tests. False True https://clsi.org/standards/products/automation-and-informatics/documents/auto16/ B2AI_STANDARD:57 BiomedicalStandard CLSI AUTO16 CLSI Next-Generation In Vitro Diagnostic Interface Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 B2AI_TOPIC:26 B2AI_TOPIC:28 Format for a multiple alignment of protein or DNA sequences. True False https://bioinfo.nhri.edu.tw/gcg/doc/11.0/clustalw+.html B2AI_STANDARD:58 BiomedicalStandard MSF CLUSTAL-W Alignment Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 B2AI_TOPIC:26 B2AI_TOPIC:28 Format for the tree (or “dendrogram”) used to guide the a multiple sequence alignment process. True False https://bioinfo.nhri.edu.tw/gcg/doc/11.0/clustalw+.html B2AI_STANDARD:59 BiomedicalStandard DND CLUSTAL-W Dendrogram Guide File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:9 ...we propose the CODE-EHR minimum standards framework to be used by researchers and clinicians to improve the design of studies and enhance transparency of study methods. The CODE-EHR framework aims to develop robust and effective utilisation of health-care data for research purposes. True False doi:10.1016/S2589-7500(22)00151-0 B2AI_STANDARD:60 BiomedicalStandard CODE-EHR CODE-EHR best-practice framework for the use of structured electronic health-care records in clinical research Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:15 The CXI format was created as common format for all the data in the Coherent X-ray Imaging Data Bank (CXIDB). Naturally its scope is all experimental data collected during Coherent X-ray Imaging experiments as well as all data generated during the analysis of the experimental data. True False https://www.cxidb.org/cxi.html B2AI_STANDARD:61 BiomedicalStandard CXI Coherent X-ray Imaging Data Bank format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:5 The CCPN Data Model for macromolecular NMR is intended to cover all data needed for macromolecular NMR spectroscopy from the initial experimental data to the final validation. It serves for exchange of data between programs, for storage, data harvesting, and database deposition. The data model proper is an abstract description of the relevant data and their relationships - it is implemented in the modeling language UML. From this CCPN autogenerates interfaces (APIs) for various languages, format description and I/O routines, and documentation. True False https://sites.google.com/site/ccpnwiki/home/documentation/ccpnmr-analysis/core-concepts/the-ccpn-data-model doi:10.1002/prot.20449 B2AI_STANDARD:62 BiomedicalStandard CCPN Collaborative Computing Project for the NMR community data model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:5 B2AI_ORG:68 Biomedical metadata. True False https://docs.nih-cfde.org/en/latest/c2m2/draft-C2M2_specification/ https://osf.io/bq6k9/ B2AI_STANDARD:63 BiomedicalStandard CFDE C2M2 Common Fund Data Ecosystem Crosscut Metadata Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines This dataset outlines a proposed set of core, minimal metadata elements that can be used to describe biomedical datasets, such as those resulting from research funded by the National Institutes of Health. It can inform efforts to better catalog or index such data to improve discoverability. The proposed metadata elements are based on an analysis of the metadata schemas used in a set of NIH-supported data sharing repositories. Common elements from these data repositories were identified, mapped to existing data-specific metadata standards from to existing multidisciplinary data repositories, DataCite and Dryad, and compared with metadata used in MEDLINE records to establish a sustainable and integrated metadata schema. True False https://figshare.com/articles/dataset/Common_Metadata_Elements_for_Cataloging_Biomedical_Datasets/1496573 https://figshare.com/articles/dataset/Common_Metadata_Elements_for_Cataloging_Biomedical_Datasets/1496573?file=3377663 B2AI_STANDARD:64 BiomedicalStandard Common Metadata Common Metadata Elements for Cataloging Biomedical Datasets Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_ORG:30 Developed in conjunction with the University of Chicago, the COST is a patient-reported outcome measure that describes the financial distress experienced by cancer patients. Since its initial publication, an additional item from the FACIT System has been included to screen for financial toxicity and to provide a good global summary item for financial toxicity. True False https://www.facit.org/measures/FACIT-COST doi:10.1002/cncr.30369 B2AI_STANDARD:65 BiomedicalStandard FACIT-COST COmprehensive Score for financial Toxicity A FACIT Measure of Financial Toxicity Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:40 A widely-used, XML-based format for electronic health records. Superceded by FHIR document standards. True True https://www.healthit.gov/topic/standards-technology/consolidated-cda-overview http://www.hl7.org/implement/standards/product_brief.cfm?product_id=492 B2AI_STANDARD:66 BiomedicalStandard C-CDA Consolidated Clinical Document Architecture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines A reporting guideline for qualitative research interviews and focus groups comprising 32 criteria, the list of which is available from http://www.cnfs.net/modules/module2/story_content/external_files/13_COREQ_checklist_000017.pdf True False doi:10.1093/intqhc/mzm042 http://www.cnfs.net/modules/module2/story_content/external_files/13_COREQ_checklist_000017.pdf B2AI_STANDARD:67 BiomedicalStandard COREQ Consolidated criteria for reporting qualitative research Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines The Consolidated Health Economic Evaluation Reporting Standards (CHEERS) statement is an attempt to consolidate and update previous health economic evaluation guidelines efforts into one current, useful reporting guidance. The primary audiences for the CHEERS statement are researchers reporting economic evaluations and the editors and peer reviewers assessing them for publication. True True doi:10.1136/bmj.f1049 https://www.ispor.org/heor-resources/good-practices/article/consolidated-health-economic-evaluation-reporting-standards-2022-cheers-2022-statement-updated-reporting-guidance-for-health-economic-evaluations B2AI_STANDARD:68 BiomedicalStandard CHEERS Consolidated Health Economic Evaluation Reporting Standards Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:4 CONSORT, which stands for Consolidated Standards of Reporting Trials, encompasses various initiatives developed by the CONSORT Group to alleviate the problems arising from inadequate reporting of randomized controlled trials (RCTs) True False https://www.consort-statement.org/ doi:10.1136/bmj.c332 B2AI_STANDARD:69 BiomedicalStandard CONSORT Consolidated Standards of Reporting Trials Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines A suite of open industry standards and specifications that provide several means to end-to-end interoperability between personal medical devices and health information systems. True False https://www.pchalliance.org/continua-design-guidelines https://members.pchalliance.org/document/dl/2148 B2AI_STANDARD:70 BiomedicalStandard Continua Continua Design Guidelines Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 HDF5-based critical care data exchange format which stores multiparametric data in an efficient, self-describing, hierarchical structure and supports real-time streaming and compression. In addition to cardiorespiratory and laboratory data, the format can, in future, accommodate other large datasets such as imaging and genomics. True False https://ccdef.org/ doi:10.1088/1361-6579/abfc9b https://github.com/autonlab/auviewer B2AI_STANDARD:71 BiomedicalStandard CCDEF Critical care data exchange format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 B2AI_ORG:34 A file format that can be used to store data in an encrypted and authenticated state. Existing applications can, with minimal modification, read and write data in the encrypted format. True False https://samtools.github.io/hts-specs/crypt4gh.pdf https://github.com/samtools/hts-specs B2AI_STANDARD:72 BiomedicalStandard Crypt4GH Crypt4GH format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:27 The acronym CIF is used both for the Crystallographic Information File, the data exchange standard file format of Hall, Allen & Brown (1991) (see Documentation), and for the Crystallographic Information Framework, a broader system of exchange protocols based on data dictionaries and relational rules expressible in different machine-readable manifestations, including, but not restricted to, Crystallographic Information File and XML. True False https://en.wikipedia.org/wiki/Crystallographic_Information_File B2AI_STANDARD:73 BiomedicalStandard CIF Crystallographic Information File format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:3 Code set used to bill outpatient & office procedures. False True https://www.ama-assn.org/amaone/cpt-current-procedural-terminology https://www.cms.gov/Medicare/Fraud-and-Abuse/PhysicianSelfReferral B2AI_STANDARD:74 BiomedicalStandard CPT Current Procedural Terminology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:23 The freely available international DDI standard describes data that result from observational methods in the social, behavioral, economic, and health sciences. DDI is used to document data in over 60 countries of the world. True False https://ddialliance.org/Specification/DDI-Lifecycle/3.3/ B2AI_STANDARD:75 BiomedicalStandard DDI-Lifecycle Data Documentation Initiative Lifecycle Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:58 A simple design pattern system that can easily be consumed, whatever your code base, for OWL ontologies. True False https://oboacademy.github.io/obook/tutorial/dosdp-template/ doi:10.1186/s13326-017-0126-0 https://github.com/INCATools/dead_simple_owl_design_patterns B2AI_STANDARD:76 BiomedicalStandard DOS-DP Dead simple owl design pattern exchange format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:10 A modeling language and notation for the precise specification of business decisions and business rules. True False https://www.omg.org/dmn/ B2AI_STANDARD:77 BiomedicalStandard DMN Decision Model and Notation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 When taxonomic descriptions are prepared for input to computer programs, the form of the coding is usually dictated by the requirements of a particular program or set of programs. This restricts the type of data that can be represented, and the number of other programs that can use the data. Even when working with a particular program, it is frequently necessary to set up different versions of the same basic data, for example, when using restricted sets of taxa or characters to make special-purpose keys. The potential advantages of automation, especially in connexion with large groups, cannot be realized if the data have to be restructured by hand for every operation. The DELTA (DEscription Language for TAxonomy) system was developed to overcome these problems. It was designed primarily for easy use by people rather than for convenience in computer programming, and is versatile enough to replace the written description as the primary means of recording data. Consequently, it can be used as a shorthand method of recording data, even if computer processing of the data is not envisaged. True False https://www.delta-intkey.com/ B2AI_STANDARD:78 BiomedicalStandard DELTA Description Language for Taxonomy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies a general model for the storage of Medical Imaging information on removable media. The purpose of this Part is to provide a framework allowing the interchange of various types of medical images and related information on a broad range of physical storage media. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part10.html B2AI_STANDARD:79 BiomedicalStandard DICOMDIR DICOM Part 10 Media Storage and File Format for Media Interchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies application specific subsets of the DICOM Standard to which an implementation may claim conformance. Such a conformance statement applies to the interoperable interchange of medical images and related information on storage media for specific clinical uses. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part11.html B2AI_STANDARD:80 BiomedicalStandard DICOM Part 11 DICOM Part 11 Media Storage Application Profiles Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard facilitates the interchange of information between digital imaging computer systems in medical environments. This interchange will enhance diagnostic imaging and potentially other clinical applications. The multi-part DICOM Standard defines the services and data that shall be supplied to achieve this interchange of information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part12.html B2AI_STANDARD:81 BiomedicalStandard DICOM Part 12 DICOM Part 12 Media Formats and Physical Media for Media Interchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 PS3.14 specifies a standardized Display Function for display of grayscale images. It provides examples of methods for measuring the Characteristic Curve of a particular Display System for the purpose of either altering the Display System to match the Grayscale Standard Display Function, or for measuring the conformance of a Display System to the Grayscale Standard Display Function. Display Systems include such things as monitors with their associated driving electronics and printers producing films that are placed on light-boxes or alternators. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part14.html B2AI_STANDARD:82 BiomedicalStandard DICOM Part 14 DICOM Part 14 Grayscale Standard Display Function Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies Security and System Management Profiles to which implementations may claim conformance. Security and System Management Profiles are defined by referencing externally developed standard protocols, such as TLS, ISCL, DHCP, and LDAP, with attention to their use in a system that uses DICOM Standard protocols for information interchange. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part15.html B2AI_STANDARD:83 BiomedicalStandard DICOM Part 15 DICOM Part 15 Security and System Management Profiles Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies the DICOM Content Mapping Resource (DCMR), which defines the Templates and Context Groups used elsewhere in the Standard. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part16.html B2AI_STANDARD:84 BiomedicalStandard DCMR DICOM Part 16 Content Mapping Resource Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard contains explanatory information in the form of Normative and Informative Annexes. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part17.html B2AI_STANDARD:85 BiomedicalStandard DICOM Part 17 DICOM Part 17 Explanatory Information Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 PS3.18 specifies web services (using the HTTP family of protocols) for managing and distributing DICOM (Digital Imaging and Communications in Medicine) Information Objects, such as medical images, annotations, reports, etc. to healthcare organizations, providers, and patients. The term DICOMweb is used to designate the RESTful Web Services described here. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part18.html B2AI_STANDARD:86 BiomedicalStandard DICOMweb DICOM Part 18 Web Services Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard defines an interface between two software applications. One application, the Hosting System, provides the second application with data, such as a set of images and related data. The second application, the Hosted Application, analyzes that data, potentially returning the results of that analysis, for example in the form of another set of images and/or structured reports, to the first application. Such an Application Program Interface (API) differs in scope from other portions of the DICOM Standard in that it standardizes the data interchange between software components on the same system, instead of data interchange between different systems. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part19.html B2AI_STANDARD:87 BiomedicalStandard DICOM Part 19 DICOM Part 19 Application Hosting Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 An implementation need not employ all the optional components of the DICOM Standard. After meeting the minimum general requirements, a conformant DICOM implementation may utilize whatever SOP Classes, communications protocols, Media Storage Application Profiles, optional (Type 3) Attributes, codes and controlled terminology, etc., needed to accomplish its designed task. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part02.html B2AI_STANDARD:88 BiomedicalStandard DICOM Part 2 DICOM Part 2 Conformance Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 B2AI_ORG:40 This Part of the DICOM Standard specifies templates for the encoding of imaging reports using the HL7 Clinical Document Architecture Release 2 (CDA R2, or simply CDA) Standard. Within this scope are clinical procedure reports for specialties that use imaging for screening, diagnostic, or therapeutic purposes. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part20.html B2AI_STANDARD:89 BiomedicalStandard DICOM Part 20 DICOM Part 20 Imaging Reports using HL7 Clinical Document Architecture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies the transformations between DICOM and other representations of the same information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part21.html B2AI_STANDARD:90 BiomedicalStandard DICOM Part 21 DICOM Part 21 Transformations between DICOM and other Representations Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies an SMPTE ST 2110-10 based service, relying on RTP, for the real-time transport of DICOM metadata. It provides a mechanism for the transport of DICOM metadata associated with a video or an audio flow based on the SMPTE ST 2110-20 and SMPTE ST 2110-30, respectively. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part22.html B2AI_STANDARD:91 BiomedicalStandard DICOM Part 22 DICOM Part 22 Real-Time Communication Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies the set of Information Object Definitions (IODs) that provide an abstract definition of real-world objects applicable to communication of digital medical information. For each IOD, this Part specifies any necessary information for the semantic description of the IOD, relationships to associated real-world objects relevant to the IOD, Attributes that describe the characteristics of the IOD. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part03.html B2AI_STANDARD:92 BiomedicalStandard DICOM Part 3 DICOM Part 3 Information Object Definitions Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies the set of Service Class Definitions that provide an abstract definition of real-world activities applicable to communication of digital medical information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part04.html B2AI_STANDARD:93 BiomedicalStandard DICOM Part 4 DICOM Part 4 Service Class Specifications Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 In this Part of the Standard the structure and encoding of the Data Set is specified. In the context of Application Entities communicating over a network, a Data Set is that portion of a DICOM Message that conveys information about real world objects being managed over the network. A Data Set may have other contexts in other applications of this Standard; e.g., in media exchange the Data Set translates to file content structure. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part05.html B2AI_STANDARD:94 BiomedicalStandard DICOM Part 5 DICOM Part 5 Data Structures and Encoding Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard is PS 3.6 of a multi-part standard produced to facilitate the interchange of information between digital imaging computer systems in medical environments. This interchange will enhance diagnostic imaging and potentially other clinical applications. The multi-part DICOM Standard covers the protocols and data that shall be supplied to achieve this interchange of information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part06.html B2AI_STANDARD:95 BiomedicalStandard DICOM Part 6 DICOM Part 6 Data Dictionary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 This Part of the DICOM Standard specifies the DICOM Message Service Element (DIMSE). The DIMSE defines an Application Service Element (both the service and protocol) used by peer DICOM Application Entities for the purpose of exchanging medical images and related information. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part07.html B2AI_STANDARD:96 BiomedicalStandard DIMSE DICOM Part 7 Message Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 The Communication Protocols specified in this Part of PS3 closely fit the ISO Open Systems Interconnection Basic Reference Model (ISO 7498-1, see Figure 1-1). They relate to the following layers - Physical, Data Link, Network, Transport, Session, Presentation and the Association Control Services (ACSE) of the Application layer. The communication protocols specified by this Part are general purpose communication protocols (TCP/IP) and not specific to this Standard. True False https://www.dicomstandard.org/current http://dicom.nema.org/medical/dicom/current/output/html/part08.html B2AI_STANDARD:97 BiomedicalStandard DICOM Part 8 DICOM Part 8 Network Communication Support for Message Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 Radiology imaging, including templates for narrative reports and machine-generated output. True False https://www.dicomstandard.org/ https://www.dicomstandard.org/current B2AI_STANDARD:98 BiomedicalStandard DICOM Digital Imaging And Communications In Medicine Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:26 Describes how to use SMTP, S/MIME, and X.509 certificates to securely transport health information over the Internet. True False https://wiki.directproject.org/w/images/e/e6/Applicability_Statement_for_Secure_Health_Transport_v1.2.pdf B2AI_STANDARD:99 BiomedicalStandard Direct Standard Direct Applicability Statement for Secure Health Transport Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:12 B2AI_TOPIC:13 Allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. True False doi:10.1186/1471-2105-2-7 https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-2-7/MediaObjects/12859_2001_8_MOESM1_ESM.pdf B2AI_STANDARD:100 BiomedicalStandard DAS Distributed Sequence Annotation System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage A metadata standard developed for the earth, environmental and ecological sciences. True False https://eml.ecoinformatics.org/ doi:10.5063/F11834T2 B2AI_STANDARD:101 BiomedicalStandard EML Ecological Metadata Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:93 This standard provides a system whereby uses of plants (in their cultural context) can be described, using standardised descriptors and terms, and attached to taxonomic data sets. It resulted from discussions at the International Working Group on Taxonomic Databases for Plant Sciences (TDWG) between 1989 and 1992. Users and potential users of the standard include economic botanists and ethnobotanists whose purpose is to record all known information about the uses of a taxon; educationalists, taxonomists, biochemists, anatomists etc. who wish to record plant use, often at a broad level; economic botany collection curators who need to describe accurately the uses and values of specimens in their collections; bibliographers who need to describe plant uses referred to in publications and to apply keywords consistently for ease of data retrieval. While this standard is still in use, it is no longer actively maintained (labelled as prior on the TDWG website). True False https://www.tdwg.org/standards/economic-botany/ B2AI_STANDARD:102 BiomedicalStandard EBDCS Economic Botany Data Collection Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:26 B2AI_ORG:61 A system for classification of enzymes that also serves as a basis for assigning code numbers to them. True False https://iubmb.qmul.ac.uk/enzyme/rules.html doi:10.1126/science.150.3697.719 B2AI_STANDARD:103 BiomedicalStandard EC Enzyme Commission Number Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 Instruments designed to assess (some of) the different aspects that define the QoL of (a specific group of) cancer patients. True True https://qol.eortc.org/questionnaires/ B2AI_STANDARD:104 BiomedicalStandard EORTC QLQ EORTC Quality of Life questionnaires Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:37 A simple digital format supporting the technical aspects of exchange and storage of polygraphic signals has been specified. Implementation of the format is simple and independent of hard- or software environments. It allows for any local montages, transducers, prefiltering, sampling frequencies, etc. At present, 7 laboratories in various countries have used the format for exchanging sleep-wake recordings. These exchanges have made it possible to create a common database of sleep records, to compare the analysis algorithms local to the various laboratories to each other by applying these algorithms to identical signals, and to set up a computer-aided interlaboratory evaluation of manual and automatic analysis methods. True False https://www.edfplus.info/ B2AI_STANDARD:105 BiomedicalStandard EDF European Data Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 A multidimensional set of minimal basic measurements suitable for all common dysphonias is proposed. It includes five different approaches - perception (grade, roughness, breathiness), videostroboscopy (closure, regularity, mucosal wave and symmetry), acoustics (jitter, shimmer, Fo-range and softest intensity), aerodynamics (phonation quotient), and subjective rating by the patient. True False doi:10.1007/s004050000299 B2AI_STANDARD:106 BiomedicalStandard ELS European Laryngological Society guidelines Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 The EQ-5D-3L descriptive system comprises the following five dimensions - mobility, self-care, usual activities, pain/discomfort and anxiety/depression. Each dimension has 3 levels - no problems, some problems, and extreme problems. The patient is asked to indicate his/her health state by ticking the box next to the most appropriate statement in each of the five dimensions. This decision results into a 1-digit number that expresses the level selected for that dimension. The digits for the five dimensions can be combined into a 5-digit number that describes the patient’s health state. True True https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/ B2AI_STANDARD:107 BiomedicalStandard EQ-5D-3L EuroQol Five Dimension Three Level descriptive system Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:5 B2AI_ORG:28 An online, open and live resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable; in one word FAIR. True False https://faircookbook.elixir-europe.org/ doi:10.5281/zenodo.7156792 B2AI_STANDARD:108 BiomedicalStandard FAIR Cookbook FAIR Cookbook Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 EHR exchange, EHRs True True https://www.hl7.org/fhir/overview.html B2AI_STANDARD:109 BiomedicalStandard FHIR Fast Healthcare Interoperability Resources Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:13 A text-based data format for nucleotide and amino acid sequences. True False https://en.wikipedia.org/wiki/FASTA_format B2AI_STANDARD:110 BiomedicalStandard FASTA FASTA Sequence Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:13 A text-based data format for nucleotide and amino acid sequences, with fields for quality scores. True False https://en.wikipedia.org/wiki/FASTQ_format B2AI_STANDARD:111 BiomedicalStandard FASTQ FASTQ Sequence and Sequence Quality Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
policy B2AI_ORG:39 The Federal Policy for the Protection of Human Subjects or the “Common Rule” was published in 1991 and codified in separate regulations by 15 Federal departments and agencies, as listed below. The HHS regulations, 45 CFR part 46, include four subparts - subpart A, also known as the Federal Policy or the “Common Rule”; subpart B, additional protections for pregnant women, human fetuses, and neonates; subpart C, additional protections for prisoners; and subpart D, additional protections for children. Each agency includes in its chapter of the Code of Federal Regulations [CFR] section numbers and language that are identical to those of the HHS codification at 45 CFR part 46, subpart A. For all participating departments and agencies the Common Rule outlines the basic provisions for IRBs, informed consent, and Assurances of Compliance. Human subject research conducted or supported by each federal department/agency is governed by the regulations of that department/agency. True False https://www.hhs.gov/ohrp/regulations-and-policy/regulations/common-rule/index.html B2AI_STANDARD:112 BiomedicalStandard Common Rule Federal Policy for the Protection of Human Subjects Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 The Common Data Models Harmonization (CDMH) FHIR Implementation Guide (IG) will focus on mapping and translating observational data extracted for Patient Centered Outcome Research (PCOR) and other purposes into FHIR format. Data is extracted from the different networks each of which may use a different data model for their data representation. The project focuses on the Common Data Models (CDMs) from the following four networks:Patient Centered Outcome Research Network (PCORNet), Informatics for Integrating Biology and Bedside (i2b2) Accrual to Clinical Trials (ACT), also known as i2b2/ACT., Observational Medical Outcomes Partnership (OMOP), and Food and Drug Administration’s Sentinel True False https://build.fhir.org/ig/HL7/cdmh/ https://build.fhir.org/ig/HL7/cdmh/profiles.html B2AI_STANDARD:113 BiomedicalStandard CDMH FHIR Common Data Models Harmonization Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_TOPIC:35 B2AI_ORG:40 A standardized suite of genomics operations in FHIR designed to support a wide range of clinical scenarios, such as variant discovery; clinical trial matching; hereditary condition and pharmacogenomic screening; and variant reanalysis. True False http://build.fhir.org/ig/HL7/genomics-reporting/operations.html doi:10.1093/jamia/ocac246 https://github.com/FHIR/genomics-operations B2AI_STANDARD:114 BiomedicalStandard Genomics Operations FHIR Genomics Operations Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 The Provenance resource tracks information about the activity that created, revised, deleted, or signed a version of a resource, describing the entities and agents involved. This information can be used to form assessments about its quality, reliability, trustworthiness, or to provide pointers for where to go to further investigate the origins of the resource and the information in it. True False https://www.hl7.org/fhir/provenance.html https://www.hl7.org/fhir/provenance-definitions.html B2AI_STANDARD:115 BiomedicalStandard Provenance FHIR Provenance Resource Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 The CodeSystem resource is used to declare the existence of and describe a code system or code system supplement and its key properties, and optionally define a part or all of its content. True False http://hl7.org/fhir/codesystem.html B2AI_STANDARD:116 BiomedicalStandard CodeSystem FHIR Resource CodeSystem Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 A statement of relationships from one set of concepts to one or more other concepts - either concepts in code systems, or data element/data element concepts, or classes in class models. True False http://hl7.org/fhir/conceptmap.html B2AI_STANDARD:117 BiomedicalStandard ConceptMap FHIR Resource ConceptMap Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 A curated namespace that issues unique symbols within that namespace for the identification of concepts, people, devices, etc. Represents a System used within the Identifier and Coding data types. True False http://hl7.org/fhir/namingsystem.html B2AI_STANDARD:118 BiomedicalStandard NamingSystem FHIR Resource NamingSystem Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 A TerminologyCapabilities resource documents a set of capabilities (behaviors) of a FHIR Terminology Server that may be used as a statement of actual server functionality or a statement of required or desired server implementation. True False http://hl7.org/fhir/terminologycapabilities.html B2AI_STANDARD:119 BiomedicalStandard TerminologyCapabilities FHIR Resource TerminologyCapabilities Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 A ValueSet resource instance specifies a set of codes drawn from one or more code systems, intended for use in a particular context. Value sets link between CodeSystem definitions and their use in coded elements. True False http://hl7.org/fhir/valueset.html B2AI_STANDARD:120 BiomedicalStandard ValueSet FHIR Resource ValueSet Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:2 The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. In 1984, the first Flow Cytometry Standard format for data files was adopted as FCS 1.0. This standard was modified in 1990 as FCS 2.0 and again in 1997 as FCS 3.0. We report here on the next generation Flow Cytometry Standard data file format. FCS 3.1 is a minor revision based on suggested improvements from the community. The unchanged goal of the Standard is to provide a uniform file format that allows files created by one type of acquisition hardware and software to be analyzed by any other type. True False https://en.wikipedia.org/wiki/Flow_Cytometry_Standard doi:10.1002/cyto.a.20825 B2AI_STANDARD:121 BiomedicalStandard FCS Flow Cytometry Standard format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:5 B2AI_ORG:32 The Data Citation Principles cover the purpose, function and attributes of citations. These principles recognize the dual necessity of creating citation practices that are both human understandable and machine-actionable. True False https://force11.org/info/joint-declaration-of-data-citation-principles-final/ B2AI_STANDARD:122 BiomedicalStandard FORCE11 DC FORCE11 Data Citation Principles Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 B2AI_ORG:30 The Functional Assessment of Cancer Therapy - General (FACT-G) is a 27-item questionnaire designed to measure four domains of HRQOL in cancer patients - Physical, social, emotional, and functional well-being. Original development and validation involved 854 patients with cancer and 15 oncology specialists. An initial pool of 370 overlapping items for breast, lung, and colorectal cancer was generated by open-ended interviews with patients experienced with the symptoms of cancer and oncology professionals. Using preselected criteria, items were reduced to a 38-item general version. Factor and scaling analyses of these 38 items on 545 patients with mixed cancer diagnoses resulted in the 27-item FACT-General (FACT-G). Coefficients of reliability and validity were uniformly high. The scale's ability to discriminate patients on the basis of stage of disease, performance status rating (PSR), and hospitalization status supports its sensitivity. It has also demonstrated sensitivity to change over time. True False https://www.facit.org/measures/FACT-G B2AI_STANDARD:123 BiomedicalStandard FACT-G Functional Assessment of Cancer Therapy - General Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 B2AI_ORG:30 Functional Assessment of Chronic Illness Therapy - Dyspnea-10 item True False https://www.facit.org/measures/facit-dyspnea doi:10.1016/j.jval.2010.06.001 B2AI_STANDARD:124 BiomedicalStandard FACIT-Dyspnea Functional Assessment of Chronic Illness Therapy - Dyspnea Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 B2AI_ORG:30 The Functional Assessment of Non-Life Threatening Conditions (FANLTC) is a 26-item version of the FACT-G designed to be administered to patients with non-life threatening conditions. The item from the FACT-G making reference to anxiety about death has been removed, and the instrument measures four domains of HRQOL - Physical, social/family, emotional and functional well-being. True False https://www.facit.org/measures/FANLTC B2AI_STANDARD:125 BiomedicalStandard FANLTC Functional Assessment of Non-Life Threatening Conditions Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_TOPIC:35 WGS data processing standards that allow different groups to produce functionally equivalent (FE) results, yet still innovate on data processing pipelines. True False doi:10.1038/s41467-018-06159-4 https://github.com/CCDG/Pipeline-Standardization B2AI_STANDARD:126 BiomedicalStandard Regier2018 Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:13 Functional genomics experiments present many challenges in data archiving, sharing and querying. As the size and complexity of data generated from such experiments grows, so does the requirement for standard data formats. To address these needs, the Functional Genomics Experiment [Object Model / Markup-Language] (FuGE-OM, FuGE-ML) has been created to facilitate the development of data standards.FuGE is a model of the shared components in different functional genomics domains. FuGE facilitates the development of data standards in functional genomics in two ways. 1. FuGE provides a model of common components in functional genomics investigations, such as materials, data, protocols, equipment and software. These models can be extended to develop modular data formats with consistent structure. 2. FuGE provides a framework for capturing complete laboratory workflows, enabling the integration of pre-existing data formats. In this context, FuGE allows the capture of additional metadata that gives formats a context within the complete workflow. FuGE is available as a UML model and an XML Schema True False https://fuge.sourceforge.net/index.php B2AI_STANDARD:127 BiomedicalStandard FuGE-ML Functional Genomics Experiment Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:13 FuGEFlow represents a collaborative effort to develop of flow cytometry experimental workflow description based on the FuGE model. The Functional Genomics Experiment data model (FuGE) describes common aspects of comprehensive, high-throughput experiments. FuGE is an extendable model that provides a basis for creation of new technology-specific data formats, such as FuGEFlow for flow cytometry. True False doi:10.1186/1471-2105-10-184 B2AI_STANDARD:128 BiomedicalStandard FuGEFlow Functional Genomics Experiment model for flow cytometry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 A method to measure performance status with a high percentage of agreement between observers. True False doi:10.1186/s12885-015-1526-0 B2AI_STANDARD:129 BiomedicalStandard FAF Functionality Assessment Flowchart Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_ORG:34 The metadata model for GA4GH, an international coalition of both public and private interested parties, formed to enable the sharing of genomic and clinical data. True False https://github.com/ga4gh-metadata/metadata-schemas B2AI_STANDARD:130 BiomedicalStandard GA4GH GA4GH metadata model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 The Gating-ML specification represents a proposal on how to form unambiguous XML-based gate definitions that may be used independently as well as included as one of the components of ACS. Such a description of gates can facilitate the interchange and validation of data between different software packages with the potential of significant increase of hardware and software interoperability. The specification supports rectangular gates in n dimensions (i.e., from one-dimensional range gates up to n-dimensional hyper-rectangular regions), polygon gates in two (and more) dimensions, ellipsoid gates in n dimensions, decision tree structures, and Boolean collections of any of the types of gates. Gates can be uniquely identified and may be ordered into a hierarchical structure to describe a gating strategy. Gates may be applied on parameters as in list mode data files (e.g., FCS files) or on transformed parameters as described by any explicit parameter transformation. Therefore, since version 1.5, parameter transformation and compensation description are included as part of the Gating-ML specification. True False http://flowcyt.sourceforge.net/gating/ B2AI_STANDARD:131 BiomedicalStandard Gating-ML Gating-ML specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:26 B2AI_TOPIC:33 A text-based data format for nucleotide and amino acid sequences, with fields for a variety of sequence metadata. True False https://en.wikipedia.org/wiki/GenBank B2AI_STANDARD:132 BiomedicalStandard GB GenBank Sequence Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 genePred is a table format commonly used for gene prediction. True False https://genome.ucsc.edu/FAQ/FAQformat.html#format9 B2AI_STANDARD:133 BiomedicalStandard GenePred Gene Prediction File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:26 B2AI_TOPIC:33 The Gene Ontology project provides annotations describing attributes of biological entities such as genes and gene products. The Gene Ontology has historically provided annotations via Gene Association Format (GAF), including GAF-1 and GAF-2. Ontologies are distributed separately, using an OWL serialization or OBO format. The use of GAF has some drawbacks. Combined representation of gene/gene product data and annotations leads to redundancy/repetition No way to represent gene/gene product metadata for unannotated genes Requirement to maintain backward compatibility makes it harder to introduce enhancements such as use of an ontology for evidence types GAF formats will continue to be supported, but the need for a way to represent genes/gene products separately from annotations, as well as the need to use the evidence ontology has lead to the creation of the GPAD (Gene Product Annotation Data) and GPI (Gene Product Information) formats, defined here. Whilst GPAD and GPI have been defined for use within the Gene Ontology Consortium for GO annotation, this specification is designed to be reusable for analagous ontology-based annotation - for example, gene phenotype annotation. True False http://geneontology.org/docs/gene-product-association-data-gpad-format/ B2AI_STANDARD:134 BiomedicalStandard GPAD Gene Product Annotation Data format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 GTF (Gene Transfer Format, GTF2.2) is an extension to, and backward compatible with, GFF2. The first eight GTF fields are the same as GFF. The feature field is the same as GFF, with the exception that it also includes the following optional values, 5UTR, 3UTR, inter, inter_CNS, and intron_CNS. True False http://genome.ucsc.edu/FAQ/FAQformat.html#format4 B2AI_STANDARD:135 BiomedicalStandard GTF Gene Transfer Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 The GMX and GMT file formats are tab-delimited file formats that describe gene sets. True False https://www.genepattern.org/file-formats-guide#GMT B2AI_STANDARD:136 BiomedicalStandard GMT GenePattern GeneSet Table Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:13 Genome feature annotation file format. True False https://github.com/The-Sequence-Ontology/Specifications B2AI_STANDARD:137 BiomedicalStandard GFF General Feature Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:13 The Gene Ontology Consortium stores annotation data, the representation of gene product attributes using GO terms, in standardized tab-delimited text files. Each line in the file represents a single association between a gene product and a GO term, with an evidence code and the reference to support the link. True False http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/ B2AI_STANDARD:138 BiomedicalStandard GAF Genome Annotation File Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_ORG:34 Beacon v2 is a protocol/specification established by the Global Alliance for Genomics and Health initiative (GA4GH) that defines an open standard for federated discovery of genomic (and phenoclinic) data in biomedical research and clinical applications. True False http://docs.genomebeacons.org/ doi:10.1002/humu.24369 https://github.com/ga4gh-beacon/beacon-v2 B2AI_STANDARD:139 BiomedicalStandard Beacon Genome Beacons Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:13 B2AI_TOPIC:35 The Genome Variation Format (GVF) is a very simple file format for describing sequence alteration features at nucleotide resolution relative to a reference genome. True False https://github.com/The-Sequence-Ontology/Specifications/blob/master/gvf.md B2AI_STANDARD:140 BiomedicalStandard GVF Genome Variation Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:13 The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that is a reference implementation the Minimum Information about a Genome Sequence (MIGS/MIMS/MIMARKS), and the extensions the Minimum Information about a Metagenome Sequence (MIMS) and Minimum Information about a MARKer gene Sequence (MIMARKS). True False doi:10.1089/omi.2008.0A10 B2AI_STANDARD:141 BiomedicalStandard GCDML Genomic Contextual Data Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_ORG:93 In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. True False https://www.tdwg.org/standards/ggbn/ doi:10.1093/database/baw125 B2AI_STANDARD:142 BiomedicalStandard GGBN Global Genome Biodiversity Network Data Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:20 GlycoCT format is devised to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules to generate a consistent, machine-readable nomenclature, based on a connection table approach, instead of a linear encoding scheme. The format uses a block concept to describe frequently occurring special features of carbohydrate sequences like repeating units. It exists in two variants, a condensed form and a more verbose XML syntax. Sorting rules assure the uniqueness of the condensed form, thus making it suitable as a direct primary key for database applications, which rely on unique identifiers. GlycoCT encompasses the capabilities of the heterogeneous landscape of digital encoding schemata in glycomics and is thus a step forward on the way to a unified and broadly accepted sequence format in glycobioinformatics. True False doi:10.1016/j.carres.2008.03.011 https://github.com/glycoinfo/GlycoCT B2AI_STANDARD:143 BiomedicalStandard GlycoCT GlycoCT encoding scheme Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:13 GTrack is a tabular format that was developed as part of the Genomic HyperBrowser system to provide a uniform representation of most types of genomic datasets. GTrack is able to replace common formats such as WIG, GFF, BED, FASTA, in addition to represent chromatin capture datasets, such as Hi-C and ChIA-PET. True False doi:10.1186/1471-2105-12-494 https://github.com/gtrack/gtrack B2AI_STANDARD:144 BiomedicalStandard GTrack GTrack genomic data format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:20 B2AI_ORG:93 GUIDs are Globally Unique Identifiers which should be referentially consistent and resolvable in order to support tests of uniqueness and the acquisition of associated metadata. Further, permanent and robust resolution services need to be available. The TDWG Globally Unique Identifiers Task Group (TDWG GUID), after meeting twice in 2006, recommended the use of the Life Sciences Identifiers (LSID) to uniquely identify shared data objects in the biodiversity domain. True False http://www.tdwg.org/standards/150 https://github.com/tdwg/guid-as B2AI_STANDARD:145 BiomedicalStandard GUID-AS GUID and Life Sciences Identifiers Applicability Statements Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema B2AI_TOPIC:4 A minimum information checklist creating a consistent framework to transparently report the purpose, methods and results of the therapeutic experiments True False doi:10.1186/1756-0500-5-10 B2AI_STANDARD:146 BiomedicalStandard GIATE Guidelines for Information About Therapy Experiments Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
policy B2AI_TOPIC:9 B2AI_ORG:39 The Health Insurance Portability and Accountability Act of 1996 (HIPAA) is a federal law that required the creation of national standards to protect sensitive patient health information from being disclosed without the patient’s consent or knowledge. The US Department of Health and Human Services (HHS) issued the HIPAA Privacy Rule to implement the requirements of HIPAA. The HIPAA Security Rule protects a subset of information covered by the Privacy Rule. True False https://www.hhs.gov/hipaa/index.html https://aspe.hhs.gov/reports/health-insurance-portability-accountability-act-1996 B2AI_STANDARD:147 BiomedicalStandard HIPAA Health Insurance Portability and Accountability Act of 1996 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:17 Code set for items and supplies and non-physician services not covered by the American Medical Association's Current Procedural Terminology-4 (CPT-4) codes; Medicare, Medicaid, and private health insurers use HCPCS procedure and modifier codes for claims processing. True False https://www.cms.gov/Medicare/Coding/HCPCSReleaseCodeSets B2AI_STANDARD:148 BiomedicalStandard HCPCS Healthcare Common Procedure Coding System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:93 The 'Herbarium Information Standards and Protocols for Interchange of Data' (HISPID) is a standard format for the interchange of electronic herbarium specimen information. HISPID has been developed by a committee of representatives from all major Australian herbaria. This interchange standard was first published in 1989, with a revised version published in 1993./nHISPID3 (version 3) is an accession-based interchange standard. Although many fields refer to attributes of the taxon they should be construed as applying to the specimen represented by the record, not to the taxon per se. The interchange of taxonomic, nomenclatural, bibliographic, typification, rare and endangered plant conservation, and other related information is not dealt with in this standard, unless it specifically refers to a particular accession (record). While this standard is still in use, it is no longer actively maintained (labelled as prior on the TDWG website). True False https://www.tdwg.org/standards/hispid3/ B2AI_STANDARD:149 BiomedicalStandard HISPID3 Herbarium Information Standards and Protocols for Interchange of Data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage Histoimmunogenetics Markup Language (HML) is intended as a potentially general-purpose XML format for exchanging genetic typing data. This format supports NGS based genotyping methods, raw sequence reads, registered methodologies, reference data, complete reporting of allele and genotype ambiguity and MIRING compliant reporting. True False https://bioinformatics.bethematchclinical.org/hla-resources/hml/ https://github.com/nmdp-bioinformatics/hml B2AI_STANDARD:150 BiomedicalStandard HML Histoimmunogenetics Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 The Arden Syntax for Medical Logic Systems Version 2.10 is the latest version of a formalism for clinical knowledge representation that can be used by clinicians, knowledge engineers, administrators and others to implement clinical decision support (CDS) solutions to help improve the quality and safety of care. Arden Syntax can be used to create a knowledge base for CDS systems that, when coupled with patient data, can generate patient-specific CDS interventions for improving patient care. The key change in Version 2.10 over Version 2.9 is inclusion of a normative XML representation for Arden Syntax. This was done because the use of XML facilitates the development of tools such as syntax checkers and editors that can help increase the correctness of executable knowledge modules, and this in turn will foster the augmentation of the development and production environments for Arden, thereby increasing its utility. True True http://www.hl7.org/implement/standards/product_brief.cfm?product_id=372 doi:10.1016/j.jbi.2012.02.001 https://www.hl7.org/login/index.cfm?next=/implement/standards/product_brief.cfm?product_id=2 B2AI_STANDARD:151 BiomedicalStandard Arden HL7 Arden Syntax Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:40 Guidance and templates for basic provenance information about clinical (and other care related information), who created it, when was it created, where was it created, how it was created, and why it was created. True True http://www.hl7.org/implement/standards/product_brief.cfm?product_id=420 B2AI_STANDARD:152 BiomedicalStandard HL7 CDA Data Provenance HL7 Clinical Document Architecture Implementation Guide - Data Provenance Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:40 Resource for findings and interpretation of diagnostic tests performed on patients, groups of patients, devices, and locations, and/or specimens derived from these. The report includes clinical context such as requesting and provider information, and some mix of atomic results, images, textual and coded interpretations, and formatted representation of diagnostic reports. True False http://hl7.org/fhir/diagnosticreport.html http://hl7.org/fhir/diagnosticreport-definitions.html B2AI_STANDARD:153 BiomedicalStandard DiagnosticReport HL7 FHIR Resource DiagnosticReport Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_TOPIC:13 B2AI_ORG:40 GenomicStudy resource aims at delineating relevant information of a genomic study. A genomic study might comprise one or more analyses, each serving a specific purpose. These analyses may vary in method (e.g., karyotyping, CNV, or SNV detection), performer, software, devices used, or regions targeted. True False https://build.fhir.org/genomicstudy.html https://build.fhir.org/genomicstudy-definitions.html B2AI_STANDARD:154 BiomedicalStandard GenomicStudy HL7 FHIR Resource GenomicStudy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_TOPIC:20 B2AI_ORG:40 Resource for raw data describing a biological sequence. True False http://hl7.org/implement/standards/fhir/molecularsequence.html http://hl7.org/implement/standards/fhir/molecularsequence-definitions.html B2AI_STANDARD:155 BiomedicalStandard MolecularSequence HL7 FHIR Resource MolecularSequence Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:40 Resource for measurements and simple assertions made about a patient, device or other subject. True False http://hl7.org/implement/standards/fhir/observation.html http://hl7.org/implement/standards/fhir/observation-definitions.html B2AI_STANDARD:156 BiomedicalStandard Observation HL7 FHIR Resource Observation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:6 B2AI_TOPIC:9 B2AI_ORG:40 Resource for demographics and other administrative information about an individual or animal receiving care or other health-related services. True False http://hl7.org/implement/standards/fhir/patient.html http://hl7.org/implement/standards/fhir/patient-definitions.html B2AI_STANDARD:157 BiomedicalStandard Patient HL7 FHIR Resource Patient Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:40 Resource for any material sample taken from a biological entity, living or dead, or taken from a physical object or the environment. True False http://hl7.org/fhir/specimen.html http://hl7.org/fhir/specimen-definitions.html B2AI_STANDARD:158 BiomedicalStandard Specimen HL7 FHIR Resource Specimen Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:6 B2AI_ORG:40 Currently, it is common that a single data element is used to capture both sex and gender information, often assuming these two items are one unified idea. This specification challenges that notion and proposes that independent consideration of sex and gender, and the assessment of their differences promotes the health of women, men, and people of diverse gender identities of all ages, avoiding systematic errors that generate results with a low validity (if any) in clinical studies. The Gender Harmony model describes an approach that can improve data accuracy for sex and gender information in health care systems. True True http://www.hl7.org/implement/standards/product_brief.cfm?product_id=564 doi:10.1093/jamia/ocab196 B2AI_STANDARD:159 BiomedicalStandard GHP HL7 Gender Harmony Project Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:28 B2AI_ORG:41 The HUPO PSI Mass Spectrometry Standards Working Group (MSS WG) has developed a specification for a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. True False https://www.psidev.info/traml B2AI_STANDARD:160 BiomedicalStandard TraML HUPO-PSI TraML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:18 B2AI_ORG:44 An overview, terminology, and categorization for Wearable Consumer Electronic Devices (Wearables). It further outlines an architecture for a series of standard specifications that define technical requirements and testing methods for different aspects of Wearables, from basic security and suitableness of wearing to various functional areas like health, fitness, and infotainment, etc. False True https://standards.ieee.org/ieee/360/6244/ B2AI_STANDARD:161 BiomedicalStandard IEEE P360 IEEE 360-2022 IEEE Standard for Wearable Consumer Electronic Devices Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:46 A mechanism to record the patient privacy consent(s) and a method for Content Consumers to use to enforce the privacy consent appropriate to the use. True False https://profiles.ihe.net/ITI/TF/Volume1/ch-19.html B2AI_STANDARD:162 BiomedicalStandard BPPC IHE Basic Patient Privacy Consents Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:46 Profile for Clinical Decision Support and Appropriate Use Criteria (AUC) information as received from the CDS Mechanism 145 (CDSM) on the order and charge transaction to the revenue cycle application that is responsible to create a claim. True False https://www.ihe.net/uploadedFiles/Documents/Radiology/IHE_Rad_Suppl_CDS-OAT.pdf B2AI_STANDARD:163 BiomedicalStandard IHE CDS-OAT IHE Clinical Decision Support Order Appropriateness Tracking Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:46 The Clinical Research Document Profile (CRD) specifies a standard way to generate a clinical research document from EHR data provided in the CDA standard. True False https://www.ihe.net/uploadedFiles/Documents/QRPH/IHE_QRPH_Suppl_CRD.pdf B2AI_STANDARD:164 BiomedicalStandard CRD IHE Clinical Research Document standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:46 Standardized means to locate communities that hold patient relevant health data and the translation of patient identifiers across communities holding the same patient’s data. True False https://profiles.ihe.net/ITI/TF/Volume1/ch-27.html B2AI_STANDARD:165 BiomedicalStandard IHE XCPD IHE Cross-Community Patient Discovery Profile Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:46 Technical profiles and definitions for IT use cases, transactions, content, and metadata. True False https://profiles.ihe.net/ITI/index.html https://profiles.ihe.net/ITI/TF/index.html B2AI_STANDARD:166 BiomedicalStandard IHE ITI IHE IT Infrastructure Technical Framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:46 Profile to support the analytical workflow between analyzers of the clinical laboratory and the IT systems managing their work True False https://www.ihe.net/resources/technical_frameworks/#PaLM https://www.ihe.net/uploadedFiles/Documents/PaLM/IHE_PaLM_TF_Vol1.pdf B2AI_STANDARD:167 BiomedicalStandard LAW IHE Laboratory Analytical Workflow Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:46 Standards for medical device communication. True False https://wiki.ihe.net/index.php?title=PCD_Profiles B2AI_STANDARD:168 BiomedicalStandard IHE PCD IHE Patient Care Device Profiles Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:46 Standardized ways for multiple distributed applications to query a patient information server for a list of patients, based on user-defined search criteria, and retrieve a patient’s demographic (and, optionally, visit or visit-related) information directly into the application. True False https://profiles.ihe.net/ITI/TF/Volume1/ch-8.html B2AI_STANDARD:169 BiomedicalStandard IHE PDQ IHE Patient Demographics Query Integration Profile Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:46 The RFD Profile provides a generic polling mechanism to allow an external agency to indicate issues with data that have been captured and enable the healthcare provider to correct the data. The profile does not dictate the mechanism employed or content required to achieve such corrections. True False https://profiles.ihe.net/ITI/TF/Volume1/ch-17.html B2AI_STANDARD:170 BiomedicalStandard RFD IHE Retrieve Form for Data Capture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:53 Industry-defined format to facilitate the publication and exchange of LOINC codes for vendor IVD test results. True False https://ivdconnectivity.org/livd/ B2AI_STANDARD:171 BiomedicalStandard LIVD IICC Digital Format for Publication of LOINC to Vendor IVD Test Results Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:19 The Image Cytometry Standard (ICS) is a digital multidimensional image file format used in life sciences microscopy. It stores not only the image data, but also the microscopic parameters describing the optics during the acquisition. True False https://en.wikipedia.org/wiki/Image_Cytometry_Standard doi:10.1002/cyto.990110502 B2AI_STANDARD:172 BiomedicalStandard ICS Image Cytometry Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:15 B2AI_TOPIC:28 B2AI_ORG:20 The purpose of imzML is to facilitate the exchange and processing of mass spectrometry imaging data. This website is intended to provide all information neccesary to implement imzML.imzML was developed in the framework of the EU funded project COMPUTIS. The main goals during the development were complete description of MS imaging experiments and efficient storage of (very large) data sets. imzML is it not limited to MS imaging, but is also useful for other MS applications generating large data sets such as LC-FTMS. The current version is mzML 1.1.0. The metadata part of imzML is based on the mzML format by HUPO-PSI True False https://ms-imaging.org/imzml/ doi:10.1016/j.jprot.2012.07.026 B2AI_STANDARD:173 BiomedicalStandard imzML imzML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:14 Diseases and diagnostic categories True False https://www.cdc.gov/nchs/icd/icd-10-cm.htm B2AI_STANDARD:174 BiomedicalStandard ICD-10-CM International Classification of Diseases 10th Revision Clinical Modification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:100 Diseases and diagnostic categories True False https://icd.who.int/en B2AI_STANDARD:175 BiomedicalStandard ICD-11 International Classification of Diseases 11th Revision Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:14 Diseases and diagnostic categories True False https://www.cdc.gov/nchs/icd/icd9cm.htm B2AI_STANDARD:176 BiomedicalStandard ICD-9-CM International Classification of Diseases 9th Revision Clinical Modification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:15 A design directive for transparent ML systems in medical image analysis. The INTRPRT guideline suggests human-centered design principles, recommending formative user research as the first step to understand user needs and domain requirements. True False doi:10.1038/s41746-022-00699-2 B2AI_STANDARD:177 BiomedicalStandard INTRPRT INTRPRT guidelines for transparent machine learning for medical image analysis Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:21 Alignment can be interpreted as a set of uni-directional mappings for transforming input RDF graph into output RDF graph. It is persisted in IPSM Alignment Format (IPSM-AF) that is based on a well known Alignment API Format. True False https://inter-iot.readthedocs.io/projects/ipsm/en/latest/Configuration/Alignment-format/IPSM-alignment-format/ https://github.com/INTER-IoT/ipsm-alignments B2AI_STANDARD:178 BiomedicalStandard IPSM-AF IPSM Alignment Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 B2AI_ORG:47 ISA-TAB-Nano specifies the format for representing and sharing information about nanomaterials, small molecules and biological specimens along with their assay characterization data (including metadata, and summary data) using spreadsheet or TAB-delimited files. True False https://wiki.nci.nih.gov/display/icr/isa-tab-nano doi:10.1186/1472-6750-13-2 B2AI_STANDARD:179 BiomedicalStandard ISA-TAB-Nano ISA-Tab-Nano format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:49 A means for communicating part or all of the electronic health record (EHR) of one or more identified subjects of care between EHR systems, or between EHR systems and a centralised EHR data repository. It can also be used for EHR communication between an EHR system or repository and clinical applications or middleware components (such as decision support components), or personal health applications and devices, that need to access or provide EHR data, or as the representation of EHR data within a distributed (federated) record system. False True http://www.en13606.org/ https://www.iso.org/standard/67868.html B2AI_STANDARD:180 BiomedicalStandard EN13606 ISO 13606 standard for Electronic Health Record Communication Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:50 Standards for medical device communication. True False https://www.itu.int/en/ITU-T/studygroups/2013-2016/16/Pages/rm/ehealth.aspx B2AI_STANDARD:181 BiomedicalStandard ITU-T E-health ITU H.810, H.811, H.812, H.812.5, and H.813 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_ORG:51 The JCAMP-DX was one of the earliest specifications providing a standard file format for data exchange in mass spectrometry. It was initially developed for infrared spectrometry and related chemical and physical information between spectrometer data systems of different manufacture. It was also used later for nuclear magnetic resonance spectroscopy. JCAMP-DX is an ASCII based format and therefore not very compact even though it includes standards for file compression. All data are stored as labeled fields of variable length using printable ASCII characters. JCAMP-DX was officially released in 1988. JCAMP-DX was found impractical for today's large MS data sets, but it is still used for exchanging moderate numbers of spectra. IUPAC is currently in charge of its maintenance and the latest protocol is from 2005. True False https://iupac.org/what-we-do/digital-standards/jcamp-dx/ B2AI_STANDARD:182 BiomedicalStandard JCAMP-DX Joint Committee on Atomic and Molecular Physical Data standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat A format used by the khmer tool to represent k-mer counts and their occurences. True False https://khmer.readthedocs.io/en/v2.0/dev/binary-file-formats.html#countgraph doi:10.12688/f1000research.6924.1 B2AI_STANDARD:183 BiomedicalStandard Countgraph K-mer countgraph Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 A standard way of measuring the ability of cancer patients to perform ordinary tasks. The Karnofsky Performance Status scores range from 0 to 100. A higher score means the patient is better able to carry out daily activities. Karnofsky Performance Status may be used to determine a patient's prognosis, to measure changes in a patient’s ability to function, or to decide if a patient could be included in a clinical trial. Also called KPS. True False http://www.npcrc.org/files/news/karnofsky_performance_scale.pdf doi:10.1200/JCO.1984.2.3.187 B2AI_STANDARD:184 BiomedicalStandard KPS Karnofsky Performance Scale Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:21 B2AI_ORG:52 The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. True False https://www.kegg.jp/kegg/xml/ B2AI_STANDARD:185 BiomedicalStandard KGML KEGG Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
deprecated B2AI_TOPIC:20 The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. True False doi:10.1136/amiajnl-2011-000763 B2AI_STANDARD:186 BiomedicalStandard LS-DAM Life sciences domain analysis model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:53 Tests, observations, diagnostics, and other clinical procedures. True True loinc.org B2AI_STANDARD:187 BiomedicalStandard LOINC Logical Observation Identifier Names and Codes Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:27 B2AI_ORG:82 PDBx/mmCIF became the standard PDB archive format in 2014. All PDB data processing and annotation will be performed using PDBx/mmCIF at all wwPDB sites. PDBx/mmCIF consists of categories of information represented as tables and keyword value pairs. True False https://mmcif.wwpdb.org/ B2AI_STANDARD:188 BiomedicalStandard mmCIF Macromolecular Crystallographic Information File Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:23 MSAML was formulated to make manipulation and extraction of multiple sequence alignment information easier by logically defining the parts of an alignment for use in an XML conformant application. True False http://xml.coverpages.org/msaml-desc-dec.html B2AI_STANDARD:189 BiomedicalStandard MSAML Markup Components for Describing Multiple Sequence Alignments Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:3 B2AI_TOPIC:27 An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule. True False https://en.wikipedia.org/wiki/Chemical_table_file B2AI_STANDARD:190 BiomedicalStandard MDL MDL molfile Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:3 The MDL reaction format is used to store information on chemical reactions. True False https://open-babel.readthedocs.io/en/latest/FileFormats/MDL_RXN_format.html B2AI_STANDARD:191 BiomedicalStandard RXN MDL reaction Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:6 B2AI_TOPIC:31 B2AI_ORG:60 Measuring Sex, Gender Identity, and Sexual Orientation recommends that the National Institutes of Health (NIH) adopt new practices for collecting data on sex, gender, and sexual orientation - including collecting gender data by default, and not conflating gender with sex as a biological variable. The report recommends standardized language to be used in survey questions that ask about a respondent's sex, gender identity, and sexual orientation. Better measurements will improve data quality, as well as the NIH's ability to identify LGBTQI+ populations and understand the challenges they face. True False https://nap.nationalacademies.org/catalog/26424/measuring-sex-gender-identity-and-sexual-orientation doi:10.17226/26424 B2AI_STANDARD:192 BiomedicalStandard Measuring Sex, Gender Identity, and Sexual Orientation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:22 A system for flexible, self-documenting representation of neuroscientific imaging data with arbitrary orientation and dimensionality. True False https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference doi:10.3389/fninf.2016.00035 B2AI_STANDARD:193 BiomedicalStandard MNC Medical Imaging NetCDF (Minc) format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:17 Medical cases in the US are classified into Medicare Severity Diagnosis Related Groups (MS-DRGs) for payment based on the following information reported by the hospital - the principal diagnosis, up to 24 additional diagnoses, and up to 25 procedures performed during the stay. In a small number of MS-DRGs, classification is also based on the age, sex, and discharge status of the patient. Effective October 1, 2015, the diagnosis and procedure information is reported by the hospital using codes from the International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) and the International Classification of Diseases, Tenth Revision, Procedure Coding System (ICD-10-PCS). True False https://www.cms.gov/Medicare/Medicare-Fee-for-Service-Payment/AcuteInpatientPPS/MS-DRG-Classifications-and-Software B2AI_STANDARD:194 BiomedicalStandard MS-DRG Medicare Severity Diagnosis Related Groups codes Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:11 MEDIN is a list of information that accompanies a data set and allows other people to find out what the data set contains, where it was collected and how they can get hold of it. It is a standard for marine metadata and a set of tools to create metadata records that comply with the MEDIN Metadata Standard True False https://www.medin.org.uk/medin-discovery-metadata-standard https://github.com/medin-marine/Discovery-Standard-public-content B2AI_STANDARD:195 BiomedicalStandard MEDIN MEDIN Discovery Metadata Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 The Memorial Symptom Assessment Scale (MSAS) is a new patient-rated instrument that was developed to provide multidimensional information about a diverse group of common symptoms. True False http://www.npcrc.org/files/news/memorial_symptom_assessment_scale.pdf doi:10.1016/0959-8049(94)90182-1 B2AI_STANDARD:196 BiomedicalStandard MSAS Memorial Symptom Assessment Scale Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_TOPIC:28 B2AI_TOPIC:34 The conceptual and procedural meta-omics schema is developed as part of the MOD-CO project. It is entitled with MOD-CO schema, a conceptual schema for processing sample data in meta-omics research and published in various kind of schema representations. With that, the MOD-CO schema is a generic and comprehensive schema providing specifications useful for later software implementation and facilitates international standardisation processes. True False https://www.mod-co.net/wiki/Schema_Representations B2AI_STANDARD:197 BiomedicalStandard MOD-CO Meta-omics Data and Collection Objects Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_ORG:74 MINiML (MIAME Notation in Markup Language, pronounced 'minimal') is a data exchange format optimized for microarray gene expression data, as well as many other types of high-throughput molecular abundance data. MINiML assumes only very basic relations between objects - Platform (e.g., array), Sample (e.g., hybridization), and Series (experiment). MINiML captures all components of the MIAME checklist, as well as any additional information that the submitter wants to provide. MINiML uses XML Schema as syntax. True False https://www.ncbi.nlm.nih.gov/geo/info/MINiML.html B2AI_STANDARD:198 BiomedicalStandard MINiML MIAME Notation in Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:33 B2AI_TOPIC:34 This document is a standard that addresses the representation of gene expression data and relevant annotations, as well as mechanisms for exchanging these data. The field of gene expression experiments has several distinct technologies that a standard must include (e.g., single vs. dual channel experiments, cDNA vs. oligonucleotides). Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. With the acceptance of XML Metadata Interchange as an OMG standard it is possible to specify a normative UML model using a tool such as Rational Rose that describes the data structures for Gene Expression True False http://scgap.systemsbiology.net/standards/mage_miame.php B2AI_STANDARD:199 BiomedicalStandard MAGE-ML MicroArray Gene Expression Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:33 B2AI_TOPIC:34 Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the FGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support. We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML True False http://scgap.systemsbiology.net/standards/mage_miame.php B2AI_STANDARD:200 BiomedicalStandard MAGE-TAB MicroArray Gene Expression Markup Language Tab format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:1 MCL is a data exchange standard for microbiological information. In short, MCL defines terms which can be used to reference and describe microorganisms. It is designed to form a simple and generic framework leveraging the electronical exchange of information about microorganisms. MCL is loosely coupled from its actual representation technologies and is currently used to structure XML and RDF files (see examples). True False doi:10.1016/j.resmic.2010.02.005 B2AI_STANDARD:201 BiomedicalStandard MCL Microbiological Common Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:37 B2AI_ORG:57 Format for MIMIC Waveform Database records. True False https://wfdb.io/mimic_wfdb_tutorials/mimic/formatting.html B2AI_STANDARD:202 BiomedicalStandard WFDB Format MIMIC Waveform Database Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema B2AI_TOPIC:12 B2AI_TOPIC:13 Information needed to enable the unambiguous interpretation and facilitate reproduction of the results of a high throughput sequencing experiment. True False https://zenodo.org/record/5706412 https://drive.google.com/file/d/1YyvWT02puzMG_UgNmfAEJwVr60-pMvIE/view?usp=sharing B2AI_STANDARD:203 BiomedicalStandard MINSEQE Minimal Information about a high throughput SEQuencing Experiment Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema This is a reporting guideline for self-monitoring and quantified-self experiments and their use for research purposes. False False doi:10.3233/978-1-61499-423-7-79 B2AI_STANDARD:204 BiomedicalStandard MISME Minimal Information about a Self-Monitoring Experiment Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema A set of guidelines for the consistent annotation and curation of computational models in biology. True False http://co.mbine.org/standards/miriam B2AI_STANDARD:205 BiomedicalStandard MIRIAM Minimal Information Required In the Annotation of Models Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema B2AI_TOPIC:2 The fundamental tenet of scientific research is that the published results of any study have to be open to independent validation or refutation. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) establishes criteria for recording and reporting information about the flow cytometry experiment overview, samples, instrumentation and data analysis. It promotes consistent annotation of clinical, biological and technical issues surrounding a flow cytometry experiment by specifying the requirements for data content and by providing a structured framework for capturing information. True False https://isac-net.org/page/MIFlowCyt doi:10.1002/cyto.a.20623 B2AI_STANDARD:206 BiomedicalStandard MIFlowCyt Minimum Information about a Flow Cytometry Experiment Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema B2AI_TOPIC:28 B2AI_ORG:41 Information from whole proteomics experiments; where samples came from, and how analyses of them were performed. True False https://www.psidev.info/miape B2AI_STANDARD:207 BiomedicalStandard MIAPE Minimum Information About a Proteomics Experiment Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema Minimum Information About an RNAi Experiment (MIARE) is a set of reporting guidelines that describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results. MIARE forms part of a larger effort to develop RNAi data standards that include a data model, data exchange format, controlled vocabulary and supporting software tools. True False http://miare.sourceforge.net/HomePage B2AI_STANDARD:208 BiomedicalStandard MIARE Minimum Information About a RNAi Experiment Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema B2AI_ORG:38 The minimum information about any (x) sequence (MIxS) is.a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about the Genomic Standards Consortium (GSC) checklists. True False https://genomicsstandardsconsortium.github.io/mixs/ doi:10.1038/nbt.1823 https://github.com/GenomicsStandardsConsortium/mixs/ B2AI_STANDARD:209 BiomedicalStandard MIxS Minimum information about any sequence Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema A reporting guideline for plant phenotyping experiments. Comprises a checklist, i.e., a list of attributes that may be necessary to fully describe an experiment so that it is understandable and replicable. Should be consulted by people recording and depositing the data. Covers description of the following aspects of plant phenotyping experiment - study, environment, experimental design, sample management, biosource, treatment and phenotype. To read more, please visit http://cropnet.pl/phenotypes True False https://www.miappe.org/ B2AI_STANDARD:210 BiomedicalStandard MIAPPE Minimum Information About Plant Phenotyping Experiments Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema B2AI_TOPIC:35 MIASM was developed for the collection of somatic variations to promote standards for annotations of somatic variation data, and to promote data integration with other data resources. True False http://structure.bmc.lu.se/MIASM/miasm.html doi:10.1002/humu.20832 B2AI_STANDARD:211 BiomedicalStandard MIASM Minimum Information About Somatic Mutation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema The MIQAS set of rules accompanied with the standardized XML and tab-delimited file formats will serve two goals - to encourage research groups that wish to publish a QTL paper to provide and submit the necessary information that would make meta-analysis possible. to allow easy interchange of data between different QTL and association analysis databases. Databases that implement the standardized XML format will typically write an import and an export filter to read data from and dump data into that an XML file. This is the same approach as used for the exchange of sequences between NCBI, Ensembl and DDBJ at the early stages of the Human Genome Project. True False http://miqas.sourceforge.net/ B2AI_STANDARD:212 BiomedicalStandard MIQAS Minimum Information for QTLs and Association Studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema MIABIS represents the minimum information required to initiate collaborations between biobanks and to enable the exchange of biological samples and data. The aim is to facilitate the reuse of bio-resources and associated data by harmonizing biobanking and biomedical research. True False doi:10.1089/bio.2015.0070 B2AI_STANDARD:213 BiomedicalStandard MIABIS Minimum information required to initiate collaborations between biobanks Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
minimuminformationschema B2AI_TOPIC:28 B2AI_ORG:41 This module identifies the minimum information required to report the use of quantification techniques in a proteomics experiment, sufficient to support both the effective interpretation and assessment of the data and the potential recreation of the results of the data analysis. True False https://www.psidev.info/attachments/miape-quant-091-documents B2AI_STANDARD:214 BiomedicalStandard MIAPE-Quant Minimum information required to report the use of quantification techniques in a proteomics experiment Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:27 An extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF); provides an extensible data representation for deposition, archiving, and public dissemination of predicted 3D models of proteins. True False doi:10.1101/2022.12.06.518550 http://github.com/ihmwg/ModelCIF B2AI_STANDARD:215 BiomedicalStandard ModelCIF ModelCIF Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
multimodal The Multilevel Healthcare Information Modeling (MLHIM) specifications enables the exchange of syntactically and semantically interoperable data extracts between distributed, independently developed, biomedical databases and clinical applications, promoting syntactic and semantic integration of Translational Research data. The Semantic MedWeb is an implementation of a MLHIM-based database development platform (open source code available at https://github.com/mlhim/SemanticMedWeb) True False https://mlhim-specifications.readthedocs.io/en/master/ B2AI_STANDARD:216 BiomedicalStandard MLHIM Multilevel Healthcare Information Modeling specifications Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:23 The multiple alignment format stores a series of multiple alignments in a format that is easy to parse and relatively easy to read. This format stores multiple alignments at the DNA level between entire genomes. Previously used formats are suitable for multiple alignments of single proteins or regions of DNA without rearrangements, but would require considerable extension to cope with genomic issues such as forward and reverse strand directions, multiple pieces to the alignment, and so forth. True False http://genome.ucsc.edu/FAQ/FAQformat.html#format5 B2AI_STANDARD:217 BiomedicalStandard MAF Multiple Alignment Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 mz5 is a complete reimplementation of the mzML ontology that is based on the efficient, industrial strength storage backend HDF5. True False doi:10.1074/mcp.O111.011379 B2AI_STANDARD:218 BiomedicalStandard mz5 mz5 format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:28 B2AI_ORG:41 mzData is an XML format for representing mass spectrometry data in such a way as to completely describe the instrumental aspects of the experiment. This format is deprecated and has been superseded by mzML. True False https://psidev.info/mass-spectrometry-workgroup#mzdata B2AI_STANDARD:219 BiomedicalStandard mzData mzData format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:28 B2AI_ORG:41 A large number of different proteomics search engines are available that produce output in a variety of different formats. It is intended that mzIdentML will provide a common format for the export of identification results from any search engine. The format was originally developed under the name AnalysisXML as a format for several types of computational analyses performed over mass spectra in the proteomics context. True False https://www.psidev.info/mzidentml B2AI_STANDARD:220 BiomedicalStandard mzIndentML mzIndentML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:28 B2AI_ORG:41 From 2005-2008 there has existed two separate XML formats for encoding raw spectrometer output, mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. It was recognized that the existence of two separate formats for essentially the same thing generated confusion and required extra programming effort. Therefore the PSI, with full participation by ISB, has developed a new format by taking the best aspects of each of the precursor formats to form a single one. It is intended to replace the previous two formats. This new format was originally given a working name of dataXML. The final name is mzML. True False https://psidev.info/mzML doi:10.1007/978-1-60761-444-9_22 http://www.peptideatlas.org/tmp/mzML1.1.0.html B2AI_STANDARD:221 BiomedicalStandard mzML mzML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:28 B2AI_ORG:41 The mzQuantML standard format is intended to store the systematic description of workflows quantifying molecules (principly peptides and proteins) by mass spectrometry. A large number of different software packages are available that produce output in a variety of different formats. It is intended that mzQuantML will provide a common format for the export of identification results from any software package. The format was originally developed under the name AnalysisXML as a format for several types of computational analyses performed over mass spectra in the proteomics context. It has been decided to split development into two formats, mzIdentML for peptide and protein identification and mzQuantML (described here), covering quantitative proteomic data derived from MS. The development of mzQuantML is driven by some general principles, specific use cases and the goal of supporting specific techniques, as listed below. These were discussed and agreed at the development meeting in Tubingen in July 2011. True False https://www.psidev.info/mzquantml B2AI_STANDARD:222 BiomedicalStandard mzQuantML mzQuantML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
deprecated fileformat B2AI_TOPIC:28 mzXML an open, generic XML (extensible markup language) representation of MS data. This format is now deprecated and it has been superseded by mzML. True False doi:10.1038/nbt1031 B2AI_STANDARD:223 BiomedicalStandard mzXML mzXML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:71 Terminology content, tools, and services to accurately code, analyze and share cancer and biomedical research, clinical and public health information. Includes NCI Thesaurus and Metathesaurus. True True https://evs.nci.nih.gov/ B2AI_STANDARD:224 BiomedicalStandard NCI EVS National Cancer Institute Enterprise Vocabulary Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:66 Standard for the collection and transmission of emergency medical services (EMS) operations and patient care data. True False https://nemsis.org/technical-resources/ B2AI_STANDARD:225 BiomedicalStandard NEMSIS National Emergency Medical Services Information System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:81 This guiding principle is expressed in the CDM design through prioritization of analytic functionality, and a parsimonious approach based upon analytic utility. At times, this results in decisions that are not based in relational database modeling principles such as normalization. The model is designed to facilitate routine and rapid execution of distributed complex analytics. To meet this design requirement, some fields are duplicated across multiple tables to support faster analytic operations for distributed querying. The PCORnet CDM is based on the FDA Mini-Sentinel CDM. This allows PCORnet to more easily leverage the large array of analytic tools and expertise developed for the MSCDM v4.0, including data characterization approaches and the various tools for complex distributed analytics. True False http://pcornet.org/pcornet-common-data-model/ https://pcornet.org/wp-content/uploads/2022/01/PCORnet-Common-Data-Model-v60-2020_10_221.pdf B2AI_STANDARD:226 BiomedicalStandard PCORNet CDM National Patient-Centered Clinical Research Network Common Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:93 Natural Collections Description (NCD) (A data standard for exchanging data describing natural history collections) is a proposed data standard for describing collections of natural history materials at the collection level; one NCD record describes one entire collection. Collection descriptions are electronic records that document the holdings of an organisation as groups of items, which complement the more traditional item-level records such as are produced for a single specimen or a library book. NCD is tailored to natural history. It lies between general resource discovery standards such as Dublin Core (DC) and rich collection description standards such as the Encoded Archival Description (EAD). The NCD standard covers all types of natural history collections, such as specimens, original artwork, archives, observations, library materials, datasets, photographs or mixed collections such as those that result from expeditions and voyages of discovery. True False https://www.tdwg.org/standards/ncd/ B2AI_STANDARD:227 BiomedicalStandard NCD Natural Collections Description standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:1 B2AI_ORG:74 This is a XML Schema specification of BioProject data. A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. True False doi:10.1093/nar/gkr1163 https://www.ncbi.nlm.nih.gov/data_specs/schema/other/bioproject/ B2AI_STANDARD:228 BiomedicalStandard BioProject Schema NCBI BioProject XML Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:63 Allows pharmacy benefit payers to communicate formulary and benefit Information to prescriber systems. False True https://standards.ncpdp.org/Access-to-Standards.aspx B2AI_STANDARD:229 BiomedicalStandard NCPDP F&B NCPDP Formulary and Benefit Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_ORG:64 Guiding principles and a foundation for the capture and use of high-quality data for post-market evaluation of medical devices True True https://nestcc.org/data-quality-and-methods/ https://mdic.org/wp-content/uploads/2020/02/NESTcc-Data-Quality-Framework.pdf B2AI_STANDARD:230 BiomedicalStandard NESTcc DQF NESTcc Data Quality Framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
A data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data. True False https://www.nwb.org/ doi:10.1101/523035 https://github.com/NeurodataWithoutBorders B2AI_STANDARD:231 BiomedicalStandard NWB Neurodata Without Borders Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:22 B2AI_ORG:99 The Neuroimaging Data Model (NIDM) is a collection of specification documents and examples that outline a domain specific extension to the W3C Provenance Data Model (PROV-DM) for the exchange and sharing of human brain imaging data. The goal of the data model is to capture data, information about the data and processes that generated the data (i.e. provenance). This information can be converted to RDF and therefore queried using SPARQL. This representation allows machine accessible representations of brain imaging data and will provide links to related resources such as publications, virtual machines, people and funding agencies. True False http://nidm.nidash.org/ B2AI_STANDARD:232 BiomedicalStandard NIDM Neuroimaging Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:22 The Neuroimaging Informatics Technology Initiative (nifti) file format was envisioned about a decade ago as a replacement to the then widespread, yet problematic, analyze 7.5 file format. The main problem with the previous format was perhaps the lack of adequate information about orientation in space, such that the stored data could not be unambiguously interpreted. Although the file was used by many different imaging software, the lack of adequate information on orientation obliged some, most notably spm, to include, for every analyze file, an accompanying file describing the orientation, such as a file with extension .mat. True False https://nifti.nimh.nih.gov/ https://nifti.nimh.nih.gov/nifti-2 B2AI_STANDARD:233 BiomedicalStandard NIFTI Neuroimaging Informatics Technology Initiative file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage NeuroML is a model description language developed in XML (extensible Markup Language) that was created to facilitate data archiving, data and model exchange, database creation, and model publication in the neurosciences. One of the goals of the NeuroML project is to develop standards for model specification that will allow for greater simulator interoperability and model exchange. True False https://neuroml.org/ B2AI_STANDARD:234 BiomedicalStandard NeuroML NeuroML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_ORG:11 The purpose of the Neurophysiology Data Translation Format (NDF) is to provide a means of sharing neurophysiology experimental data and derived data between services and tools developed within the CARMEN project (www.carmen.org.uk). This document specifes the NDF. The specification supports the types of data that are currently used by members of the CARMEN consortium and provides a capability to support future data types. It is capable of accommodating external data file formats as well as metadata such as user defined experimental descriptions and the history (provenance) of derived data. True False doi:10.3389/conf.fnins.2010.13.00118 B2AI_STANDARD:235 BiomedicalStandard NDF Neurophysiology Data Translation Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:26 NHX is based on the New Hampshire (NH) standard (also called Newick tree format). True False http://www.phylosoft.org/NHX/ B2AI_STANDARD:236 BiomedicalStandard NHX New Hampshire eXtended Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:26 The Newick Standard for representing trees in computer-readable form makes use of the correspondence between trees and nested parentheses, noticed in 1857 by the famous English mathematician Arthur Cayley. True False http://evolution.genetics.washington.edu/phylip/newicktree.html B2AI_STANDARD:237 BiomedicalStandard Newick Newick tree Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:25 B2AI_TOPIC:26 To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats True False http://www.nexml.org/ https://github.com/nexml/nexml B2AI_STANDARD:238 BiomedicalStandard NeML NeXML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 A sequence file. The .nib format packs 2 bases per byte and handles one record per nib file. True False https://genomebrowser.wustl.edu/goldenPath/help/blatSpec.html B2AI_STANDARD:239 BiomedicalStandard nib Nibble sequence format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_ORG:9 Format and ontology used to represent experiments, spectral and derived data, and supporting metadata. True False https://bmrb.io/standards/ doi:10.1007/s10858-018-0220-3 B2AI_STANDARD:240 BiomedicalStandard NMR-STAR NMR Self-defining Text Archive and Retrieval format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:17 B2AI_ORG:21 nmrML is an open mark-up language for NMR data. It is currently under heavy development and is not yet ready for public use. The development of this standard is coordinated by Workpackage 2 of the COSMOS - COordination Of Standards In MetabOlomicS Project. COSMOS is a global effort to enable free and open sharing of metabolomics data. Coordinated by Dr Christoph Steinbeck of the EMBL-European Bioinformatics Institute, COSMOS brings together European data providers to set and promote community standards that will make it easier to disseminate metabolomics data through life science e-infrastructures. This Coordination Action has been financed with €2 million by the European Commission's Seventh Framework Programme. The nmrML data standard will be approved by the Metabolomics Standards Initiative and was derived from an earlier nmrML that was developed by the Metabolomics Innovation Centre (TMIC). True False https://nmrml.org/ B2AI_STANDARD:241 BiomedicalStandard nmrML nmrML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:25 Observ-Tab is a simple spreadsheet format to represent and exchange phenotype data. True False doi:10.1002/humu.22070 B2AI_STANDARD:242 BiomedicalStandard Observ-Tab Observ-Tab format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:4 B2AI_ORG:76 Open community data standard designed to standardize the structure and content of observational data and to enable efficient analyses that can produce reliable evidence. True False https://ohdsi.github.io/CommonDataModel/ doi:10.3233/978-1-61499-564-7-574 https://github.com/OHDSI/CommonDataModel B2AI_STANDARD:243 BiomedicalStandard OMOP CDM Observational Medical Outcomes Partnership Common Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:4 B2AI_ORG:76 An improved replacement to the previously reported LAERTES system. One of the initial uses of CEM has been its use in generating lists of negative control concepts to be used in empirical calibration. True False https://github.com/OHDSI/CommonEvidenceModel/wiki/Postprocessing-Negative-Controls doi:10.1007/s40264-014-0189-0 https://github.com/OHDSI/CommonEvidenceModel B2AI_STANDARD:244 BiomedicalStandard OMOP CEM Observational Medical Outcomes Partnership Common Evidence Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 A biology-oriented language for building ontologies, based on OWL. True False https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html https://owlcollab.github.io/oboformat/doc/obo-syntax.html B2AI_STANDARD:245 BiomedicalStandard OBO Open Biomedical Ontology Flat File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:18 Data standards and tools for standardizing, storing, and visualizing mobile health data, including integration with FHIR standards. True False https://www.openmhealth.org/ https://github.com/openmhealth B2AI_STANDARD:246 BiomedicalStandard Open mHealth Open mHealth Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:19 B2AI_ORG:77 multi-spectral imaging data True False https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/# B2AI_STANDARD:247 BiomedicalStandard OME-TIFF Open Microscopy Environment TIFF specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:19 B2AI_ORG:77 OME-XML is a file format for storing microscopy information (both pixels and metadata) using the OME Data Model. True False https://docs.openmicroscopy.org/ome-model/5.6.3/ome-xml/ doi:10.1186/gb-2005-6-5-r47 B2AI_STANDARD:248 BiomedicalStandard OME-XML Open Microscopy Environment XML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:27 B2AI_ORG:19 A compressed file that contains all the information needed to describe a modeling and simulation experiment. True False http://co.mbine.org/specifications/omex.version-1.pdf B2AI_STANDARD:249 BiomedicalStandard OMEX Open Modeling EXchange format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:54 OpenICE is an initiative to create a community implementation of an Integrated Clinical Environment. The initiative encompasses not only software implementation but also an architecture for a wider clinical ecosystem to enable new avenues of clinical research. OpenICE seeks to integrate an inclusive framework of healthcare devices and clinical applications to existing Healthcare IT ecosystems. True False https://www.openice.info/ https://github.com/mdpnp/mdpnp B2AI_STANDARD:250 BiomedicalStandard OpenICE Open-Source Integrated Clinical Environment Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:9 B2AI_ORG:79 This document contains the definitive statement of archetype semantics, in the form of an object model for archetypes. The model presented here can be used as a basis for building software that processes archetypes, independent of their persistent representation; equally, it can be used to develop the output side of parsers that process archetypes in a linguistic format, such as the openEHR Archetype Definition Language (ADL), XML-instance and so on. As a specification, it can be treated as an API for archetypes. True False https://specifications.openehr.org/releases/AM/latest/AOM1.4.html B2AI_STANDARD:251 BiomedicalStandard AOM14 openEHR Archetype Object Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:79 openEHR' is the name of a technology for e-health, consisting of open specifications, clinical models and software that can be used to create standards, and build information and interoperability solutions for healthcare. The various artefacts of openEHR are produced by the openEHR community and managed by openEHR International, an international non-profit organisation originally established in 2003 and previously managed by the openEHR Foundation. True False https://www.openehr.org/about/what_is_openehr https://specifications.openehr.org/releases/BASE/latest/architecture_overview.html B2AI_STANDARD:252 BiomedicalStandard openEHR openEHR Architecture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines The quality of research in hospital epidemiology (infection control) must be improved to be robust enough to influence policy and practice. In order to raise the standards of research and publication, a CONSORT equivalent for these largely quasi-experimental studies has been prepared by the authors of two relevant systematic reviews undertaken for the HTA and the Cochrane Collaboration. The statement was revised following widespread consultation with learned societies, editors of journals and researchers. It consists of a 22 item checklist, and a summary table. The emphasis is on transparency to improve the quality of reporting and on the use of appropriate statistical techniques.The statement has been endorsed and welcomed by a number of professional special interest groups and societies including the Association of Medical Microbiologists (AMM), Bristish Society for Antimicrobial Chemotherapy (BSAC) and the Infection Control Nurses' Association (ICNA) Research and Development Group. Like CONSORT, ORION considers itself a work in progress, which requires ongoing dialogue for successful promotion and dissemination. The statement is therefore offered for further public discussion and journals are encouraged to trial it as part of their reviewing and editing process and feedback to the authors. True False https://www.ucl.ac.uk/antimicrobial-resistance/reporting-guidelines/orion-statement-consort-equivalent-infection-control-intervention-studies doi:10.1016/S1473-3099(07)70082-8 https://www.ucl.ac.uk/drupal/site_antimicrobial-resistance/sites/antimicrobial-resistance/files/checklist_authors.pdf B2AI_STANDARD:253 BiomedicalStandard ORION Outbreak Reports and Intervention Studies Of Nosocomial infection Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:54 This standard specifies the characteristics necessary for the safe integration of MEDICAL DEVICES and other equipment, via an electronic interface, from different MANUFACTURERS into a single medical system for the care of a single high acuity PATIENT. This standard establishes requirements for a medical system that is intended to have greater error resistance and improved PATIENT safety, treatment efficacy and workflow efficiency than can be achieved with independently used MEDICAL DEVICES. False False https://mdpnp.org/mdice.html https://www.astm.org/f2761-09r13.html B2AI_STANDARD:254 BiomedicalStandard ICE Patient-Centric Integrated Clinical Environment Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:26 The profile HMM calculated from multiple sequnce alignment data in this service is stored in Profile HMM save format (usually with .hmm extension). It is an ASCII file containing a lot of header and descriptive records followed by large numerical matrix which holds probabilistic model of the motif. The file of this format is useful to search against sequnce databases to find out other proteins which share the same motif. This HMM file should not be edited manually (especially the matrix part) because it contains consistent numerical model as a whole. True False http://hmmer.org/ https://www.genome.jp/tools/motif/hmmformat.htm B2AI_STANDARD:255 BiomedicalStandard HMMER Format Pfam / HMMER Profile file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:4 B2AI_ORG:34 B2AI_ORG:58 Patient phenotypes. True False http://phenopackets.org/ https://github.com/phenopackets/phenopacket-schema B2AI_STANDARD:256 BiomedicalStandard Phenopackets Phenopackets schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 An HL7 messaging and content reference standard for national, syndromic surveillance electronic health record technology certification; A basis for local and state syndromic surveillance messaging implementation guides; A resource for planning for the increasing use of electronic health record technology and for providing details on health data elements that may become a part of future public health syndromic surveillance messaging requirements; Optional elements of interest for adding laboratory results to syndromic surveillance messages using ORU^R01 message structure (see details in the PHIN messaging Standard, National Condition Reporting case Notification, ORU^R01 message Structure Specification profile, Version 2.1, 2014) True False https://knowledgerepository.syndromicsurveillance.org/hl7-version-251-phin-messaging-guide-syndromic-surveillance-emergency-department-urgent-care-and https://www.cdc.gov/nssp/documents/guides/syndrsurvmessagguide2_messagingguide_phn.pdf B2AI_STANDARD:257 BiomedicalStandard PHIN Guide PHIN Messaging Guide for Syndromic Surveillance Emergency Department, Urgent Care, Inpatient and Ambulatory Care Settings Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 B2AI_TOPIC:12 phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events. True False http://www.phyloxml.org/ doi:10.1186/1471-2105-10-356 B2AI_STANDARD:258 BiomedicalStandard phyloXML phyloXML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:18 B2AI_ORG:4 Definitions and performance criteria for measuring step counting on consumer wearable or app-based physical activity monitoring devices. True True https://webstore.ansi.org/standards/ansi/cta20562016ansi B2AI_STANDARD:259 BiomedicalStandard ANSI/CTA-2056 Physical Activity Monitoring for Fitness Wearables Step Counting Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:1 A formal specification for biological sample metadata structure. The PEP specification accommodates typical features of data-intensive bioinformatics projects with many biological samples. True False http://pep.databio.org/ doi:10.1093/gigascience/giab077 https://github.com/pepkit/pepspec B2AI_STANDARD:260 BiomedicalStandard PEP Portable Encapsulated Project specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:1 A self-describing serialized format for bulk biomedical data called the Portable Format for Biomedical (PFB) data. The Portable Format for Biomedical data is based upon Avro and encapsulates a data model, a data dictionary, the data itself, and pointers to third party controlled vocabularies. In general, each data element in the data dictionary is associated with a third party controlled vocabulary to make it easier for applications to harmonize two or more PFB files. True False https://anvilproject.org/ncpi/technologies#portable-format-for-bioinformatics-pfb doi:10.1101/2022.07.19.500678 https://github.com/uc-cdis/pypfb B2AI_STANDARD:261 BiomedicalStandard PFB Portable Format for Bioinformatics Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines An evidence-based minimum set of items for reporting in systematic reviews and meta-analyses.The aim of the PRISMA Statement is to help authors improve the reporting of systematic reviews and meta-analyses. We have focused on randomized trials, but PRISMA can also be used as a basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. PRISMA may also be useful for critical appraisal of published systematic reviews, although it is not a quality assessment instrument to gauge the quality of a systematic review. True False https://www.prisma-statement.org/ doi:10.1136/bmj.n71 B2AI_STANDARD:262 BiomedicalStandard PRISMA Preferred Reporting Items for Systematic Reviews and Meta-Analyses Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:27 B2AI_ORG:82 An exchange format for reporting experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, bibliographic citations, primary and secondary structure, information, and crystallographic structure factors and NMR experimental data True False https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html B2AI_STANDARD:263 BiomedicalStandard PDB Protein Data Bank Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:26 B2AI_ORG:41 The work on PSI-PAR was initiated as part of the ProteomeBinders project and carried out by EMBL-EBI and the PSI-MI work group. The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. For detailed information on all PSI activities, please see PSI Home Page. The PSI-PAR format is a standardized means of representing protein affinity reagent data and is designed to facilitate the exchange of information between different databases and/or LIMS systems. PSI-PAR is not a proposed database structure. The PSI-PAR format consists of the PSI-MI XML2.5 schema (originally designed for molecular interactions) and the PSI-PAR controlled vocabulary. In addition, PSI-PAR documentation and examples are available on this web page. The scope of PSI-PAR is PAR and target protein production and characterization. True False https://www.psidev.info/psi-par doi:10.1074/mcp.M900185-MCP200 B2AI_STANDARD:264 BiomedicalStandard PSI-PAR Proteomics Standards Initiative Protein Affinity Reagent format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:26 B2AI_ORG:41 GelML is a data exchange format for describing the results of gel electrophoresis experiments. GelML is developed as a HUPO-PSI working group. True False https://www.psidev.info/gelml/1.0 B2AI_STANDARD:265 BiomedicalStandard PSI GelML PSI GelML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:28 B2AI_ORG:41 The PSI-MI XML 2.5 is a community standard for molecular interactions which has been jointly developed by major data providers (BIND, CellZome, DIP, GSK, HPRD, Hybrigenics, IntAct, MINT, MIPS, Serono, U. Bielefeld, U. Bordeaux, U. Cambridge, and others).This format is stable and used for several years now - published in October 2007 (Broadening the Horizon Ð Level 2.5 of the HUPO-PSI Format for Molecular Interactions; Samuel Kerrien et al. BioMed Central. 2007.), it has been adapted for many different usages. It can be used for storing any kind of molecular interaction data - complexes and binary interactions not only protein-protein interactions, can describe nucleic acids interactions and others hierarchical complexes modelling by using interactionRef in participants instead of an interactor Data representation in PSI-MI 2.5 XML relies heavily on the use of controlled vocabularies. They can be accessed easily via the Ontology Lookup Service, PSI-MI, PSI-MOD. True False https://www.psidev.info/mif B2AI_STANDARD:266 BiomedicalStandard PSI-MI XML PSI-MI XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:28 An XML format for quality-related data of mass spectrometry and other high-throughput experiments. Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml True False doi:10.1074/mcp.M113.035907 B2AI_STANDARD:267 BiomedicalStandard qcML qcML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:33 The RDML file format is developed by the RDML consortium (http://www.rdml.org) and can be used free of charge. The RDML file format was created to encourage the exchange, publication, revision and re-analysis of raw qPCR data. The core of an RDML file is an experiment, not a PCR run. Therefore all the information is collected which is required to understand an experiment. The structure of the file format was inspired by a database structure. In the file are several master elements, which are then referred to in other parts of the file. This structure allows to reduce the amount of redundant information and encourages the user to provide useful information. The Real-time PCR Data Markup Language (RDML) is a structured and universal data standard for exchanging quantitative PCR (qPCR) data. The data standard should contain sufficient information to understand the experimental setup, re-analyse the data and interpret the results. The data standard is a compressed text file in Extensible Markup Language (XML) and enables transparent exchange of annotated qPCR data between instrument software and third-party data analysis packages, between colleagues and collaborators, and between authors, peer reviewers, journals and readers. To support the public acceptance of this standard, both an on-line RDML file generator is available for end users, as well as RDML software libraries to be used by software developers, enabling import and export of RDML data files. True False http://www.rdml.org B2AI_STANDARD:268 BiomedicalStandard RDML Real-time PCR Data Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines REFLECT stands for Reporting guidElines For randomized controLled trials for livEstoCk and food safeTy. It is an evidence-based minimum set of items for trials reporting production, health, and food-safety outcomes.The aim of the REFLECT Statement is to help authors improve the reporting livestock trials with production, health, and food-safety outcomes. We have focused on both types of randomized trials, field trials and challenge studies in livestock, and the interventions may be therapeutic or preventive. The REFLECT Statement consists of a 22-item checklist (MS Word version ; PDF word version). It is an evolving document that is subject to change periodically as new evidence emerges. This website contains the current definitive version of the REFLECT Statement. True False https://meridian.cvm.iastate.edu/reflect/ doi:10.4315/0362-028x-73.3.579 B2AI_STANDARD:269 BiomedicalStandard REFLECT Reporting guidelines for randomized controlled trials for livestock and food safety Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines Despite years of research and hundreds of reports on tumor markers in oncology, the number of markers that have emerged as clinically useful is pitifully small. Often initially reported studies of a marker show great promise, but subsequent studies on the same or related markers yield inconsistent conclusions or stand in direct contradiction to the promising results. It is imperative that we attempt to understand the reasons why multiple studies of the same marker lead to differing conclusions. A variety of methodological problems have been cited to explain these discrepancies. Unfortunately, many tumor marker studies have not been reported in a rigorous fashion, and published articles often lack sufficient information to allow adequate assessment of the quality of the study or the generalizability of study results. The development of guidelines for the reporting of tumor marker studies was a major recommendation of the National Cancer Institute-European Organisation for Research and Treatment of Cancer (NCI-EORTC) First International Meeting on Cancer Diagnostics in 2000. As for the successful CONSORT initiative for randomized trials and for the STARD statement for diagnostic studies, we suggest guidelines to provide relevant information about the study design, preplanned hypotheses, patient and specimen characteristics, assay methods, and statistical analysis methods. In addition, the guidelines provide helpful suggestions on how to present data and important elements to include in discussions. The goal of these guidelines is to encourage transparent and complete reporting so that the relevant information will be available to others to help them to judge the usefulness of the data and understand the context in which the conclusions apply. True False https://www.equator-network.org/reporting-guidelines/reporting-recommendations-for-tumour-marker-prognostic-studies-remark/ doi:10.1038/sj.bjc.6602678 https://www.equator-network.org/wp-content/uploads/2016/10/REMARK-checklist-for-EQUATOR-website-002.docx B2AI_STANDARD:270 BiomedicalStandard REMARK Reporting recommendations for tumour Marker prognostic studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:31 A common schema that encodes how the different elements of assessment data and / or the metadata relate to one another. True False https://www.repronim.org/reproschema/ https://github.com/ReproNim/reproschema B2AI_STANDARD:271 BiomedicalStandard ReproSchema ReproSchema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:9 B2AI_ORG:89 A standard data structure that allows Sentinel Data Partners to quickly execute distributed programs against local data. True False https://www.sentinelinitiative.org/methods-data-tools/sentinel-common-data-model https://dev.sentinelsystem.org/projects/SCDM/repos/sentinel_common_data_model/browse B2AI_STANDARD:272 BiomedicalStandard SCDM Sentinel Common Data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat The Sequence Alignment/Map (SAM) format is a TAB-delimited text format consisting of a header section, which is optional, and an alignment section. True False http://samtools.sourceforge.net/ doi:10.1093/bioinformatics/btp352 B2AI_STANDARD:273 BiomedicalStandard SAM Sequence Alignment/Map Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:12 B2AI_TOPIC:13 B2AI_TOPIC:33 B2AI_ORG:74 Used by The Sequence Read Archive (SRA) and the European Nucleotide Archive (ENA) to store raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. True False https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/ doi:10.1093/nar/gkq1019 B2AI_STANDARD:274 BiomedicalStandard SRA-XML Sequence Read Archive Metadata XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 Simple Omnibus Format in Text (SOFT) is designed for rapid batch submission (and download) of data. SOFT is a simple line-based, plain text format, meaning that SOFT files may be readily generated from common spreadsheet and database applications. A single SOFT file can hold both data tables and accompanying descriptive information for multiple, concatenated Platforms, Samples, and/or Series records. True False https://www.ncbi.nlm.nih.gov/geo/info/soft-seq.html B2AI_STANDARD:275 BiomedicalStandard SOFT Simple Omnibus Format in Text Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:3 A typographical line notation for specifying chemical structure. True False http://opensmiles.org/ http://opensmiles.org/opensmiles.html B2AI_STANDARD:276 BiomedicalStandard SMILES Simplified Molecular Input Line Entry Specification Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 SED-ML is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. It follows the requirements defined in the MIASE guidelines. True False https://sed-ml.org/ B2AI_STANDARD:277 BiomedicalStandard SED-ML Simulation Experiment Description Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:12 B2AI_TOPIC:13 B2AI_TOPIC:35 B2AI_ORG:74 Sequence variant data model. Represents all variants as a sequence of four operations. Start at the boundary before the first nucleotide in the sequence S, advance P nucleotides, delete D nucleotides, then Insert the nucleotides in the string. True False doi:10.1093/bioinformatics/btz856 B2AI_STANDARD:278 BiomedicalStandard SPDI SPDI data model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:37 A new and more flexible data structure, named the Standard EEG Data Structure (SEDS), was proposed to meet the needs of both small-scale EEG data batch processing in single-site studies and large-scale EEG data sharing and analysis in single-/multisite studies (especially on cloud platforms). False False doi:10.1016/j.softx.2021.100933 B2AI_STANDARD:279 BiomedicalStandard SEDS Standard EEG Data Structure Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:48 The ISBER Biospecimen Science Working Group has developed a SPREC that identifies and records the main pre-analytical factors that may have impact on the integrity of sampled clinical fluids and solid biospecimens and their simple derivatives during collection, processing and storage. SPREC comprises 7 elements for both fluid and solid samples, defining the sample and primary container type, periods of cold and warm ischemia, and subsequent handling steps including speed and temperature of centrifugation and final storage temperature. The ability to manage and track pre-analytical variations impacting biospecimen integrity is fundamental to the provision of high quality tissue samples for research, and the effective and efficient interconnectivity and interoperability between national and international Biobanks. True False https://www.isber.org/page/SPREC doi:10.1089/bio.2017.0109 B2AI_STANDARD:280 BiomedicalStandard SPREC Standard PREanalytical Code Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines The objective of the STARD initiative is to improve the accuracy and completeness of reporting of studies of diagnostic accuracy, to allow readers to assess the potential for bias in the study (internal validity) and to evaluate its generalisability (external validity).The STARD statement consist of a checklist of 25 items and recommends the use of a flow diagram which describe the design of the study and the flow of patients. True False https://www.equator-network.org/reporting-guidelines/stard/ doi:10.1136/bmjopen-2016-012799 B2AI_STANDARD:281 BiomedicalStandard STARD Standards for Reporting of Diagnostic Accuracy Studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:26 A system for marking up features in a multiple alignment. True False https://sonnhammer.sbc.su.se/Stockholm.html B2AI_STANDARD:282 BiomedicalStandard Stockholm Stockholm Multiple Alignment Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines Making sense of rapidly evolving evidence on genetic associations is crucial to making genuine advances in human genomics and the eventual integration of this information in the practice of medicine and public health. Assessment of the strengths and weaknesses of this evidence, and hence the ability to synthesize it, has been limited by inadequate reporting of results. The STrengthening the REporting of Genetic Association studies (STREGA) initiative builds on the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement and provides additions to 12 of the 22 items on the STROBE checklist. The additions concern population stratification, genotyping errors, modelling haplotype variation, Hardy-Weinberg equilibrium, replication, selection of participants, rationale for choice of genes and variants, treatment effects in studying quantitative traits, statistical methods, relatedness, reporting of descriptive and outcome data, and the volume of data issues that are important to consider in genetic association studies. The STREGA recommendations do not prescribe or dictate how a genetic association study should be designed but seek to enhance the transparency of its reporting, regardless of choices made during design, conduct, or analysis. True False https://www.equator-network.org/reporting-guidelines/strobe-strega/ doi:10.1002/gepi.20410 B2AI_STANDARD:283 BiomedicalStandard STREGA Strengthening the Reporting of Genetic Association studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_ORG:91 STROBE stands for an international, collaborative initiative of epidemiologists, methodologists, statisticians, researchers and journal editors involved in the conduct and dissemination of observational studies, with the common aim of STrengthening the Reporting of OBservational studies in Epidemiology. The STROBE Statement is being endorsed by a growing number of biomedical journals. Incomplete and inadequate reporting of research hampers the assessment of the strengths and weaknesses of the studies reported in the medical literature. Readers need to know what was planned (and what was not), what was done, what was found, and what the results mean. Recommendations on the reporting of studies that are endorsed by leading medical journals can improve the quality of reporting.Observational research comprises several study designs and many topic areas. We aimed to establish a checklist of items that should be included in articles reporting such research - the STROBE Statement. We considered it reasonable to initially restrict the recommendations to the three main analytical designs that are used in observational research - cohort, case-control, and cross-sectional studies. We want to provide guidance on how to report observational research well. Our recommendations are not prescriptions for designing or conducting studies. Also, the checklist is not an instrument to evaluate the quality of observational research. True False https://www.strobe-statement.org/ doi:10.1016/j.jclinepi.2007.11.008 B2AI_STANDARD:284 BiomedicalStandard STROBE Strengthening the Reporting of Observational studies in Epidemiology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:27 SDF is one of a family of chemical-data file formats developed by MDL; it is intended especially for structural information. SDF stands for structure-data file, and SDF files actually wrap the molfile (MDL Molfile) format. True False https://en.wikipedia.org/wiki/Chemical_table_file#SDF B2AI_STANDARD:285 BiomedicalStandard SDF Structure Data Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples. True False https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html https://github.com/Bioconductor/SummarizedExperiment B2AI_STANDARD:286 BiomedicalStandard SummarizedExperiment SummarizedExperiment container Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:1 Standard for in silico representation of genetic designs. SBOL is designed to allow synthetic biologists and genetic engineers to electronically exchange designs . Send and receive genetic designs to and from biofabrication centers. Facilitate storage of genetic designs in repositories Embed genetic designs in publications. True False https://sbolstandard.org/ https://sbolstandard.org/#specifications B2AI_STANDARD:287 BiomedicalStandard SBOL Synthetic Biology Open Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:1 An effort to standardize the graphical notation used in maps of biological processes. True False https://sbgn.github.io/ doi:10.1038/nbt.1558 https://sbgn.github.io/downloads/specifications/pd_level1_version2.pdf B2AI_STANDARD:288 BiomedicalStandard SBGN Systems Biology Graphical Notation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:1 B2AI_ORG:19 The Systems Biology Markup Language (SBML) is a machine-readable exchange format for computational models of biological processes. Its strength is in representating phenomena at the scale of biochemical reactions, but it is not limited to that. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chances for errors in translation and assuring a common starting point for analyses and simulations. True False http://sbml.org/ doi:10.1515/jib-2017-0081 B2AI_STANDARD:289 BiomedicalStandard SBML Systems Biology Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:1 Systems Biology has benefited tremendously from the development and use of SBML, which is a markup language to specify models composed of molecular species, and their interactions (including reactions). SBML is a common format that many systems biology software understand and thus it has become the way in which models are shared and communicated. Despite the popularity of SBML, that has resulted in many models being available in electronic format, there is currently no standard way of communicating the results of the operations carried out with such models (e.g. simulations). Here we propose a new markup language which is complementary to SBML and which is intended to specify results from operations carried out on models SBRML. In fact, this markup language is useful also to communicate experimental data as long as it is possible to express the data in terms of a reference SBML model. Thus SBRML is a means of specifying quantitative results in the context of a systems biology model. False False https://sbrml.sourceforge.net/SBRML/Welcome.html B2AI_STANDARD:290 BiomedicalStandard SBRML Systems Biology Results Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:13 A tab-delimited genome position index file format. The format can handle individual chromosomes up to 512 Mbp (2^29 bases) in length. True False http://www.htslib.org/doc/tabix.html doi:10.1093/bioinformatics/btq671 https://samtools.github.io/hts-specs/tabix.pdf B2AI_STANDARD:291 BiomedicalStandard Tabix Tabix index file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_ORG:93 The development of an abstract model for a taxonomic concept, which can capture the various models represented and understood by the various data providers, is central to this project. This model is presented as an XML schema document that is proposed as a standard to allow exchange of data between different data models. It aims to capture data as understood by the data owners without distortion, and facilitate the query of different data resources according to the common schema model. The TCS schema was conceived to allow the representation of taxonomic concepts as defined in published taxonomic classifications, revisions and databases. As such, it specifies the structure for XML documents to be used for the transfer of defined concepts. Valid transfer documents may either explicitly detail the defining components of taxon concepts, transfer GUIDs referring to defined taxon concepts (if and when these are available) or a mixture of the two. True False http://www.tdwg.org/standards/117 https://github.com/tdwg/tcs B2AI_STANDARD:292 BiomedicalStandard TCS Taxonomic Concept Transfer Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:93 This document defines how TDWG standards should be presented. Each standard is a logical directory or folder containing two or more files - a cover page outlining basic meta data for the standard and one or more normative files specifying the standard itself. Rules are specified for the naming of standards and files. Human readable files should be in English, follow basic layout principles and be marked up in XHTML. The legal statements that all documents must contain are defined. True False http://www.tdwg.org/standards/147 B2AI_STANDARD:293 BiomedicalStandard TDWG SDS Taxonomic Databases Working Group Standards Documentation Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:3 ToxML is an open data exchange standard that allows the representation and communication of toxicological and related data in a well-structured electronic format. True False doi:10.1080/1062936X.2013.783506 B2AI_STANDARD:294 BiomedicalStandard ToxML ToxML standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_ORG:12 Evidence-based public health decisions are based on evaluations of intervention studies with randomized and nonrandomized designs. Transparent reporting is crucial for assessing the validity and efficacy of these intervention studies, and, it facilitates synthesis of the findings for evidence-based recommendations. Therefore, the mission of the Transparent Reporting of Evaluations with Nonrandomized Designs (TREND) group is to improve the reporting standards of nonrandomized evaluations of behavioral and public health intervention True False https://www.cdc.gov/trendstatement/index.html doi:10.2105/ajph.94.3.361 https://www.cdc.gov/trendstatement/pdf/trendstatement_TREND_Checklist.pdf B2AI_STANDARD:295 BiomedicalStandard TREND Transparent Reporting of Evaluations with Nonrandomized Designs Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:26 Trusted Instant Messaging (TIM+) defines a protocol that facilitates real-time communication and incorporates secure messaging concepts to ensure information is transmitted securely between known, trusted entities both within and across enterprises. TIM+ will determine the availability or presence of trusted endpoints and support text-based communication and file transfers. True False https://directtrust.app.box.com/s/p3vp3g4bv52cyi4nbpyfpdal6t7z2qdz B2AI_STANDARD:296 BiomedicalStandard TIM+ Trusted Instant Messaging Plus Applicability Statement Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:4 Originally developed as part of the FP7 Transatlantic Tumor Model Repositories project, TumorML has been developed as an XML-based domain-specific vocabulary that includes elements from existing vocabularies, to deal with storing and transmitting existing cancer models among research communities. True False doi:10.1145/2544063.2544064 B2AI_STANDARD:297 BiomedicalStandard TumorML TumorML standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:3 B2AI_ORG:31 An alphanumeric identifier based on a substance's molecular structure and/or descriptive information. True False https://precision.fda.gov/uniisearch B2AI_STANDARD:298 BiomedicalStandard UNII Unique Ingredient Identifiers Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:13 B2AI_TOPIC:35 Variant Call Format (VCF) is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. True False https://en.wikipedia.org/wiki/Variant_Call_Format https://github.com/samtools/hts-specs B2AI_STANDARD:299 BiomedicalStandard VCF Variant Call Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_ORG:29 A text format devised by Ensembl for the eponymous Variant Effect Predictor tool. True False https://useast.ensembl.org/info/docs/tools/vep/vep_formats.html B2AI_STANDARD:300 BiomedicalStandard VEP Variant Effect Predictor format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:34 variant representation True False https://vrs.ga4gh.org/en/latest/index.html doi:10.1016/j.xgen.2021.100027 B2AI_STANDARD:301 BiomedicalStandard VRS Variation Representation Specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:35 A Locus-specific Database (LSDB) describes the variants discovered on a single gene or members of a gene family and other related functional elements. LSDBs are curated by experts on their respective loci, and as such are typically the best resources of such information available. But LSDBs vary widely in format and completeness, making data integration and exchange among them difficult and time-consuming. To address these difficulties, the VarioML format has been developed for the full range of variation data use-cases, providing semantically well-defined components which can be easily composed to fit specific needs. Using VarioML, data owners can now efficiently enable the integration, federation, and exchange of their variant data. The discoverabiliaty, extensibility, and quality of variation data is immediately enhanced. Critical new avenues of research and knowledge discovery are opened, as data using the VarioML standard can be integrated with the global library of purely genetic data. VarioML is a central prerequisite for effective modelling of phenotype data and genotype-to-phenotype relationships. It removes the long-standing technical obstacles to the effective passing of variant data from discovery laboratories into the biomedical database world. Now all that is needed is the broad participation of the genotype-to-phenotype research community. True False https://github.com/VarioML/VarioML B2AI_STANDARD:302 BiomedicalStandard VarioML VarioML format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:93 TDWG vocabularies are a collection of standardized terms and their definitions. Vocabulary standards differ from other Biodiversity Information Standards (TDWG) standards in that they are likely to change more often over time as they evolve to meet the changing needs of the biodiversity informatics community. These changes may be incremental, making it impractical to apply the full TDWG standards process to every change. The TDWG Vocabulary Maintenance Specification details the categories of changes that can be made to a TDWG vocabulary standard, the mechanisms used to achieve those changes, and the entities that are responsible for shepherding those changes through the process. True False https://www.tdwg.org/standards/vms/ B2AI_STANDARD:303 BiomedicalStandard VMS Vocabulary Maintenance Standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:9 A statistically robust Voice Handicap Index (VHI). An 85-item version of this instrument was administered to 65 consecutive patients seen in the Voice Clinic at Henry Ford Hospital. The data were subjected to measures of internal consistency reliability and the initial 85-item version was reduced to a 30-item final version. This final version was administered to 63 consecutive patients on two occasions in an attempt to assess test-retest stability, which proved to be strong. The findings of the latter analysis demonstrated that a change between two administrations of 18 points represents a significant shift in psychosocial function. False False doi:10.1044/1058-0360.0603.66 B2AI_STANDARD:304 BiomedicalStandard VHI Voice Handicap Index Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:99 Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. This document describes a consensus among participating stakeholders in the Health Care and the Life Sciences domain on the description of datasets using the Resource Description Framework (RDF). This specification meets key functional requirements, reuses existing vocabularies to the extent that it is possible, and addresses elements of data description, versioning, provenance, discovery, exchange, query, and retrieval. True False https://www.w3.org/TR/hcls-dataset/ B2AI_STANDARD:305 BiomedicalStandard HCLS W3C HCLS Dataset Description Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:12 B2AI_TOPIC:13 Wiggle files and its bedgraph variant allow you to plot quantitative data as either shades of color (dense mode) or bars of varying height (full and pack mode) on the genome. True False https://genome.ucsc.edu/goldenPath/help/wiggle.html B2AI_STANDARD:306 BiomedicalStandard WIG Wiggle Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:19 B2AI_ORG:101 A proprietary image format based on TIFF. False False https://openwetware.org/wiki/Dissecting_LSM_files B2AI_STANDARD:307 BiomedicalStandard LSM Zeiss LSM series confocal microscope image Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual B2AI_TOPIC:37 Audio data compression scheme optimized for speech coding, adopted in October 1998 as the standard speech codec by 3GPP (3d Generation Partnership Project) and now widely used in GSM (Global System for Mobile Communications). True False https://www.loc.gov/preservation/digital/formats/fdd/fdd000254.shtml B2AI_STANDARD:308 DataStandard AMR Adaptive Multi-Rate Speech Codec Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:28 Mass spectra output format used by AB SCIEX intstruments. False False doi:10.1074/mcp.R112.019695 B2AI_STANDARD:309 DataStandard WIFF Analyst native acquisition file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:15 Analyze 7.5 can store voxel-based volumes and consists of two files - One file with the actual data in a binary format with the filename extension .img and another file (header with filename extension .hdr) with information about the data such as voxel size and number of voxel in each dimension. True False https://analyzedirect.com/documents/AD_AnalyzeImage75_File_Format.pdf B2AI_STANDARD:310 DataStandard HDR/IMG Analyze file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:5 A language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware like CPUs and GPUs. The Arrow memory format also supports zero-copy reads for lightning-fast data access without serialization overhead. True False https://arrow.apache.org/ https://github.com/apache/arrow B2AI_STANDARD:311 DataStandard Arrow Apache Arrow Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_ORG:5 Avro is a row-oriented remote procedure call and data serialization framework developed within Apache's Hadoop project. It uses JSON for defining data types and protocols, and serializes data in a compact binary format. True False https://avro.apache.org/ https://github.com/apache/avro B2AI_STANDARD:312 DataStandard Avro Apache Avro Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:99 ADMS is a profile of DCAT, used to describe semantic assets (or just 'Assets'), defined as highly reusable metadata (e.g. xml schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies) that are used for eGovernment system development. True False https://www.w3.org/TR/vocab-adms/ B2AI_STANDARD:313 DataStandard ADMS Asset Description Metadata Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:37 File format for sound that wraps various sound bitstreams, ranging from uncompressed waveform to MIDI. True False https://www.loc.gov/preservation/digital/formats/fdd/fdd000005.shtml B2AI_STANDARD:314 DataStandard AIFF Audio Interchange File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 B2AI_TOPIC:37 AVI files can contain both audio and video data in a file container that allows synchronous audio-with-video playback. True False https://en.wikipedia.org/wiki/Audio_Video_Interleave B2AI_STANDARD:315 DataStandard AVI Audio Video Interleave digital multimedia container format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 A bitmap image format. True False https://en.wikipedia.org/wiki/BMP_file_format B2AI_STANDARD:316 DataStandard BMP Bitmap format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. Think JSON, except binary. Or think Protocol Buffers, except faster. True False https://capnproto.org/ https://github.com/capnproto/capnproto B2AI_STANDARD:317 DataStandard Cap'n'Proto Cap'n'Proto Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 CellML language is an open standard based on the XML markup language. CellML is being developed by the Auckland Bioengineering Institute at the University of Auckland and affiliated research groups. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. True False https://www.cellml.org/ doi:10.1186/1471-2105-11-178 B2AI_STANDARD:318 DataStandard CellML CellML language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A file format for providing citation metadata for software or datasets in plaintext files that are easy to read by both humans and machines. True False https://citation-file-format.github.io/ https://github.com/citation-file-format/citation-file-format B2AI_STANDARD:319 DataStandard CFF citation-file-format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
workflowlanguage specification for describing data analysis workflows and tools True False https://www.commonwl.org/ doi:10.48550/arXiv.2105.07028 https://github.com/common-workflow-language/common-workflow-language B2AI_STANDARD:320 DataStandard CWL Common Workflow Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 The CURATE(D) steps are a teaching and representation tool. This model is useful for onboarding data curators and orienting researchers preparing to share their data. It serves as a demonstration for the type of work involved in robust data curation, and was created to fit within institution-specific data repository workflows. True False https://datacurationnetwork.org/outputs/workflows/ https://docs.google.com/document/d/1RWt2obXOOeJRRFmVo9VAkl4h41cL33Zm5YYny3hbPZ8/edit B2AI_STANDARD:321 DataStandard CURATE(D) CURATE(D) Checklists Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:22 Reference guide for processes, best practices, and principles in data management. False True https://www.dama.org/cpages/body-of-knowledge B2AI_STANDARD:322 DataStandard DAMA-DMBOK DAMA Data Management Body of Knowledge Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:99 An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. True False https://www.w3.org/TR/vocab-dcat-1/ B2AI_STANDARD:323 DataStandard DCAT Data Catalog Vocabulary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 The DataCite Metadata Schema is a list of core metadata properties chosen for the accurate and consistent identification of a resource for citation and retrieval purposes, along with recommended use instructions. The resource that is being identified can be of any kind, but it is typically a dataset. We use the term ‘dataset’ in its broadest sense. We mean it to include not only numerical data, but any other research data outputs. True False https://schema.datacite.org/ https://schema.datacite.org/meta/kernel-4.3/metadata.xsd B2AI_STANDARD:324 DataStandard DataCite DataCite Metadata Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Describe datasets. True False https://huggingface.co/docs/datasets/dataset_card B2AI_STANDARD:325 DataStandard Dataset Cards Dataset Cards Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datasheets B2AI_TOPIC:5 ...we propose that every dataset be accompanied with a datasheet that documents its motivation, composition, collection process, recommended uses, and so on. True False https://arxiv.org/abs/1803.09010 B2AI_STANDARD:326 DataStandard Datasheets Datasheets for Datasets Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:21 eXtensible Graph Markup and Modeling Language is an XML application based on GML which is used for graph description. XGMML uses tags to describe nodes and edges of a graph. The purpose of XGMML is to make possible the exchange of graphs between differents authoring and browsing tools for graphs. True False http://xml.coverpages.org/xgmml.html B2AI_STANDARD:327 DataStandard XGMML eXtensible Graph Markup and Modeling Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:5 B2AI_ORG:83 Simple and research software appropriate goalposts to inform those who publish and/or preserve research software. True False https://www.rd-alliance.org/group/fair-research-software-fair4rs-wg/outcomes/fair-principles-research-software-fair4rs doi:10.1038/s41597-022-01710-x B2AI_STANDARD:328 DataStandard FAIR4RS FAIR Principles for Research Software Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem deprecated FIPS codes are numbers which uniquely identify geographic areas. As of database version 55, FIPS has been merged with the Geographic Names Information System (GNIS). True False https://transition.fcc.gov/oet/info/maps/census/fips/fips.txt B2AI_STANDARD:329 DataStandard FIPS Federal Information Processing System Codes for States and Counties Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 FieldML is a declarative language for building hierarchical models represented by generalized mathematical fields. FieldML is developed as a data model and accompanying API. Find out more about the FieldML API, where to get the latest release and how to contribute to its development. FieldML is a declarative language for representing hierarchical models using generalized mathematical fields. FieldML can be used to represent the dynamic 3D geometry and solution fields from computational models of cells, tissues and organs. It enables model interchange for the bioengineering and general engineering analysis communities. Example uses are models of tissue structure, the distribution of proteins and other biochemical compounds, anatomical annotation, and other biological annotation. True False doi:10.1007/s11517-013-1097-7 B2AI_STANDARD:330 DataStandard FieldML FieldML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:37 FLAC (Free Lossless Audio Codec) is an audio coding format for lossless compression of digital audio. True False https://en.wikipedia.org/wiki/FLAC https://xiph.org/flac/format.html B2AI_STANDARD:331 DataStandard FLAC Free Lossless Audio Codec Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Describe datasets. True False https://specs.frictionlessdata.io/data-package/ https://github.com/frictionlessdata/specs B2AI_STANDARD:332 DataStandard Frictionless Frictionless Data Package Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:34 Provides a way for an API to expose a set of metadata to help discovery and aggregation of services via computational methods. True False https://github.com/ga4gh-discovery/ga4gh-service-info B2AI_STANDARD:333 DataStandard serviceinfo GA4GH serviceinfo Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
workflowlanguage B2AI_TOPIC:20 A schema moving Galaxy's workflow description language toward standards such as the Common Workflow Language. True False https://github.com/galaxyproject/gxformat2 B2AI_STANDARD:334 DataStandard gxformat2 Galaxy workflow Format 2 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:14 B2AI_ORG:98 The Geographic Names Information System (GNIS) is the Federal and national standard for geographic nomenclature. The U.S. Geological Survey's National Geospatial Program developed the GNIS in support of the U.S. Board on Geographic Names as the official repository of domestic geographic names data, the official vehicle for geographic names use by all departments of the Federal Government, and the source for applying geographic names to Federal electronic and printed products. True False https://www.usgs.gov/us-board-on-geographic-names/domestic-names https://www.usgs.gov/u.s.-board-on-geographic-names/download-gnis-data B2AI_STANDARD:335 DataStandard GNIS ID Geographic Names Information System Feature IDs Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:6 The GENC Standard specifies a profile of ISO 3166 codes for the representation of names of countries and their subdivisions. True False https://www.dni.gov/index.php/who-we-are/organizations/ic-cio/ic-cio-related-menus/ic-cio-related-links/ic-technical-specifications/geopolitical-entities-names-and-codes https://evs.nci.nih.gov/ftp1/GENC/ B2AI_STANDARD:336 DataStandard GENC Geopolitical Entities, Names, and Codes Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat markuplanguage B2AI_TOPIC:21 An XML file format and language for describing graphs. True False http://graphml.graphdrawing.org/specification.html B2AI_STANDARD:337 DataStandard GraphML Graph Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:15 A bitmap image format. True False https://en.wikipedia.org/wiki/GIF B2AI_STANDARD:338 DataStandard GIF Graphics Interchange Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format. True False https://www.hdfgroup.org/solutions/hdf5/ B2AI_STANDARD:339 DataStandard HDF5 HDF5 format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format. True False https://hdmf-common-schema.readthedocs.io/en/latest/format.html doi:10.1109/bigdata47090.2019.9005648 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8500680/ B2AI_STANDARD:340 DataStandard HDMF HDMF format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 B2AI_ORG:47 General-purpose ISA-Tab file format - an extensible, hierarchical structure that focuses on the description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships). True False https://isa-specs.readthedocs.io/en/latest/isatab.html https://github.com/ISA-tools/ISAdatasets B2AI_STANDARD:341 DataStandard ISA-Tab ISA-Tab format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:6 B2AI_ORG:49 The purpose of ISO 3166 is to define internationally recognized codes of letters and/or numbers that we can use when we refer to countries and their subdivisions. However, it does not define the names of countries – this information comes from United Nations sources (Terminology Bulletin Country Names and the Country and Region Codes for Statistical Use maintained by the United Nations Statistics Divisions). True False https://www.iso.org/iso-3166-country-codes.html https://en.wikipedia.org/wiki/List_of_ISO_3166_country_codes B2AI_STANDARD:342 DataStandard ISO 3166 ISO 3166 Country Codes Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:49 A way of presenting dates and times that is clearly defined and understandable to both people and machines. True False https://www.iso.org/iso-8601-date-and-time-format.html B2AI_STANDARD:343 DataStandard ISO 8601 ISO 8601 Date and time format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 A method of lossy compression for digital images. True False https://en.wikipedia.org/wiki/JPEG B2AI_STANDARD:344 DataStandard JPEG Joint Photographic Experts Group Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 JSON validation True False https://json-schema.org/ https://github.com/json-schema-org/json-schema-spec B2AI_STANDARD:345 DataStandard JSON-schema JSON-schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:21 linked knowledge True False https://github.com/biolink/kgx/blob/master/specification/kgx-format.md B2AI_STANDARD:346 DataStandard KGX Knowledge Graph Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 LinkML is a flexible modeling language that allows you to author schemas in YAML that describe the structure of your data. Additionally, it is a framework for working with and validating data in a variety of formats (JSON, RDF, TSV), with generators for compiling LinkML schemas to other frameworks. True False https://linkml.io/linkml https://github.com/linkml/linkml B2AI_STANDARD:347 DataStandard LinkML LinkML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:99 A product of the W3C Math Working Group, MathML is a low-level specification for describing mathematics as a basis for machine to machine communication which provides a much needed foundation for the inclusion of mathematical expressions in Web pages. It is also important in publishing workflows for science and technology and wherever mathematics has to be handled by software. True False https://www.w3.org/Math/whatIsMathML.html B2AI_STANDARD:348 DataStandard MathML MathML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 B2AI_ORG:56 Format used by Microsoft Excel spreadsheet software. False False https://www.iso.org/standard/71691.html B2AI_STANDARD:349 DataStandard xlsx Microsoft Excel spreadsheet container file Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
modelcards B2AI_TOPIC:5 B2AI_ORG:37 Structured documentation detailing performance characteristics of machine learning models. True False https://modelcards.withgoogle.com/about https://arxiv.org/abs/1810.03993 https://github.com/tensorflow/model-card-toolkit/blob/master/model_card_toolkit/schema/v0.0.2/model_card.schema.json B2AI_STANDARD:350 DataStandard Model Cards Model Cards Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:37 MP3 (formally MPEG-1 Audio Layer III or MPEG-2 Audio Layer III) is a coding format for digital audio. True False https://en.wikipedia.org/wiki/MP3 https://www.iso.org/standard/26797.html B2AI_STANDARD:351 DataStandard MP3 MPEG-1 Audio Layer 3 MPEG-2 Audio Layer 3 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 B2AI_TOPIC:37 B2AI_ORG:49 A digital multimedia container format most commonly used to store video and audio, but it can also be used to store other data such as subtitles and still images. Like most modern container formats, it allows streaming over the Internet. True False https://en.wikipedia.org/wiki/MP4_file_format https://www.loc.gov/preservation/digital/formats/fdd/fdd000155.shtml B2AI_STANDARD:352 DataStandard MPEG-4 MPEG-4 Part 14 digital multimedia container format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_ORG:8 A standardized format for chromatographic data representation. True False https://www.unidata.ucar.edu/software/netcdf/ https://www.astm.org/e1947-98r14.html B2AI_STANDARD:353 DataStandard netCDF Network Common Data Form Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 An exchange format for neural network models produced using Torch, Caffe, TensorFlow, Theano, Chainer, Caffe2, PyTorch, or MXNet. True False https://www.khronos.org/nnef https://github.com/KhronosGroup/NNEF-Tools B2AI_STANDARD:354 DataStandard NNEF Neural Network Exchange Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 B2AI_ORG:49 This standard specifies an XML implementation for the OGC and ISO Observations and Measurements (O&M) conceptual model (OGC Observations and Measurements v2.0 also published as ISO/DIS 19156), including a schema for Sampling Features. This encoding is an essential dependency for the OGC Sensor Observation Service (SOS) Interface Standard. More specifically, this standard defines XML schemas for observations, and for features involved in sampling when making observations. These provide document models for the exchange of information describing observation acts and their results, both within and between different scientific and technical communities. True False https://www.ogc.org/standards/om B2AI_STANDARD:355 DataStandard OMXML OGC and ISO Observations and Measurements standard in XML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:37 File format and bitstream encoding for for spoken content, targeted at a wide range of devices other than mobile phones. True False https://speex.org/docs/manual/speex-manual/node8.html B2AI_STANDARD:356 DataStandard OGG Speex Ogg Speex Audio Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 ONNX is an open format built to represent machine learning models. True False https://onnx.ai/ https://github.com/onnx/onnx/blob/main/docs/IR.md B2AI_STANDARD:357 DataStandard ONNX Open Neural Network Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Standard for describing program interfaces. True False https://spec.openapis.org/oas/latest.html https://github.com/OAI/OpenAPI-Specification/ B2AI_STANDARD:358 DataStandard OpenAPI OpenAPI Specification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 Apache Parquet is a free and open-source column-oriented data storage format in the Apache Hadoop ecosystem. True False https://parquet.apache.org/ B2AI_STANDARD:359 DataStandard parquet Parquet Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:43 PURLs are Web addresses or Uniform Resource Locators (URLs) that act as permanent identifiers in the face of a dynamic and changing Web infrastructure. Instead of resolving directly to Web resources (documents, data, services, people, etc.) PURLs provide a level of indirection that allows the underlying Web addresses of resources to change over time without negatively affecting systems that depend on them. This capability provides continuity of references to network resources that may migrate from machine to machine for business, social or technical reasons. True False https://sites.google.com/site/persistenturls/ https://code.google.com/archive/p/persistenturls/ B2AI_STANDARD:360 DataStandard PURL Persistent Uniform Resource Locator Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:15 B2AI_TOPIC:32 A file format to present documents, including text formatting and images, in a manner independent of application software, hardware, and operating systems. True False https://en.wikipedia.org/wiki/PDF B2AI_STANDARD:361 DataStandard PDF Portable Document Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 A raster-graphics file format that supports lossless data compression. True False https://en.wikipedia.org/wiki/Portable_Network_Graphics B2AI_STANDARD:362 DataStandard PNG Portable Network Graphics Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:15 B2AI_TOPIC:32 A page description language. True False https://en.wikipedia.org/wiki/PostScript B2AI_STANDARD:363 DataStandard PS Postscript Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
markuplanguage B2AI_TOPIC:5 PMML (Predictive Model Markup Language) uses XML to represent mining models. The structure of the models is described by an XML Schema. One or more mining models can be contained in a PMML document. A PMML document is an XML document with a root element of type PMML True False https://dmg.org/pmml/v4-4-1/GeneralStructure.html B2AI_STANDARD:364 DataStandard PMML Predictive Model Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:37 Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data. True False https://developers.google.com/protocol-buffers/ https://github.com/protocolbuffers/protobuf B2AI_STANDARD:365 DataStandard protobuf Protocol Buffers Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:99 The PROV Family of Documents defines a model, corresponding serializations and other supporting definitions to enable the inter-operable interchange of provenance information in heterogeneous environments such as the Web. True False https://www.w3.org/TR/prov-overview/ B2AI_STANDARD:366 DataStandard PROV Provenance Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 Serialization format for a Python object structure. “Pickling” is the process whereby a Python object hierarchy is converted into a byte stream, and “unpickling” is the inverse operation, whereby a byte stream (from a binary file or bytes-like object) is converted back into an object hierarchy. True False https://docs.python.org/3.8/library/pickle.html https://github.com/python/cpython/blob/3.8/Lib/pickle.py B2AI_STANDARD:367 DataStandard pickle Python pickle format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:97 The Qualitative Data Exchange Schema (QuDEx) allows users to discover, find, retrieve and cite complex qualitative data collections in context. True False https://www.data-archive.ac.uk/managing-data/standards-and-procedures/metadata-standards/qudex/ https://dam.data-archive.ac.uk/standards/qudex_v03_01.xsd B2AI_STANDARD:368 DataStandard QuDEx Qualitative Data Exchange Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
guidelines B2AI_TOPIC:5 B2AI_ORG:83 A framework for implementing effective curation workflows for achieving greater FAIR-ness and long-term usability of research data and code. True False https://www.rd-alliance.org/group/cure-fair-wg/outcomes/10-things-curating-reproducible-and-fair-research https://curating4reproducibility.org/10things/ B2AI_STANDARD:369 DataStandard RDA 10 Things RDA CURE-FAIR 10 Things for Curating Reproducible and FAIR Research Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:99 RDF Schema (RDFS) is the RDF vocabulary description language. RDFS defines classes and properties that may be used to describe classes, properties and other resources. True False https://www.w3.org/TR/rdf-schema/ B2AI_STANDARD:370 DataStandard RDFS RDF Schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:6 The Registry Interchange Format - Collections and Services (RIF-CS) Schema was developed as a data interchange format for supporting the electronic exchange of collection and service descriptions. It organises information about collections and services into the format required by the ANDS Collections Registry. True False https://services.ands.org.au/documentation/rifcs/1.2.0/guidelines/rif-cs.html B2AI_STANDARD:371 DataStandard RIF-CS Registry Interchange Format - Collections and Services schema Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A community effort to establish a lightweight approach to packaging research data with their metadata. It is based on schema.org annotations in JSON-LD, and aims to make best-practice in formal metadata description accessible and practical for use in a wider variety of situations, from an individual researcher working with a folder of data, to large data-intensive computational research environments. True False https://www.researchobject.org/ro-crate/ doi:10.3233/DS-210053 https://www.researchobject.org/ro-crate/specification.html B2AI_STANDARD:372 DataStandard RO-CRATE Research Object Crate Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:99 describe anything True False https://www.w3.org/TR/rdf-schema/ B2AI_STANDARD:373 DataStandard RDF Resource Description Framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 A new simple format for storing tensors safely (as opposed to pickle) and that is still fast (zero-copy). True False https://github.com/huggingface/safetensors B2AI_STANDARD:374 DataStandard Safetensors Safetensors Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 B2AI_ORG:99 Scalable Vector Graphics (SVG) Version 1.1, a modularized language for describing two-dimensional vector and mixed vector/raster graphics in XML. True False https://www.w3.org/Graphics/SVG/About.html B2AI_STANDARD:375 DataStandard SVG Scalable Vector Graphics Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 B2AI_ORG:99 A language for validating RDF graphs against a set of conditions. These conditions are provided as shapes and other constructs expressed in the form of an RDF graph. RDF graphs that are used in this manner are called shapes graphs in SHACL and the RDF graphs that are validated against a shapes graph are called data graphs. As SHACL shape graphs are used to validate that data graphs satisfy a set of conditions they can also be viewed as a description of the data graphs that do satisfy these conditions. Such descriptions may be used for a variety of purposes beside validation, including user interface building, code generation and data integration. True False https://www.w3.org/TR/shacl/ B2AI_STANDARD:376 DataStandard SHACL Shapes Constraint Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 A raster graphics file format. True False https://en.wikipedia.org/wiki/Silicon_Graphics_Image B2AI_STANDARD:377 DataStandard SGI Silicon Graphics image format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 SSSOM is a Simple Standard for Sharing Ontological Mappings, providing a TSV-based representation for ontology term mappings, a comprehensive set of standard metadata elements to describe mappings, and a standard translation between the TSV and the Web Ontology Language (OWL). True False https://mapping-commons.github.io/sssom/ doi:10.1093/database/baac035 https://github.com/mapping-commons/sssom B2AI_STANDARD:378 DataStandard SSSOM Simple Standard for Sharing Ontological Mappings Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 Statismo defines a storage format (Statistical Image And Shape Models) based on HDF5, which includes all the information necessary to use the model, as well as meta-data about the model creation, which helps to make model building reproducible. True False https://github.com/statismo/statismo B2AI_STANDARD:379 DataStandard statismo Statismo format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:88 SDMX is an initiative to foster standards for the exchange of statistical information. True False https://sdmx.org/ B2AI_STANDARD:380 DataStandard SDMX Statistical Data and Metadata eXchange standard Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 STL files describe only the surface geometry of a three-dimensional object without any representation of color, texture or other common CAD model attributes. The STL format specifies both ASCII and binary representations. True False https://www.loc.gov/preservation/digital/formats/fdd/fdd000504.shtml B2AI_STANDARD:381 DataStandard STL STereoLithography File Format Family Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:93 The goal of the Structured Descriptive Data (SDD) standard is to allow capture, transport, caching and archiving of descriptive data in all the forms shown above, using a platform- and application-independent, international standard. Such a standard is crucial to enabling lossless porting of data between existing and future software platforms including identification, data-mining and analysis tools, and federated databases. True False https://www.tdwg.org/standards/sdd/ https://github.com/tdwg/sdd B2AI_STANDARD:382 DataStandard SDD Structured Descriptive Data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 An image file format for storing raster graphics images. True False https://en.wikipedia.org/wiki/TIFF B2AI_STANDARD:383 DataStandard TIFF Tagged Image File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 A tar (tape archive) file format is an archive created by tar, a UNIX-based utility used to package files together for backup or distribution purposes. It contains multiple files (also known as a tarball) stored in an uncompressed format along with metadata about the archive. Tar files are not compressed archive files. They are often compressed with file compression utilities such as gzip or bzip2. True False https://www.loc.gov/preservation/digital/formats/fdd/fdd000531.shtml B2AI_STANDARD:384 DataStandard TAR TAR archive file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:93 The TDWG Access Protocol for Information Retrieval (TAPIR) is a Web Service protocol and XML schema to perform queries across distributed databases of varied physical and logical structure. It was originally designed to be used by federated networks. TAPIR is intended for communication between applications, using HTTP as the transport mechanism. TAPIR's flexibility makes it suitable to both very simple service implementations where the provider only responds to a set of pre-defined queries, or more advanced implementations where the provider software can dynamically parse complex queries referencing output models supplied by the client. True False https://www.tdwg.org/standards/tapir/ B2AI_STANDARD:385 DataStandard TAPIR TDWG Access Protocol for Information Retrieval Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:5 B2AI_ORG:84 A common syntax for communication of quantities and their units. True False https://unitsofmeasure.org/ucum B2AI_STANDARD:386 DataStandard UCUM The Unified Code for Units of Measure Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:37 Waveform Audio File Format (WAVE or WAV due to its filename extension is an audio file format standard. True False https://en.wikipedia.org/wiki/WAV https://sites.google.com/site/musicgapi/technical-documents/wav-file-format B2AI_STANDARD:387 DataStandard WAV Waveform Audio File Format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:99 The Web Ontology Language (OWL) is a family of knowledge representation languages or ontology languages for authoring ontologies or knowledge bases. The languages are characterized by formal semantics and RDF/XML-based serializations for the Semantic Web. OWL is endorsed by the World Wide Web Consortium (W3C) and has attracted academic, medical and commercial interest. The OWL 2 Web Ontology Language, informally OWL 2, is an ontology language for the Semantic Web with formally defined meaning. OWL 2 ontologies provide classes, properties, individuals, and data values and are stored as Semantic Web documents. OWL 2 ontologies can be used along with information written in RDF, and OWL 2 ontologies themselves are primarily exchanged as RDF documents. True False https://www.w3.org/OWL/ B2AI_STANDARD:388 DataStandard OWL Web Ontology Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
workflowlanguage The Workflow Description Language (WDL) is a way to specify data processing workflows with a human-readable and -writeable syntax. WDL makes it straightforward to define analysis tasks, chain them together in workflows, and parallelize their execution. The language makes common patterns simple to express, while also admitting uncommon or complicated behavior; and strives to achieve portability not only across execution platforms, but also different types of users. Whether one is an analyst, a programmer, an operator of a production system, or any other sort of user, WDL should be accessible and understandable. True False https://openwdl.org/ https://github.com/openwdl/wdl B2AI_STANDARD:389 DataStandard WDL Workflow Description Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual deprecated fileformat B2AI_TOPIC:15 X PixMap (XBM) is an image file format used by the X Window System. Replaced by XPM. True False https://en.wikipedia.org/wiki/X_PixMap B2AI_STANDARD:390 DataStandard XBM X PixMap bitmap image format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
audiovisual fileformat B2AI_TOPIC:15 X PixMap (XPM) is an image file format used by the X Window System. True False https://en.wikipedia.org/wiki/X_PixMap B2AI_STANDARD:391 DataStandard XPM X PixMap image format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 An open source project and Python package that introduces labels in the form of dimensions, coordinates, and attributes on top of raw NumPy-like arrays, which allows for more intuitive, more concise, and less error-prone user experience. True False https://xarray.dev/ https://github.com/pydata/xarray B2AI_STANDARD:392 DataStandard xarray xarray Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 A human-readable data-serialization language. It is commonly used for configuration files and in applications where data is being stored or transmitted. True False https://en.wikipedia.org/wiki/YAML B2AI_STANDARD:393 DataStandard YAML YAML Ain't Markup Language Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A format for storage of large N-dimensional typed arrays. Has implementations in multiple programming languages. True False https://zarr.dev/ B2AI_STANDARD:394 DataStandard Zarr Zarr Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
fileformat B2AI_TOPIC:5 An archive file format that supports lossless data compression. True False https://en.wikipedia.org/wiki/ZIP_(file_format) B2AI_STANDARD:395 DataStandard ZIP ZIP compressed file format Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Adapter refers to a set of newly introduced weights, typically within the layers of a transformer model. Adapters provide an alternative to fully fine-tuning the model for each downstream task, while maintaining performance. AdapterHub builds on the HuggingFace transformers framework, requiring as little as two additional lines of code to train adapters for a downstream task. True False https://adapterhub.ml/ doi:10.48550/arXiv.2007.07779 https://github.com/adapter-hub/Hub B2AI_STANDARD:396 ModelRepository AdapterHub AdapterHub Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 A community-driven, fully open resource where standardized pre-trained models can be shared, explored, tested, and downloaded for further adaptation or direct deployment in multiple end user-facing tools (e.g., ilastik, deepImageJ, QuPath, StarDist, ImJoy, ZeroCostDL4Mic, CSBDeep). True False https://bioimage.io/#/ doi:10.1101/2022.06.07.495102 https://github.com/bioimage-io/bioimage.io B2AI_STANDARD:397 ModelRepository Bioimage Bioimage Model Zoo Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
dataregistry B2AI_TOPIC:5 machine learning models, with focus on language models and NLP True False https://huggingface.co/models https://github.com/huggingface/huggingface_hub B2AI_STANDARD:398 ModelRepository HF Models Hugging Face 🤗 Models Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 machine learning models True False https://modelzoo.co/ B2AI_STANDARD:399 ModelRepository modelzoo.co Model Zoo Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
dataregistry B2AI_TOPIC:5 OpenML is an open platform for sharing datasets, algorithms, and experiments True True https://www.openml.org/ https://github.com/openml/OpenML B2AI_STANDARD:400 ModelRepository OpenML OpenML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 machine learning models True False https://pytorch.org/hub/ https://github.com/pytorch/hub B2AI_STANDARD:401 ModelRepository PyTorch Hub PyTorch Hub Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:37 machine learning models True False https://tfhub.dev/ B2AI_STANDARD:402 ModelRepository TFHub Tensorflow Hub Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:7 B2AI_ORG:4 Definitions for terms used in human bioacoustics. False True https://webstore.ansi.org/Standards/ASA/ANSIASAS3202015R2020 B2AI_STANDARD:403 OntologyOrVocabulary ASA/ANSI S3.20 Acoustical Society of America / American National Standards Institute S3.20 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 concepts related to Alzheimer's Disease True False https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO B2AI_STANDARD:404 OntologyOrVocabulary ADO Alzheimer's Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Antibiotic resistance genes and mutations True False doi:10.1093/nar/gkz935 https://github.com/arpcard/aro B2AI_STANDARD:405 OntologyOrVocabulary ARO Antibiotic Resistance Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Terms and relations for interoperation between epidemic models and public health application software. True False https://github.com/ApolloDev/apollo-sv B2AI_STANDARD:406 OntologyOrVocabulary APOLLO_SV Apollo Structured Vocabulary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 General terms for AI True False https://bioportal.bioontology.org/ontologies/AIO https://github.com/berkeleybop/artificial-intelligence-ontology B2AI_STANDARD:407 OntologyOrVocabulary AIO Artificial Intelligence Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 Upper level ontology. True False http://basic-formal-ontology.org/ doi:10.3233/AO-160164 https://github.com/BFO-ontology/BFO B2AI_STANDARD:408 OntologyOrVocabulary BFO Basic Formal Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Biodiversity data, including data on museum collections and environmental/metagenomic samples. True False https://github.com/BiodiversityOntologies/bco B2AI_STANDARD:409 OntologyOrVocabulary BCO Biological Collections Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:15 Sample preparation, visualization and imaging methods used in biomedical research. True False http://cellimagelibrary.org/ https://github.com/CRBS/Biological_Imaging_Methods_Ontology/ B2AI_STANDARD:410 OntologyOrVocabulary FBBI Biological Imaging Methods Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. True False doi:10.1186/2041-1480-5-34 https://github.com/obophenotype/biological-spatial-ontology B2AI_STANDARD:411 OntologyOrVocabulary BSPO Biological Spatial Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. True False http://www.brenda-enzymes.org/ doi:10.1093/nar/gkq968 https://github.com/BRENDA-Enzymes/BTO B2AI_STANDARD:412 OntologyOrVocabulary BTO BRENDA tissue / enzyme source Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A structured controlled vocabulary of Caenorhabditis elegans phenotypes. True False doi:10.1186/1471-2105-12-32 https://github.com/obophenotype/c-elegans-phenotype-ontology B2AI_STANDARD:413 OntologyOrVocabulary WBPHENOTYPE C. elegans phenotype ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 Entities related to cardiovascular diseases. True False https://github.com/OpenLHS/CVDO B2AI_STANDARD:414 OntologyOrVocabulary CVDO Cardiovascular Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Standardize and integrate cell line information and to support computer-assisted reasoning. True False http://www.clo-ontology.org/ doi:10.1186/2041-1480-5-3 https://github.com/CLO-Ontology/CLO B2AI_STANDARD:415 OntologyOrVocabulary CLO Cell Line Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Cell Types True False https://cell-ontology.github.io/ doi:10.1186/s13326-016-0088-7 https://github.com/obophenotype/cell-ontology B2AI_STANDARD:416 OntologyOrVocabulary CL Cell Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:3 B2AI_ORG:29 A distinct role hierarchy for chemicals. True False doi:10.26434/chemrxiv.12591221.v1 https://github.com/obophenotype/chiro B2AI_STANDARD:417 OntologyOrVocabulary CHIRO CHEBI Integrated Role Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:3 B2AI_ORG:29 Chemicals True False https://www.ebi.ac.uk/chebi/ doi:10.1093/nar/gkv1031 https://github.com/ebi-chebi/ChEBI B2AI_STANDARD:418 OntologyOrVocabulary CHEBI Chemical Entities of Biological Interest Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:3 Descriptors commonly used in cheminformatics software applications and the algorithms which generate them. True False doi:10.1371/journal.pone.0025513 https://github.com/semanticchemistry/semanticchemistry B2AI_STANDARD:419 OntologyOrVocabulary CHEMINF Chemical Information Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:3 A chemical methods ontology. True False https://github.com/rsc-ontologies/rsc-cmo B2AI_STANDARD:420 OntologyOrVocabulary CHMO Chemical Methods Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 An ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. True False doi:10.5281/zenodo.6522019 https://github.com/OpenLHS/LABO B2AI_STANDARD:421 OntologyOrVocabulary LABO clinical LABoratory Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 Morphological and physiological measurement records generated from clinical and model organism research and health programs. True False doi:10.1186/2041-1480-4-26 https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology B2AI_STANDARD:422 OntologyOrVocabulary CMO Clinical measurement ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:13 Code set for active and inactive vaccines available in the US. True False https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx B2AI_STANDARD:423 OntologyOrVocabulary CVX Clinical Vaccines Administered Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species. True False https://github.com/obophenotype/caro/ B2AI_STANDARD:424 OntologyOrVocabulary CARO Common Anatomy Reference Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_TOPIC:7 Common Terminology Criteria for Adverse Events (CTCAE) is widely accepted throughout the oncology community as the standard classification and severity grading scale for adverse events in cancer therapy clinical trials and other oncology settings. True False https://bioportal.bioontology.org/ontologies/CTCAE https://ctep.cancer.gov/protocoldevelopment/electronic_applications/ctc.htm B2AI_STANDARD:425 OntologyOrVocabulary CTCAE Common Terminology Criteria for Adverse Events Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A formalization of concepts and relations relevant to evolutionary comparative analysis. True False doi:10.4137/EBO.S2320 https://github.com/evoinfo/cdao B2AI_STANDARD:426 OntologyOrVocabulary CDAO Comparative Data Analysis Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Nutritional attributes of material entities that contribute to human diet. True False https://cdno.info/ doi:10.3389/fnut.2022.928837 https://github.com/Southern-Cross-Plant-Science/cdno B2AI_STANDARD:427 OntologyOrVocabulary CDNO Compositional Dietary Nutrition Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Capture confidence information about annotations. True False doi:10.1093/database/bav043 https://github.com/BgeeDB/confidence-information-ontology B2AI_STANDARD:428 OntologyOrVocabulary CIO Confidence Information Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:16 A classification of the diverse roles performed in the work leading to a published research output in the sciences. True False https://github.com/data2health/contributor-role-ontology B2AI_STANDARD:429 OntologyOrVocabulary CRO Contributor Role Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:75 Terms from a wide range of OBO projects to improve interoperability. True False https://github.com/OBOFoundry/COB B2AI_STANDARD:430 OntologyOrVocabulary COB Core Ontology for Biology and Biomedicine Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 Ontologically represent and standardize various aspects of coronavirus infectious. True False doi:10.1038/s41597-020-0523-6 https://github.com/cido-ontology/cido B2AI_STANDARD:431 OntologyOrVocabulary CIDO Coronavirus Infectious Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 B2AI_ORG:33 A structured resource integrating basic terms and concepts in the context of clinical trials. True False https://github.com/ClinicalTrialOntology/CTO/ B2AI_STANDARD:432 OntologyOrVocabulary CTO CTO Core Ontology of Clinical Trials Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 B2AI_ORG:34 Data use rules True False https://github.com/EBISPOT/DUO B2AI_STANDARD:433 OntologyOrVocabulary DUO Data Use Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
An ontology developed to facilitate information curation in the area of medical devices, experimental scaffolds and biomaterials. True False https://bioportal.bioontology.org/ontologies/DEB doi:10.1002/adfm.201909910 https://github.com/ProjectDebbie/Ontology_DEB B2AI_STANDARD:434 OntologyOrVocabulary DEB Devices, Experimental scaffolds and Biomaterials Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 This ontology network aims at representing the main sets of entities and relationships used in the context of DevOps infrastructure. It is the result of a collaboration between Huawei Research Ireland and the Ontology Engineering Group at Universidad Politécnica de Madrid. It originally started from an analysis of the Configuration Management Databases used by Huawei Research Ireland for the management of a large part of its DevOps infrastructure, and has evolved into an ontology that may be used as a starting point for the standardisation of the representation of CMDB-related data across vendors. True False https://oeg-upm.github.io/devops-infra/index.html https://github.com/oeg-upm/devops-infra B2AI_STANDARD:435 OntologyOrVocabulary devops-infra Devops Infrastructure Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. True False https://github.com/DiseaseOntology/DiseaseDriversOntology B2AI_STANDARD:436 OntologyOrVocabulary DISDRIV Disease Drivers Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Commonly encountered and/or high level Drosophila phenotypes. True False https://github.com/FlyBase/flybase-controlled-vocabulary/wiki doi:10.1186/2041-1480-4-30 https://github.com/FlyBase/drosophila-phenotype-ontology B2AI_STANDARD:437 OntologyOrVocabulary DPO Drosophila Phenotype Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:8 B2AI_TOPIC:26 Drug Target Ontology (DTO) is being developed at the University of Miami in the research group of Stephan Schürer. DTO was developed as part of the Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg/overview), is supported by grant (IDG Knowledge Management Center, (U54CA189205). DTO is a novel semantic framework to formalize knowledge about drug targets and is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. True False https://bioportal.bioontology.org/ontologies/DTO doi:10.1186/s13326-017-0161-x http://drugtargetontology.org/ B2AI_STANDARD:438 OntologyOrVocabulary DTO Drug Target Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:8 The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology True False https://github.com/DIDEO/DIDEO B2AI_STANDARD:439 OntologyOrVocabulary DIDEO Drug-drug Interaction and Drug-drug Interaction Evidence Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:29 Data types, identifiers, and formats True False doi:10.1093/bioinformatics/btt113 https://github.com/edamontology/edamontology B2AI_STANDARD:440 OntologyOrVocabulary EDAM EMBRACE Data And Methods Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Affective phenomena such as emotions, moods, appraisals and subjective feelings. True False https://github.com/jannahastings/emotion-ontology B2AI_STANDARD:441 OntologyOrVocabulary MFOEM Emotion Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:11 Environmental systems, components, and processes. True False http://environmentontology.org/ https://github.com/EnvironmentOntology/envo B2AI_STANDARD:442 OntologyOrVocabulary ENVO Environment Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:11 Exposures to experimental treatments of plants and model organisms. True False https://github.com/EnvironmentOntology/environmental-exposure-ontology B2AI_STANDARD:443 OntologyOrVocabulary ECTO Environmental conditions, treatments and exposures ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 The Evidence Graph Ontology (EVI) extends core concepts from the W3C Provenance Ontology [PROV-O] to describe evidence for correctness of findings in biomedical publications. The semantic data model in EVI is expressed using OWL2 Web Ontology Language. True False https://evidencegraph.github.io/EVI/index.html https://github.com/EvidenceGraph/EVI B2AI_STANDARD:444 OntologyOrVocabulary EVI Evidence Graph Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry An ontology for experimental and other evidence statements. True False https://www.evidenceontology.org/ doi:10.1093/nar/gkab1025 https://github.com/evidenceontology/evidenceontology B2AI_STANDARD:445 OntologyOrVocabulary ECO Evidence ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model org... True False https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 doi:10.1186/2041-1480-4-26 https://github.com/rat-genome-database/XCO-experimental-condition-ontology B2AI_STANDARD:446 OntologyOrVocabulary XCO Experimental condition ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:11 Vocabularies for describing exposure data to inform understanding of environmental health. True False https://github.com/CTDbase/exposure-ontology B2AI_STANDARD:447 OntologyOrVocabulary EXO Exposure ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Phenotypes observed in fission yeast. True False doi:10.1093/bioinformatics/btt266 https://github.com/pombase/fypo B2AI_STANDARD:448 OntologyOrVocabulary FYPO Fission Yeast Phenotype Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:8 Food-Drug interactions automatically extracted from scientific literature. True False https://gitub.u-bordeaux.fr/erias/fideo https://github.com/getbordea/fideo/ B2AI_STANDARD:449 OntologyOrVocabulary FIDEO Food Interactions with Drugs Evidence Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and agriculture tha... True False https://foodon.org/ doi:10.1038/s41538-018-0032-6 https://github.com/FoodOntology/foodon/ B2AI_STANDARD:450 OntologyOrVocabulary FOODON Food Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Represent food intake data and associate it with metabolomic data True False doi:10.1093/bioinformatics/btab626 https://github.com/pcastellanoescuder/FoodBiomarkerOntology B2AI_STANDARD:451 OntologyOrVocabulary FOBI Food-Biomarker Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Application ontology used to convert vertebrate trait data in spreadsheets to triples. True False https://futres.org/ https://github.com/futres/fovt B2AI_STANDARD:452 OntologyOrVocabulary FOVT FuTRES Ontology of Vertebrate Traits Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:6 Terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation. True False https://gsso.research.cchmc.org/ https://github.com/Superraptor/GSSO B2AI_STANDARD:453 OntologyOrVocabulary GSSO Gender, Sex, and Sexual Orientation Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:12 B2AI_ORG:36 Function of genes and gene products. True False http://geneontology.org/ doi:10.1093/nar/gkaa1113 https://github.com/geneontology/go-ontology B2AI_STANDARD:454 OntologyOrVocabulary GO Gene Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Vocabulary necessary to identify, document and research foodborne pathogens. True False http://genepio.org/ https://github.com/GenEpiO/genepio B2AI_STANDARD:455 OntologyOrVocabulary GENEPIO Genomic Epidemiology Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 B2AI_TOPIC:6 Genomics cohort attributes. True False https://github.com/IHCC-cohorts/GECKO B2AI_STANDARD:456 OntologyOrVocabulary GECKO Genomics Cohorts Knowledge Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:58 Genotypes True False https://github.com/monarch-initiative/GENO-ontology B2AI_STANDARD:457 OntologyOrVocabulary GENO Genotype Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:14 B2AI_ORG:96 An ontology of geographical entities True False https://github.com/ufbmi/geographical-entity-ontology/ B2AI_STANDARD:458 OntologyOrVocabulary GEO Geographical Entity Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:35 The Global Medical Device Nomenclature (GMDN) is a comprehensive set of terms, within a structured category hierarchy, which name and group ALL medical device products including implantables, medical equipment, consumables, and diagnostic devices. False True https://www.gmdnagency.org/ B2AI_STANDARD:459 OntologyOrVocabulary GMDN Global Medical Device Nomenclature Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage). True False https://gnome.glyomics.org/ doi:10.5281/zenodo.6678279 https://github.com/glygen-glycan-data/GNOme B2AI_STANDARD:460 OntologyOrVocabulary GNO Glycan Naming and Subsumption Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:92 Surveillance system level data. True False https://w3id.org/hso https://github.com/SVA-SE/HSO B2AI_STANDARD:461 OntologyOrVocabulary HSO Health Surveillance Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 An index to the HL7-supported Code Systems. True False https://www.hl7.org/documentcenter/public/standards/vocabulary/vocabulary_tables/infrastructure/vocabulary/vocabulary.html#voc-systems B2AI_STANDARD:462 OntologyOrVocabulary HL7 Vocabulary HL7 Vocabulary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Concepts related to homology, as well as other concepts used to describe similarity and non-homology. True False doi:10.1016/j.tig.2009.12.012 https://github.com/BgeeDB/homology-ontology B2AI_STANDARD:463 OntologyOrVocabulary HOM Homology Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:25 B2AI_ORG:80 Orphanet provides phenotypic annotations of the rare diseases in the Orphanet nomenclature using the Human Phenotype Ontology (HPO). HOOM is a module that qualifies the annotation between a clinical entity and phenotypic abnormalities according to a frequency and by integrating the notion of diagnostic criterion. True False https://bioportal.bioontology.org/ontologies/HOOM https://www.orphadata.com/ontologies/ B2AI_STANDARD:464 OntologyOrVocabulary HOOM HPO - ORDO Ontological Module Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A systematic description of the ancestry concepts used in the NHGRI-EBI Catalog True False doi:10.1186/s13059-018-1396-2 https://github.com/EBISPOT/ancestro B2AI_STANDARD:465 OntologyOrVocabulary HANCESTRO Human Ancestry Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Life cycle stages for Human. True False https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv https://github.com/obophenotype/developmental-stage-ontologies B2AI_STANDARD:466 OntologyOrVocabulary HSAPDV Human Developmental Stages Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 An ontology for describing the classification of human diseases organized by etiology. True False http://www.disease-ontology.org https://github.com/DiseaseOntology/HumanDiseaseOntology B2AI_STANDARD:467 OntologyOrVocabulary DOID Human Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Phenotypic Features True False https://hpo.jax.org/ https://github.com/obophenotype/human-phenotype-ontology B2AI_STANDARD:468 OntologyOrVocabulary HPO Human Phenotype Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:28 B2AI_ORG:41 A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. True False https://www.psidev.info/groups/controlled-vocabularies B2AI_STANDARD:469 OntologyOrVocabulary XLMOD HUPO-PSI cross-linking and derivatization reagents controlled vocabulary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 An ontology for representing clinical data about hypertension. True False https://github.com/aellenhicks/htn_owl B2AI_STANDARD:470 OntologyOrVocabulary HTN Hypertension Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology... True False https://github.com/infectious-disease-ontology/infectious-disease-ontology B2AI_STANDARD:471 OntologyOrVocabulary IDO Infectious Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 An ontology of information entities. True False https://github.com/information-artifact-ontology/IAO B2AI_STANDARD:472 OntologyOrVocabulary IAO Information Artifact Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 An ontology of clinical informed consents True False https://github.com/ICO-ontology/ICO B2AI_STANDARD:473 OntologyOrVocabulary ICO Informed Consent Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry An integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs). True False http://db-mml.sjtu.edu.cn/ICEberg/ doi:10.1038/s41597-021-01112-5 https://github.com/ontoice/ICEO B2AI_STANDARD:474 OntologyOrVocabulary ICEO Integrative and Conjugative Element Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:87 Comprehensive, curated and interlinked data of artificial intelligence tasks, benchmarks, AI performance metrics, benchmark results and research papers. True False https://openbiolink.github.io/ITOExplorer/ https://github.com/OpenBioLink/ITO B2AI_STANDARD:475 OntologyOrVocabulary ITO Intelligence Task Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry An ontology of interactions and interaction networks. True False doi:10.1186/2041-1480-6-2 https://github.com/INO-ontology/ino B2AI_STANDARD:476 OntologyOrVocabulary INO Interaction Network Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:1 biological, biomedical, and related concepts True False doi:10.1007/s00354-019-00074-y https://github.com/kushidat/IOBC B2AI_STANDARD:477 OntologyOrVocabulary IOBC Interlinking Ontology for Biological Concepts Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Algorithms for simulating biology, their parameters, and their outputs. True False http://co.mbine.org/standards/kisao https://github.com/SED-ML/KiSAO B2AI_STANDARD:478 OntologyOrVocabulary KISAO Kinetic Simulation Algorithm Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Standard terms for annotating mammalian phenotypic data. True False doi:10.1007/s00335-012-9421-3 https://github.com/mgijax/mammalian-phenotype-ontology B2AI_STANDARD:479 OntologyOrVocabulary MP Mammalian Phenotype Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:13 Code set for active and inactive manufacturers of vaccines in the US. True False https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx B2AI_STANDARD:480 OntologyOrVocabulary MVX Manufacturers of Vaccines Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:28 B2AI_ORG:41 A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. True False http://www.psidev.info/groups/controlled-vocabularies doi:10.1093/database/bat009 https://github.com/HUPO-PSI/psi-ms-CV B2AI_STANDARD:481 OntologyOrVocabulary MS Mass spectrometry ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A representation of the variety of methods used to make clinical and phenotype measurements. True False https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 doi:10.1186/2041-1480-4-26 https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology/ B2AI_STANDARD:482 OntologyOrVocabulary MMO Measurement method ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Life cycle stages for Medaka True False https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv https://github.com/obophenotype/developmental-stage-ontologies B2AI_STANDARD:483 OntologyOrVocabulary OLATDV Medaka Developmental Stages Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 B2AI_ORG:58 Terms for medical procedures, interventions, therapies, treatments, and recommendations. True False https://github.com/monarch-initiative/MAxO B2AI_STANDARD:484 OntologyOrVocabulary MAXO Medical Action Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:8 B2AI_ORG:74 Formal ontological representations of medication terminology, pharmacologic classifications, and asserted authoritative relationships between them. Replaces NDF-RT. Provided through UMLS. True True https://evs.nci.nih.gov/ftp1/NDF-RT/Introduction%20to%20MED-RT.pdf B2AI_STANDARD:485 OntologyOrVocabulary MED-RT Medication Reference Terminology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 Mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable. True False https://github.com/jannahastings/mental-functioning-ontology B2AI_STANDARD:486 OntologyOrVocabulary MFOMD Mental Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry All aspects of mental functioning. True False https://github.com/jannahastings/mental-functioning-ontology B2AI_STANDARD:487 OntologyOrVocabulary MF Mental Functioning Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 An OWL ontology and application profile to capture metadata information for ontologies, vocabularies or semantic resources/artefacts in general. True False doi:10.1007/978-3-319-70863-8_17 https://github.com/sifrproject/MOD-Ontology B2AI_STANDARD:488 OntologyOrVocabulary MOD Metadata vocabulary for Ontology Description and Publication Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Major Histocompatibility Complex (MHC) restriction in experiments. True False https://github.com/IEDB/MRO B2AI_STANDARD:489 OntologyOrVocabulary MRO MHC Restriction Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry An application ontology to formalize annotation of phylogenetic data. True False https://www.evoio.org/wiki/MIAPA doi:10.1089/omi.2006.10.231 https://github.com/evoinfo/miapa/ B2AI_STANDARD:490 OntologyOrVocabulary MIAPA MIAPA Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Minimum information regarding potential drug-drug interaction information. True False https://github.com/MPIO-Developers/MPIO B2AI_STANDARD:491 OntologyOrVocabulary MPIO Minimum PDDI Information Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
modelcards B2AI_TOPIC:5 An OWL2-based artifact that represents and formalizes model card report information. The current release of this ontology utilizes standard concepts and properties from OBO Foundry ontologies. True False doi:10.1186/s12859-022-04797-6 https://github.com/UTHealth-Ontology/MCRO B2AI_STANDARD:492 OntologyOrVocabulary MCRO Model Card Report Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:20 B2AI_TOPIC:26 B2AI_ORG:41 Vocabulary for the annotation of experiments concerned with protein-protein interactions. True False https://github.com/HUPO-PSI/psi-mi-CV B2AI_STANDARD:493 OntologyOrVocabulary MI Molecular Interactions Controlled Vocabulary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:29 Processes at the molecular level True False https://www.ebi.ac.uk/ols/ontologies/mop https://github.com/rsc-ontologies/rxno B2AI_STANDARD:494 OntologyOrVocabulary MOP Molecular Process Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 B2AI_ORG:58 Diseases True False https://mondo.monarchinitiative.org/ doi:10.1093/nar/gkw1128 https://github.com/monarch-initiative/mondo B2AI_STANDARD:495 OntologyOrVocabulary MONDO Mondo Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Mouse anatomy covering embryonic development and postnatal stages. True False http://www.informatics.jax.org/expression.shtml https://github.com/obophenotype/mouse-anatomy-ontology B2AI_STANDARD:496 OntologyOrVocabulary EMAPA Mouse Developmental Anatomy Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes. True False http://www.pathbase.net/ https://github.com/PaulNSchofield/mpath B2AI_STANDARD:497 OntologyOrVocabulary MPATH Mouse pathology ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:3 Connects organic name reactions to their roles in an organic synthesis and to processes in MOP True False https://github.com/rsc-ontologies/rxno B2AI_STANDARD:498 OntologyOrVocabulary RXNO Name Reaction Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:8 B2AI_ORG:31 Information about finished drug products, unfinished drugs and compounded drug products True False https://www.accessdata.fda.gov/scripts/cder/ndc/index.cfm B2AI_STANDARD:499 OntologyOrVocabulary NDC National Drug Code Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:74 An ontology representation of the NCBI organismal taxonomy. True False http://www.ncbi.nlm.nih.gov/taxonomy https://github.com/obophenotype/ncbitaxon B2AI_STANDARD:500 OntologyOrVocabulary NCBITAXON NCBI organismal classification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:74 A reference terminology that includes broad coverage of the cancer domain, including cancer related diseases. True False https://github.com/NCI-Thesaurus/thesaurus-obo-edition B2AI_STANDARD:501 OntologyOrVocabulary NCIT NCI Thesaurus OBO Edition Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Human and animal behaviours and behavioural phenotypes True False https://github.com/obo-behavior/behavior-ontology/ B2AI_STANDARD:502 OntologyOrVocabulary NBO Neuro Behavior Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:22 A Comprehensive Hierarchical Nomenclature for Structures of the Primate Brain (human and macaque) True False http://braininfo.rprc.washington.edu/aboutBrainInfo.aspx#NeuroNames doi:10.1007/s12021-011-9128-8 B2AI_STANDARD:503 OntologyOrVocabulary NeuroNames Neuronames Brain Hierarchy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. True False https://github.com/SpeciesFileGroup/nomen B2AI_STANDARD:504 OntologyOrVocabulary NOMEN Nomenclatural ontology for biological names Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:33 An ontology for non-coding RNA, both of biological origin, and engineered. True False https://github.com/OmniSearch/ncro B2AI_STANDARD:505 OntologyOrVocabulary NCRO Non-Coding RNA Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Terms for nutrition assessment, diagnosis, intervention, and monitoring/evaluation. False True https://www.ncpro.org/ B2AI_STANDARD:506 OntologyOrVocabulary NCPT Nutrition Care Process Terminology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 Terms that are used to annotate ontology terms for all OBO ontologies. True False https://github.com/information-artifact-ontology/ontology-metadata B2AI_STANDARD:507 OntologyOrVocabulary OMO OBO Metadata Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A structured controlled vocabulary to provide a representation of the data from electronic health records involved in the care of pregnancy. True False https://github.com/ontoneo-project/Ontoneo B2AI_STANDARD:508 OntologyOrVocabulary ONTONEO Obstetric and Neonatal Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Vocabulary for the description of the most widely-used computational approach for studying digital evolution. True False https://gitlab.com/fortunalab/ontoavida B2AI_STANDARD:509 OntologyOrVocabulary ONTOAVIDA OntoAvida ontology for Avida digital evolution platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Annotation and modeling of biobank repository and biobanking administration. True False https://github.com/biobanking/biobanking B2AI_STANDARD:510 OntologyOrVocabulary OBIB Ontology for Biobanking Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Description of life-science and clinical investigations. True False http://obi-ontology.org doi:10.1371/journal.pone.0154556 https://github.com/obi-ontology/obi B2AI_STANDARD:511 OntologyOrVocabulary OBI Ontology for Biomedical Investigations Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 B2AI_TOPIC:7 Treatment of disease and diagnosis and on carcinomas and other pathological entities. True False https://github.com/OGMS/ogms B2AI_STANDARD:512 OntologyOrVocabulary OGMS Ontology for General Medical Science Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Data exchange standards and common data elements in the microRNA (miR) domain. True False https://github.com/OmniSearch/omit B2AI_STANDARD:513 OntologyOrVocabulary OMIT Ontology for MIRNA Target Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Research output of nutritional epidemiologic studies. True False doi:10.3390/nu11061300 https://github.com/cyang0128/Nutritional-epidemiologic-ontologies B2AI_STANDARD:514 OntologyOrVocabulary ONE Ontology for Nutritional Epidemiology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Description of concepts in the nutritional studies domain. True False doi:10.1186/s12263-018-0601-y https://github.com/enpadasi/Ontology-for-Nutritional-Studies B2AI_STANDARD:515 OntologyOrVocabulary ONS Ontology for Nutritional Studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 B2AI_TOPIC:7 Adverse clinical events. True False https://github.com/OAE-ontology/OAE/ B2AI_STANDARD:516 OntologyOrVocabulary OAE Ontology of Adverse Events Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Biological and clinical statistics. True False https://github.com/obcs/obcs B2AI_STANDARD:517 OntologyOrVocabulary OBCS Ontology of Biological and Clinical Statistics Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A collection of biological attributes (traits) covering all kingdoms of life. True False https://wiki.geneontology.org/index.php/Extensions/x-attribute https://github.com/obophenotype/bio-attribute-ontology B2AI_STANDARD:518 OntologyOrVocabulary OBA Ontology of Biological Attributes Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. True False https://github.com/linikujp/OGSF B2AI_STANDARD:519 OntologyOrVocabulary OGSF Ontology of Genetic Susceptibility Factor Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Host-pathogen interactions and virulence factors. True False doi:10.1093/nar/gky999 https://github.com/OHPI/ohpi B2AI_STANDARD:520 OntologyOrVocabulary OHPI Ontology of Host Pathogen Interactions Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions. True False https://github.com/ohmi-ontology/ohmi B2AI_STANDARD:521 OntologyOrVocabulary OHMI Ontology of Host-Microbiome Interactions Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various... True False https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview doi:10.1186/s13326-016-0087-8 https://github.com/ufbmi/OMRSE B2AI_STANDARD:522 OntologyOrVocabulary OMRSE Ontology of Medically Related Social Entities Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:96 Organizational components of trauma centers and trauma systems. True False https://github.com/OOSTT/OOSTT B2AI_STANDARD:523 OntologyOrVocabulary OOSTT Ontology of Organizational Structures of Trauma centers and Trauma systems Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Entities and relations associated with precision medicine and related investigations at different conditions. True False https://github.com/OPMI/opmi B2AI_STANDARD:524 OntologyOrVocabulary OPMI Ontology of Precision Medicine and Investigation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:33 An application ontology designed to annotate next-generation sequencing experiments performed on RNA. True False https://github.com/safisher/ornaseq B2AI_STANDARD:525 OntologyOrVocabulary ORNASEQ Ontology of RNA Sequencing Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 B2AI_TOPIC:7 A biomedical ontology in the domain of vaccine adverse events. True False https://github.com/OVAE-Ontology/ovae B2AI_STANDARD:526 OntologyOrVocabulary OVAE Ontology of Vaccine Adverse Events Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 Content of dental practice health records. True False doi:10.1186/s13326-020-00222-0 https://github.com/oral-health-and-disease-ontologies/ohd-ontology B2AI_STANDARD:527 OntologyOrVocabulary OHD Oral Health and Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:7 B2AI_ORG:80 The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. True False https://bioportal.bioontology.org/ontologies/ORDO https://www.orphadata.com/ontologies/ B2AI_STANDARD:528 OntologyOrVocabulary ORDO Orphanet Rare Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Species-neutral phenotypes observed in pathogen-host interactions. True False doi:10.1093/nar/gkab1037 https://github.com/PHI-base/phipo B2AI_STANDARD:529 OntologyOrVocabulary PHIPO Pathogen Host Interaction Phenotype Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:7 An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly. True False doi:10.1093/nar/gkp832 https://github.com/DiseaseOntology/PathogenTransmissionOntology B2AI_STANDARD:530 OntologyOrVocabulary TRANS Pathogen Transmission Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:21 A controlled vocabulary for annotating gene products to pathways. True False http://rgd.mcw.edu/rgdweb/ontology/search.html doi:10.1186/2041-1480-5-7 https://github.com/rat-genome-database/PW-Pathway-Ontology B2AI_STANDARD:531 OntologyOrVocabulary PW Pathway ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:4 Ontology to reproducibly study visualizations of clinical performance True False https://github.com/Display-Lab/psdo B2AI_STANDARD:532 OntologyOrVocabulary PSDO Performance Summary Display Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:3 B2AI_TOPIC:7 B2AI_TOPIC:12 B2AI_TOPIC:21 B2AI_TOPIC:25 B2AI_ORG:58 An application ontology for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds. True False https://github.com/monarch-initiative/phenio B2AI_STANDARD:533 OntologyOrVocabulary PHENIO Phenomics Integrated Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Phenotypic qualities (properties, attributes or characteristics). True False https://github.com/pato-ontology/pato B2AI_STANDARD:534 OntologyOrVocabulary PATO Phenotype And Trait Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Groups of interacting organisms such as populations and communities. True False https://github.com/PopulationAndCommunityOntology/pco B2AI_STANDARD:535 OntologyOrVocabulary PCO Population and Community Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:3 Process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes. True False https://github.com/proco-ontology/PROCO B2AI_STANDARD:536 OntologyOrVocabulary PROCO Process Chemistry Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:26 B2AI_ORG:41 PSI-MOD is an ontology consisting of terms that describe protein chemical modifications True False https://www.psidev.info/groups/protein-modifications doi:10.1038/nbt0808-864 https://github.com/HUPO-PSI/psi-mod-CV B2AI_STANDARD:537 OntologyOrVocabulary PSI-MOD Protein modification Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:26 An ontological representation of protein-related entities True False https://github.com/PROconsortium/PRoteinOntology/ B2AI_STANDARD:538 OntologyOrVocabulary PR PRotein Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:2 Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics. True False https://github.com/obophenotype/provisional_cell_ontology B2AI_STANDARD:539 OntologyOrVocabulary PCL Provisional Cell Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:1 B2AI_TOPIC:11 Effects of radiation on biota in terrestrial and space environments. True False https://github.com/Radiobiology-Informatics-Consortium/RBO B2AI_STANDARD:540 OntologyOrVocabulary RBO Radiation Biology Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:85 A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research. True True https://www.rsna.org/practice-tools/data-tools-and-standards/radlex-radiology-lexicon B2AI_STANDARD:541 OntologyOrVocabulary RadLex RadLex radiology lexicon Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Ontology of rat strains. True False http://rgd.mcw.edu/rgdweb/search/strains.html doi:10.1186/2041-1480-4-36 https://github.com/rat-genome-database/RS-Rat-Strain-Ontology B2AI_STANDARD:542 OntologyOrVocabulary RS Rat Strain Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 Relationship types shared across multiple ontologies. True False https://oborel.github.io/ https://github.com/oborel/obo-relations B2AI_STANDARD:543 OntologyOrVocabulary RO Relation Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:8 B2AI_ORG:74 Medication terminology. Provided through UMLS. True True https://www.nlm.nih.gov/research/umls/rxnorm/index.html B2AI_STANDARD:544 OntologyOrVocabulary RxNorm RxNorm Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:58 Provenance of scientific claims and the evidence that supports them. True False https://github.com/monarch-initiative/SEPIO-ontology B2AI_STANDARD:545 OntologyOrVocabulary SEPIO Scientific Evidence and Provenance Information Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:99 An ontology for describing sensors and their observations, the involved procedures, the studied features of interest, the samples used to do so, and the observed properties, as well as actuators. True False https://www.w3.org/TR/vocab-ssn/ https://github.com/w3c/sdw B2AI_STANDARD:546 OntologyOrVocabulary SSN Semantic Sensor Network Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects. True False http://www.sequenceontology.org/ doi:10.1016/j.jbi.2010.03.002 https://github.com/The-Sequence-Ontology/SO-Ontologies B2AI_STANDARD:547 OntologyOrVocabulary SO Sequence types and features ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Sickle Cell Disease terminology. True False https://scdontology.h3abionet.org/ https://github.com/scdodev/scdo-ontology B2AI_STANDARD:548 OntologyOrVocabulary SCDO Sickle Cell Disease Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Software tools, their types, tasks, versions, provenance and associated data. True False doi:10.1186/2041-1480-5-25 https://github.com/allysonlister/swo B2AI_STANDARD:549 OntologyOrVocabulary SWO Software ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:3 Translate each code descriptor from the official CPT code set into language that is easily understood by the average patient and/or his or her caregiver. The objective is to simplify the highly technical CPT code descriptors into something more patient-focused and patient-friendly. False True https://commerce.ama-assn.org/catalog/media/Consumer-and-Clinician-Descriptors-in-CPT-Data-Files.pdf B2AI_STANDARD:550 OntologyOrVocabulary CFDs Standard Current Procedural Terminology Consumer Friendly Descriptors Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 B2AI_ORG:47 Statistical tests and methods True False http://stato-ontology.org/ https://github.com/ISA-tools/stato B2AI_STANDARD:551 OntologyOrVocabulary STATO Statistics Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient. True False http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page doi:10.1093/nar/gkab1063 https://github.com/DiseaseOntology/SymptomOntology B2AI_STANDARD:552 OntologyOrVocabulary SYMP Symptom Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
codesystem B2AI_TOPIC:9 B2AI_ORG:74 Standard for electronic exchange of clinical health information. Provided through UMLS. True True https://www.nlm.nih.gov/healthit/snomedct/index.html B2AI_STANDARD:553 OntologyOrVocabulary SNOMED CT Systematized Nomenclature of Medicine - Clinical Terms Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:74 SNOMED, not SNOMED-CT True False https://bioportal.bioontology.org/ontologies/SNMI B2AI_STANDARD:554 OntologyOrVocabulary SNMI Systematized Nomenclature of Medicine, International Version Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:1 B2AI_ORG:29 Terms commonly used in Systems Biology and computational modeling. True False https://github.com/EBI-BioModels/SBO B2AI_STANDARD:555 OntologyOrVocabulary SBO Systems Biology Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:1 A vocabulary of taxonomic ranks (species, family, phylum, etc). True False doi:10.1186/2041-1480-4-34 https://github.com/phenoscape/taxrank B2AI_STANDARD:556 OntologyOrVocabulary TAXRANK Taxonomic rank vocabulary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 A terminology for the skills necessary to make data FAIR and to keep it FAIR. True False https://obofoundry.org/ontology/t4fs.html doi:10.5281/zenodo.4772741 https://github.com/terms4fairskills/FAIRterminology B2AI_STANDARD:557 OntologyOrVocabulary T4FS terms4FAIRskills Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:8 B2AI_ORG:96 An ontology to support comparative effectiveness researchers studying claims data. True False doi:10.1186/s13326-017-0121-5 https://github.com/ufbmi/dron B2AI_STANDARD:558 OntologyOrVocabulary DRON The Drug Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:62 The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. True False https://bioportal.bioontology.org/ontologies/OBOE https://github.com/NCEAS/oboe/ B2AI_STANDARD:559 OntologyOrVocabulary OBOE The Extensible Observation Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:12 B2AI_TOPIC:13 A formal ontology of genes and genomes of biological organisms. True False https://bitbucket.org/hegroup/ogg/src/master/ B2AI_STANDARD:560 OntologyOrVocabulary OGG The Ontology of Genes and Genomes Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:8 An ontology to describe entities related to prescription of drugs True False doi:10.3390/ijerph182212025 https://github.com/OpenLHS/PDRO B2AI_STANDARD:561 OntologyOrVocabulary PDRO The Prescription of Drugs Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Terms involving toxicity courses and processes. True False https://toxpilot.nibiohn.go.jp/ https://github.com/txpo-ontology/TXPO/ B2AI_STANDARD:562 OntologyOrVocabulary TXPO Toxic Process Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Anatomy True False https://obophenotype.github.io/uberon/ doi:10.1186/gb-2012-13-1-r5 https://github.com/obophenotype/uberon B2AI_STANDARD:563 OntologyOrVocabulary UBERON Uberon Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:74 Biomedical terminology and hierarchical relationships between concepts. True True https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html B2AI_STANDARD:564 OntologyOrVocabulary Metathesaurus UMLS Metathesaurus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. True False https://github.com/obophenotype/upheno B2AI_STANDARD:565 OntologyOrVocabulary UPHENO Unified phenotype ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 The Units Ontology - a tool for integrating units of measurement in science True False https://obofoundry.org/ontology/uo.html doi:10.1093/database/bas033 B2AI_STANDARD:566 OntologyOrVocabulary UO Units of measure ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:5 Metrical units for use in conjunction with PATO. True False https://github.com/bio-ontology-research-group/unit-ontology B2AI_STANDARD:567 OntologyOrVocabulary UO Units of measurement ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:27 Universal Medical Device Nomenclature System (UMDNS) is a nomenclature that has been officially adopted by many nations. UMDNS facilitates identifying, processing, filing, storing, retrieving, transferring, and communicating data about medical devices. The nomenclature is used in applications ranging from hospital inventory and work-order controls to national agency medical device regulatory systems. False True https://www.ecri.org/solutions/umdns B2AI_STANDARD:568 OntologyOrVocabulary UMDNS Universal Medical Device Nomenclature System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Vaccine and vaccination ontology. True False doi:10.1186/2041-1480-3-17 https://github.com/vaccineontology/VO B2AI_STANDARD:569 OntologyOrVocabulary VO Vaccine Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_ORG:58 Vertebrate breed names. True False https://github.com/monarch-initiative/vertebrate-breed-ontology B2AI_STANDARD:570 OntologyOrVocabulary VBO Vertebrate Breed Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Extinct and extant vertebrate taxa. True False https://github.com/phenoscape/vertebrate-taxonomy-ontology B2AI_STANDARD:571 OntologyOrVocabulary VTO Vertebrate Taxonomy Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Traits covering vertebrates. True False https://github.com/AnimalGenome/vertebrate-trait-ontology B2AI_STANDARD:572 OntologyOrVocabulary VT Vertebrate trait ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry Support ontology for the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). True False doi:10.5281/zenodo.6685957 https://github.com/VEuPathDB-ontology/VEuPathDB-ontology B2AI_STANDARD:573 OntologyOrVocabulary EUPATH VEuPathDB ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 Anatomical, cellular, and gene function phenotypes occurring throughout the development of Xenopus laevis. True False doi:10.1186/s12859-022-04636-8 https://github.com/obophenotype/xenopus-phenotype-ontology B2AI_STANDARD:574 OntologyOrVocabulary XPO Xenopus Phenotype Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
obofoundry B2AI_TOPIC:25 All phenotypes of the Zebrafish model organism. True False https://github.com/obophenotype/zebrafish-phenotype-ontology B2AI_STANDARD:575 OntologyOrVocabulary ZP Zebrafish Phenotype Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:6 B2AI_ORG:12 B2AI_ORG:40 A code set for use in coding race and ethnicity data. True False https://www.cdc.gov/phin/resources/vocabulary/documents/cdc-race--ethnicity-background-and-purpose.pdf https://phinvads.cdc.gov/vads/ViewValueSet.action?id=B246B692-6DF8-E111-B875-001A4BE7FA90 B2AI_STANDARD:576 DataStandardOrTool PHVS_Race_HL7_2x CDC Race and Ethnicity Code Set Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_TOPIC:6 B2AI_ORG:45 Best practices for the structure, content, construction, and semantics of language tags for use in cases where it is desirable to indicate the language used in an information object. True False https://www.rfc-editor.org/rfc/rfc5646 B2AI_STANDARD:577 DataStandardOrTool RFC 5646 IETF Request for Comment 5646 Tags for Identifying Languages Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:31 B2AI_ORG:50 Standard notation for printing telephone numbers, E-mail addresses and Web addresses. True False https://www.itu.int/rec/T-REC-E.123-200102-I/en B2AI_STANDARD:578 DataStandardOrTool ITU–T E.123 International Telecommunication Union E.123 Notation for national and international telephone numbers, e-mail addresses and web addresses Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:31 B2AI_ORG:50 Number structure and functionality for the five categories of numbers used for international public telecommunication - geographic areas, global services, Networks, groups of countries (GoC) and resources for trials. True False https://www.itu.int/rec/T-REC-E.164-201011-I/en B2AI_STANDARD:579 DataStandardOrTool ITU–T E.164 International Telecommunication Union E.164 The international public telecommunication numbering plan Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 A new clinical database, ACRIMA, has been made publicly available, containing 705 labelled images. It is composed of 396 glaucomatous images and 309 normal images. Additionally, python scripts used to obtain the presented results are also available. True False http://www.cvblab.webs.upv.es/project/acrima_en/ doi:10.1186/s12938-019-0649-y https://figshare.com/articles/dataset/CNNs_for_Automatic_Glaucoma_Assessment_using_Fundus_Images_An_Extensive_Validation/7613135 B2AI_STANDARD:580 ReferenceDataOrDataset ACRIMA ACRIMA dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Speech dataset. ~500 utterances classified by emotion True False http://m3c.web.auth.gr/research/aesdd-speech-emotion-recognition/ B2AI_STANDARD:581 ReferenceDataOrDataset AESDD Acted Emotional Speech Dynamic Database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:7 B2AI_TOPIC:12 B2AI_TOPIC:16 B2AI_TOPIC:21 B2AI_TOPIC:25 B2AI_TOPIC:33 B2AI_ORG:58 The Alliance of Genome Resources contains a subset of model organism data from member databases that is harmonized to the same model. This is the graph ingest of Alliance data prepared for loading into the Monarch Initiative graph resource. True False https://monarch-initiative.github.io/monarch-ingest/Sources/Alliance/ https://data.monarchinitiative.org/monarch-kg-dev/latest/rdf/alliance.nt.gz B2AI_STANDARD:582 ReferenceDataOrDataset Alliance ingest Alliance of Genome Resources Knowledge Graph Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:27 B2AI_ORG:24 AlphaFold DB provides open access to over 200 million protein structure predictions to accelerate scientific research. True False https://alphafold.ebi.ac.uk/ doi:10.1038/s41586-021-03819-2 B2AI_STANDARD:583 ReferenceDataOrDataset AlphaFold DB AlphaFold protein structure database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 The OCTAGON dataset is a set of Angiography by Octical Coherence Tomography images (OCT-A) used to the segmentation of the Foveal Avascular Zone (FAZ). The dataset includes 144 healthy OCT-A images and 69 diabetic OCT-A images, divided into four groups, each one with 36 and about 17 OCT-A images, respectively. False True http://www.varpa.es/research/ophtalmology.html doi:10.1371/journal.pone.0212364 B2AI_STANDARD:584 ReferenceDataOrDataset OCTAGON Angiography by Optical Coherence Tomography segmentation dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 90 fundus images with annotations for retinal arteriovenous (AV) nicking. True False https://people.eng.unimelb.edu.au/thivun/projects/AV_nicking_quantification/ doi:10.1109/TBME.2013.2271035 B2AI_STANDARD:585 ReferenceDataOrDataset AV Nicking Arteriovenous Nicking dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 30000 audio samples of spoken digits True False doi:10.48550/arXiv.1807.03418 https://github.com/soerenab/AudioMNIST B2AI_STANDARD:586 ReferenceDataOrDataset AudioMNIST AudioMNIST Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:34 Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species, produced from multiple data types (bulk RNA-Seq, single-cell RNA-Seq, Affymetrix, in situ hybridization, and EST data) and from multiple data sets (including GTEx data). True False https://bgee.org/ doi:10.1093/nar/gkaa793 B2AI_STANDARD:587 ReferenceDataOrDataset Bgee Bgee Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
text B2AI_TOPIC:16 Biomedical text relation annotations and labels for novel findings True False https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/ doi:10.1093/bib/bbac282 B2AI_STANDARD:588 ReferenceDataOrDataset BioRED Biomedical Relation Extraction Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 195 phase-contrast microscopy images that were divided into 16 subwindows and each subwindow labeled into 4 classes by two trained operators. True False https://figshare.com/s/d6fb591f1beb4f8efa6f doi:10.1371/journal.pone.0149399 B2AI_STANDARD:589 ReferenceDataOrDataset BioMediTech RPE BioMediTech retinal pigmented epithelium dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
text B2AI_TOPIC:16 Biomedical texts annotated for negation, speculation and linguistic scope True False https://rgai.inf.u-szeged.hu/node/105 B2AI_STANDARD:590 ReferenceDataOrDataset BioScope BioScope corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 More than 54,000 external iris images True True http://biometrics.idealtest.org/findTotalDbByMode.do?mode=Iris#/datasetDetail/4 B2AI_STANDARD:591 ReferenceDataOrDataset CASIA Iris CASIA Iris Image Database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 More than 26,000 external iris images True True http://biometrics.idealtest.org/findTotalDbByMode.do?mode=Iris#/datasetDetail/14 B2AI_STANDARD:592 ReferenceDataOrDataset CASIA Iris Subject Ageing CASIA Iris Subject Ageing dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
proteindata B2AI_TOPIC:26 B2AI_ORG:95 A free, publicly available online resource that provides information on the evolutionary relationships of protein structural domains. True False http://www.cathdb.info/ doi:10.1093/nar/gkaa1079 B2AI_STANDARD:593 ReferenceDataOrDataset CATH CATH Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
text B2AI_TOPIC:16 Biomedical texts annotated for concepts and linguistic features True False https://github.com/UCDenver-ccp/CRAFT doi:10.1007/978-94-024-0881-2_53 https://github.com/UCDenver-ccp/CRAFT B2AI_STANDARD:594 ReferenceDataOrDataset CRAFT Colorado Richly Annotated Full-Text Corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Recordings of 4 speakers in ~9000 recordings over 4 noisy locations. True False https://archive.org/details/chime-home B2AI_STANDARD:595 ReferenceDataOrDataset CHiME Computational Hearing in Multisource Environments Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Respiratory sounds and speech of healthy and COVID-19 positive individuals. True False https://github.com/iiscleap/Coswara-Data B2AI_STANDARD:596 ReferenceDataOrDataset Coswara Coswara dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
text B2AI_TOPIC:16 Biomedical texts with focus on SARS-CoV-2 True False https://ai2-semanticscholar-cord-19.s3-us-west-2.amazonaws.com/historical_releases.html https://github.com/allenai/cord19 B2AI_STANDARD:597 ReferenceDataOrDataset CORD-19 COVID-19 Open Research Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Speech dataset. 7,442 recordings from 91 actors. True False doi:10.1109/TAFFC.2014.2336244 https://github.com/CheyneyComputerScience/CREMA-D B2AI_STANDARD:598 ReferenceDataOrDataset CREMA-D Crowd-sourced Emotional Multimodal Actors Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:35 Database of human chromosomal rearrangement (CR) events and their associated diseases. For each reported CR event, dbCRID documents the type of the event, the disease or symptoms associated, and—when possible—detailed information about the CR event including precise breakpoint positions, junction sequences, genes and gene regions disrupted and experimental techniques applied to discover/analyze the CR event. True False https://web.archive.org/web/20180902234150/http://dbcrid.biolead.org/ doi:10.1093/nar/gkq1038 B2AI_STANDARD:599 ReferenceDataOrDataset dbCRID Database of Chromosomal Rearrangements In Diseases Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_TOPIC:25 B2AI_ORG:29 DECIPHER is used by the clinical community to share and compare phenotypic and genotypic data. The DECIPHER database contains data from 44,062 patients who have given consent for broad data-sharing; DECIPHER also supports more limited sharing via consortia. True True https://www.deciphergenomics.org/ doi:10/1016/j.ajhg.2009.03.010 B2AI_STANDARD:600 ReferenceDataOrDataset DECIPHER DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:12 B2AI_TOPIC:13 B2AI_TOPIC:25 B2AI_ORG:74 The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans. False True https://www.ncbi.nlm.nih.gov/gap/ B2AI_STANDARD:601 ReferenceDataOrDataset dbGaP Database of Genotypes and Phenotypes Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 In DeepDR (Deep Diabetic Retinopathy), the fundus images composed of two parts. One part is from the participants in the Shanghai Diabetic Complication Screening Project (SDCSP), Nicheng Diabetes Screening Project (NDSP), and Nationwide Screening for Complications of Diabetes (NSCD) between 2014 and 2017 for regular fundus images. The other part was captured by a retinal specialist at an Eye Clinic located in Department of Ophthalmology, Shanghai Jiao Tong University affiliated Sixth People’s Hospital, China between 2014 to 2017 for regular fundus images and between Jan 2019 to present for ultra-widefield retinal images. From the thousands of examinations available, we have extracted 2000 regular fundus images from 500 patients and 256 ultra-widefield images from another 128 patients to form our dataset. True False https://isbi.deepdr.org/data.html doi:10.1016/j.patter.2022.100512 https://github.com/deepdrdoc/DeepDRiD B2AI_STANDARD:602 ReferenceDataOrDataset DeepDRiD Deep Diabetic Retinopathy dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Human nonverbal vocal sound dataset False True https://en.babba.ai/nonverbal https://github.com/deeplyinc/Nonverbal-Vocalization-Dataset B2AI_STANDARD:603 ReferenceDataOrDataset Deeply Deeply Nonverbal Vocalization Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 20 speakers reading 5 excerpts each from public domain books. True False https://zenodo.org/record/4660670 B2AI_STANDARD:604 ReferenceDataOrDataset DAPS Device and Produced Speech Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 The Diabetic Retinopathy Image Dataset (DRiDB) has been established to help scientists from around the world to test and develop new image processing methods for early diabetic retinopathy detection in retinal fundus images. False True https://ipg.fer.hr/ipg/resources/image_database doi:10.1109/ISPA.2013.6703830 B2AI_STANDARD:605 ReferenceDataOrDataset DRiDB Diabetic retinopathy image database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 The database consists of 110 colour digital retinal images. Initially, it were obtained 124 eye fundus images selected randomly from an eye fundus image base belonging to the Ophthalmology Service at Miguel Servet Hospital, Saragossa (Spain). From this initial image base, all those eye images (14 in total) that had some type of cataract (severe and moderate) were eliminated and, finally, was obtained the image base with 110 images. True False http://www.ia.uned.es/~ejcarmona/DRIONS-DB.html doi:10.1016/j.artmed.2008.04.005 B2AI_STANDARD:606 ReferenceDataOrDataset DRIONS-DB Digital Retinal Images for Optic Nerve Segmentation DataBase Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 40 fundus images; annotations for diabetic retinopathy True True https://drive.grand-challenge.org/ doi:10.1109/TMI.2004.825627 B2AI_STANDARD:607 ReferenceDataOrDataset DRIVE Digital Retinal Images for Vessel Extraction dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 A dataset of retinal images which include both normal and glaucomatous eyes and manual segmentations from multiple human experts. True True http://cvit.iiit.ac.in/projects/mip/drishti-gs/mip-dataset2/Home.php doi:10.1109/ISBI.2014.6867807 B2AI_STANDARD:608 ReferenceDataOrDataset Drishti-GS Drishti-GS dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
clinicaldata multimodal text B2AI_TOPIC:9 B2AI_ORG:57 Deidentified, multimodal patient data from ICU stays True True https://eicu-crd.mit.edu/ B2AI_STANDARD:609 ReferenceDataOrDataset eICU-CRD eICU Collaborative Research Database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 144 audio files labelled by 40 listeners. True False https://zenodo.org/record/3727593 doi:10.1145/3243274.3243277 B2AI_STANDARD:610 ReferenceDataOrDataset EmoSynth EmoSynth Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:27 B2AI_ORG:55 An open atlas of 617 million metagenomic protein structures. True False https://esmatlas.com/ doi:10.1101/2022.07.20.500902 B2AI_STANDARD:611 ReferenceDataOrDataset ESM Atlas ESM Metagenomic Atlas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
proteindata B2AI_TOPIC:26 A hierarchical classification of protein domains according to their evolutionary relationships. Only proteins with experimentally determined spatial structures from the PDB database are currently classified in ECOD. True False http://prodata.swmed.edu/ecod/ doi:10.1371/journal.pcbi.1003926 B2AI_STANDARD:612 ReferenceDataOrDataset ECOD Evolutionary Classification of Protein Domains Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:34 Ongoing transcriptome analysis project. True False https://fantom.gsc.riken.jp/ doi:10.1101/gr.254219.119 B2AI_STANDARD:613 ReferenceDataOrDataset FANTOM FANTOM Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 Individual optical coherence tomography images and marking 38400 BScans from 269 age-related macular degeneration patients and 115 normal subjects, their ages, and their corresponding segmentation boundaries on a 5mm diameter centered at the fovea. True False http://people.duke.edu/~sf59/RPEDC_Ophth_2013_dataset.htm doi:10.1016/j.ophtha.2013.07.013 B2AI_STANDARD:614 ReferenceDataOrDataset Duke OCT Farsiu et al. Optical Coherence Tomography dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 4 speakers, 2,000 recordings, 50 of each digit per speaker. True False https://github.com/Jakobovski/free-spoken-digit-dataset B2AI_STANDARD:615 ReferenceDataOrDataset FSDD Free Spoken Digit Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 1020 high resolution colour fundus images and provides ground truth annotations for glaucoma diagnosis, optic disc and optic cup segmentation, vertical cup-to-disc ratio, size of neuroretinal rim in inferior, superior, nasal and temporal quadrants, and bounding box location for optic disc. False False https://www.dfki.uni-kl.de/g1020 doi:10.1109/IJCNN48605.2020.9207664 B2AI_STANDARD:616 ReferenceDataOrDataset G1020 G1020 dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
referencegenome B2AI_TOPIC:13 The goal of the GENCODE project is to identify and classify all gene features in the human and mouse genomes with high accuracy based on biological evidence, and to release these annotations for the benefit of biomedical research and genome interpretation. True False https://www.gencodegenes.org/human/release_24.html B2AI_STANDARD:617 ReferenceDataOrDataset GRCh38 GENCODE24 (GRCh38) reference genome Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 10 actors portraying 10 states and 12 emotions True True https://www.unige.ch/cisa/gemep B2AI_STANDARD:618 ReferenceDataOrDataset GEMEP GEneva Multimodal Emotion Portrayals corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_TOPIC:25 B2AI_TOPIC:35 A continuously updating, queryable, federated genomic data commons. False True https://www.genomicinformationcommons.org/ B2AI_STANDARD:619 ReferenceDataOrDataset GIC Genomic Information Commons Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:34 The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 54 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. True False https://gtexportal.org/home/ doi:10.1038/ng.2653. B2AI_STANDARD:620 ReferenceDataOrDataset GTex Genotype Tissue Expression project Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 B2AI_ORG:37 dataset of manually-annotated audio events True False https://research.google.com/audioset/ doi:10.1109/ICASSP.2017.7952261 B2AI_STANDARD:621 ReferenceDataOrDataset AudioSet Google AudioSet Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
clinicaldata B2AI_ORG:2 The Healthcare Cost and Utilization Project (HCUP) includes the largest collection of longitudinal hospital care data in the United States. False True https://www.hcup-us.ahrq.gov/ B2AI_STANDARD:622 ReferenceDataOrDataset HCUP Healthcare Cost and Utilization Project Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 The public database contains at the moment 15 images of healthy patients, 15 images of patients with diabetic retinopathy and 15 images of glaucomatous patients. Binary gold standard vessel segmentation images are available for each image. Also the masks determining field of view (FOV) are provided for particular datasets. True False https://www5.cs.fau.de/research/data/fundus-images/ doi:10.1155/2013/154860 B2AI_STANDARD:623 ReferenceDataOrDataset HRF High resolution fundus image database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:7 B2AI_TOPIC:25 B2AI_ORG:58 Annotations on Human Phenotype Ontology terms for Orphanet diseases. True False https://hpo-annotation-qc.readthedocs.io/en/latest/annotationFormat.html#phenotype-hpoa-format http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa B2AI_STANDARD:624 ReferenceDataOrDataset HPOA phenotype HPOA - Disease Annotations Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:12 B2AI_TOPIC:25 B2AI_ORG:58 Annotations on Human Phenotype Ontology terms for genes. True False https://hpo.jax.org/app/data/annotations http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt B2AI_STANDARD:625 ReferenceDataOrDataset HPOA genes to phenotype HPOA - Gene to Phenotype Associations Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:12 B2AI_TOPIC:25 B2AI_ORG:58 Annotations on Human Phenotype Ontology terms for genes. True False https://hpo.jax.org/app/data/annotations http://purl.obolibrary.org/obo/hp/hpoa/phenotype_to_genes.txt B2AI_STANDARD:626 ReferenceDataOrDataset HPOA phenotype to genes HPOA - Phenotype to Gene Associations Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:2 The Human Cell Atlas (HCA) is an international group of researchers using a combination of these new technologies to create cellular reference maps with the position, function and characteristics of every cell type in the human body. True False https://www.humancellatlas.org/portals/ doi:10.7554/eLife.27041 https://github.com/HumanCellAtlas/ B2AI_STANDARD:627 ReferenceDataOrDataset HCA Human Cell Atlas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:17 A freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data - 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. True False https://hmdb.ca/ doi:10.1093/nar/gkab1062 B2AI_STANDARD:628 ReferenceDataOrDataset HMDB Human Metabolome Database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
proteindata B2AI_TOPIC:26 B2AI_TOPIC:28 The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues, and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. True False https://www.proteinatlas.org/ doi:10.1126/science.1260419 B2AI_STANDARD:629 ReferenceDataOrDataset HPA Human Protein Atlas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 Dataset constituting typical diabetic retinopathy lesions and also normal retinal structures annotated at a pixel level. True True https://idrid.grand-challenge.org/ doi:10.3390/data3030025 https://ieee-dataport.org/open-access/indian-diabetic-retinopathy-image-dataset-idrid B2AI_STANDARD:630 ReferenceDataOrDataset IDRiD Indian Diabetic Retinopathy Image Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 12 hours of audiovisual data by 10 actors; 5 emotions. True True https://sail.usc.edu/iemocap/iemocap_release.htm B2AI_STANDARD:631 ReferenceDataOrDataset IEMOCAP Interactive emotional dyadic motion capture database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
proteindata B2AI_TOPIC:26 B2AI_ORG:29 InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. True False https://www.ebi.ac.uk/interpro/ doi:10.1093/nar/gkaa977 B2AI_STANDARD:632 ReferenceDataOrDataset InterPro InterPro Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Derived from LibriSpeech by concatenating the corpus utterances to simulate a conversation and capturing the audio replays with far-field microphones. True False https://github.com/chenzhuo1011/libri_css B2AI_STANDARD:633 ReferenceDataOrDataset Libri-CSS Libri-CSS dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Derived from LibriSpeech. Generated, noisy mixes of speech. True False https://github.com/JorisCos/LibriMix B2AI_STANDARD:634 ReferenceDataOrDataset LibriMix LibriMix dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 A corpus of ~1000 hours of English speech derived from read audiobooks from the LibriVox project. True False https://www.openslr.org/12 doi:10.1109/ICASSP.2015.7178964 B2AI_STANDARD:635 ReferenceDataOrDataset Librispeech Librispeech Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 A public domain speech dataset consisting of 13,100 short audio clips of a single speaker reading passages from 7 non-fiction books, with transcriptions. True False https://keithito.com/LJ-Speech-Dataset/ B2AI_STANDARD:636 ReferenceDataOrDataset LJ Speech LJ Speech Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 Longitudinal visual field data of 139 glaucoma patients. True True http://www.rodrep.com/data-sets.html doi:10.1167/iovs.13-12492 B2AI_STANDARD:637 ReferenceDataOrDataset LGVF Longitudinal Glaucomatous Visual Field data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 A linked-data commons that coordinates access to data and harmonizes data management activities at three critical stages - (1) intake, including curation, de-identification, abstraction, and quality assessment (2) annotation and labelling of images and other data using semi-automated approaches and (3) distributed access and query methods. True True https://www.midrc.org/ B2AI_STANDARD:638 ReferenceDataOrDataset MIDRC Medical Imaging and Data Resource Center Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
clinicaldata multimodal text B2AI_TOPIC:9 B2AI_ORG:57 Deidentified, multimodal patient data True True https://mimic.mit.edu/ B2AI_STANDARD:639 ReferenceDataOrDataset MIMIC Medical Information Mart for Intensive Care Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 The 1200 eye fundus color numerical images of the posterior pole of the Messidor database were acquired by 3 ophthalmologic departments. True True https://www.adcis.net/en/third-party/messidor/ doi:10.5566/ias.1155 B2AI_STANDARD:640 ReferenceDataOrDataset Messidor Methods to Evaluate Segmentation and Indexing Techniques in the field of Retinal Ophthalmology dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
A collection of 3D microstructural datasets assembed using a single 2D input slice as training data. True False https://microlib.io/ doi:10.1038/s41597-022-01744-1 https://github.com/tldr-group/microlib B2AI_STANDARD:641 ReferenceDataOrDataset MicroLib MicroLib Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 B2AI_ORG:56 A noisy speech dataset that can scale to arbitrary sizes depending on the number of speakers, noise types, and Speech to Noise Ratio. True False https://github.com/microsoft/MS-SNSD B2AI_STANDARD:642 ReferenceDataOrDataset MS-SNSD Microsoft Scalable Noisy Speech Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
clinicaldata B2AI_TOPIC:37 B2AI_ORG:57 A large collection of physiological signals and measurements from patients in intensive care units, including electrocardiograms, photoplethysmograms, respiration, invasive and non-invasive blood pressure, and more. These measurements and signals are obtained directly from the bedside monitor, and provide a detailed view into the physiology of critically ill patients. True False https://physionet.org/content/mimic4wdb/0.1.0/ doi:10.13026/a2mw-f949 B2AI_STANDARD:643 ReferenceDataOrDataset WFDB MIMIC Waveform Database for Biomedical Signal Processing Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 B2AI_ORG:59 Spoken text from public domain sources. True True https://voice.mozilla.org/ doi:10.48550/arXiv.1912.06670 https://github.com/common-voice/common-voice B2AI_STANDARD:644 ReferenceDataOrDataset Common Voice Mozilla Common Voice data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 100 hours by over 100 speakers. True True https://ecs.utdallas.edu/research/researchlabs/msp-lab/MSP-Podcast.html doi:10.1109/TAFFC.2017.2736999 B2AI_STANDARD:645 ReferenceDataOrDataset MSP-Podcast MSP Podcast Corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 20 sentences by 12 actors; 4 emotions, with video True True https://ecs.utdallas.edu/research/researchlabs/msp-lab/MSP-Improv.html doi:10.1109/TAFFC.2016.2515617 B2AI_STANDARD:646 ReferenceDataOrDataset MSP-IMPROV MSP-IMPROV Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
multimodal B2AI_TOPIC:26 B2AI_TOPIC:28 Two central approaches for mapping cellular structure – protein fluorescent imaging and protein biophysical association – each generate extensive datasets but of distinct qualities and resolutions that are typically treated separately. The MuSIC map is designed to address this challenge, by integrating immunofluorescent images in the Human Protein Atlas with ongoing affinity purification experiments from the BioPlex resource. The result is a unified hierarchical map of eukaryotic cell architecture. In the MuSIC hierarchy, nodes represent systems and arrows indicate containment of the lower system by the upper. Node color indicates known (gold) or putative novel (purple) systems. The size of each circle is based on the number of proteins in the system. The relative height of each system in the layout is determined based on the predicted diameter of the system in MuSIC. True False http://doi.org/10.18119/N9188W doi:10.1038/s41586-021-04115-9 https://github.com/idekerlab/MuSIC B2AI_STANDARD:647 ReferenceDataOrDataset MuSIC data Multi-Scale Integrated Cell data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Derived from EmotionLines. Includes more than 1400 dialogues and 13000 utterances from the Friends TV series. True False https://github.com/SenticNet/MELD B2AI_STANDARD:648 ReferenceDataOrDataset MELD Multimodal EmotionLines Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
clinicaldata B2AI_ORG:14 The National Health and Nutrition Examination Survey (NHANES) is a program of studies designed to assess the health and nutritional status of adults and children in the United States. The survey is unique in that it combines interviews and physical examinations. NHANES is a major program of the National Center for Health Statistics (NCHS). True False https://www.cdc.gov/nchs/nhanes/index.htm B2AI_STANDARD:649 ReferenceDataOrDataset NHANES National Health and Nutrition Examination Survey Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:81 Clinical data from 9 primary partners. False True https://pcornet.org/data/ B2AI_STANDARD:650 ReferenceDataOrDataset PCORNet Data National Patient-Centered Clinical Research Network data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 14k speech samples with simulated background noise and live degradation conditions. True False doi:10.21437/Interspeech.2021-299 https://github.com/gabrielmittag/NISQA/wiki/NISQA-Corpus B2AI_STANDARD:651 ReferenceDataOrDataset NISQA-Corpus NISQA Speech Quality Corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:16 B2AI_TOPIC:3 B2AI_ORG:74 204 full-text PubMed Central (PMC) articles, fully annotated for chemical entities by 12 NLM indexers for both span (i.e. named entity recognition) and normalization (i.e. entity linking) using MeSH. True False https://ftp.ncbi.nlm.nih.gov/pub/lu/NLM-Chem-BC7-corpus/ doi:10.1093/database/baac102 B2AI_STANDARD:652 ReferenceDataOrDataset NLM-Chem-BC7 NLM-Chem BioCreative VII Chemical Identification corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Clean and noisy parallel speech database. Also known as VBD, Voice Bank + DEMAND. Speech samples from VCTK dataset. True False https://datashare.is.ed.ac.uk/handle/10283/2791 doi:10.7488/ds/2117 B2AI_STANDARD:653 ReferenceDataOrDataset Noisy Noisy Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
clinicaldata B2AI_TOPIC:7 B2AI_TOPIC:25 B2AI_ORG:18 A real-world-data-derived resource with annotation for rare-disease-related phenotypes. This resource is derived from the EHRs of two academic health institutions containing more than 10 million individuals spanning wide age ranges and different disease subgroups. By leveraging ontology mapping and advanced natural-language-processing (NLP) methods, OARD automatically and efficiently extracts concepts for both rare diseases and their phenotypic traits from billing codes and lab tests as well as over 100 million clinical narratives. True False https://rare.cohd.io/ doi:10.1016/j.ajhg.2022.08.002 https://github.com/stormliucong/oard-react B2AI_STANDARD:654 ReferenceDataOrDataset OARD Open annotation for rare diseases dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 An open source Optical Coherence Tomography Image Database containing different retinal OCT images with different pathological conditions. True False https://borealisdata.ca/dataverse/OCTID doi:10.48550/arXiv.1812.07056 B2AI_STANDARD:655 ReferenceDataOrDataset OCTID Optical Coherence Tomography Image Retinal Database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 650 retinal images annotated by trained professionals from Singapore Eye Research Institute. A wide collection of image signs, critical for glaucoma diagnosis, are annotated. False False doi:10.1109/IEMBS.2010.5626137 B2AI_STANDARD:656 ReferenceDataOrDataset ORIGA-light ORIGA-light dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 Dataset with fundus images and clinical data of both eyes of the same patient for glaucoma assessment True False doi:10.1038/s41597-022-01388-1 https://figshare.com/articles/dataset/PAPILA/14798004/2 B2AI_STANDARD:657 ReferenceDataOrDataset PAPILA PAPILA dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Recordings from 20 Parkinson’s Disease patients and 20 healthy subjects. True False https://archive.ics.uci.edu/ml/datasets/Parkinson+Speech+Dataset+with++Multiple+Types+of+Sound+Recordings doi:10.1109/JBHI.2013.2245674 B2AI_STANDARD:658 ReferenceDataOrDataset PD database Parkinson's speech dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
text B2AI_TOPIC:16 B2AI_ORG:74 Biomedical texts True False https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/ B2AI_STANDARD:659 ReferenceDataOrDataset PMC OA PubMed Central Open Access Subset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 1200 fundus images with ground truth segmentations of the optic disc and optic cup, and clinical glaucoma labels. True True https://refuge.grand-challenge.org/ doi:10.1016/j.media.2019.101570 B2AI_STANDARD:660 ReferenceDataOrDataset REFUGE Retinal Fundus Glaucoma Challenge Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 750 retinal fundus images. True True https://deepblue.lib.umich.edu/data/concern/data_sets/3b591905z doi:10.1117/12.2293584 B2AI_STANDARD:661 ReferenceDataOrDataset RIGA Retinal fundus Images for Glaucoma Analysis dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 313 retinographies from normal subjects and 172 retinographies from patients with glaucoma. All of these images have been assessed by two experts and include a manual segmentation of the disc and cup. True False doi:10.5566/ias.2346 https://github.com/miag-ull/rim-one-dl B2AI_STANDARD:662 ReferenceDataOrDataset RIM-ONE DL Retinal IMage database for Optic Nerve Evaluation Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 Currently, we have released a first data set, aimed at CAD of microaneurysms and dot hemorrhages. These abnormalities are amongst the first signs of the presence of diabetic retinopathy. True True http://webeye.ophth.uiowa.edu/ROC/ doi:10.1109/TMI.2009.2033909 B2AI_STANDARD:663 ReferenceDataOrDataset ROC Retinopathy Online Challenge data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:34 We developed a pipeline that processes and unifies RNA-seq data from different studies. Using the pipeline, we have processed data from the GTEx and TCGA and have successfully corrected for study-specific biases, allowing comparative analysis across studies. True False https://github.com/mskcc/RNAseqDB doi:10.1038/sdata.2018.61 https://github.com/mskcc/RNAseqDB B2AI_STANDARD:664 ReferenceDataOrDataset RNAseqDB RNAseqDB Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 95 dyadic conversations from 21 subjects. Each subject converses with another playing one of four characters with emotions; 5 FeelTrace annotations - activation, valence, dominance, power, intensity. True True https://semaine-db.eu/ B2AI_STANDARD:665 ReferenceDataOrDataset SEMAINE SEMAINE dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
text B2AI_TOPIC:16 B2AI_ORG:74 A repository of semantic predications (subject-predicate-object triples) extracted from the entire set of PubMed citations. True True https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR.html doi:10.1093/bioinformatics/bts591 https://github.com/lhncbc/SemRep/tree/master B2AI_STANDARD:666 ReferenceDataOrDataset SemMedDB Semantic MEDLINE Database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 10,000 hours of transcribed audio True True doi:10.48550/arXiv.2106.06909 https://github.com/SpeechColab/GigaSpeech B2AI_STANDARD:667 ReferenceDataOrDataset GigaSpeech Speechcollab GigaSpeech Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 A database of free audio samples of single-word commands, English pronunciations. True False https://github.com/JohannesBuchner/spoken-command-recognition B2AI_STANDARD:668 ReferenceDataOrDataset Sound Commander Spoken Commands dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata text B2AI_TOPIC:16 B2AI_TOPIC:36 Text-aligned spoken Wikipedia articles. True False https://nats.gitlab.io/swc/ doi:10.1007/s10579-017-9410-y B2AI_STANDARD:669 ReferenceDataOrDataset SWC Spoken Wikipedia Corpora Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 89 fundus images with segmentation and annotated for different diabetic retinopathies True False https://www.it.lut.fi/project/imageret/diaretdb1/ doi:10.5244/C.21.15 B2AI_STANDARD:670 ReferenceDataOrDataset DiaRetDb1 Standard Diabetic Retinopathy Database Calibration level 1 dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
proteindata B2AI_TOPIC:26 The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. True False http://scop.mrc-lmb.cam.ac.uk/ doi:10.1093/nar/gkz1064 B2AI_STANDARD:671 ReferenceDataOrDataset SCOP Structural Classification of Proteins Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 ~400 raw images True False http://cecas.clemson.edu/~ahoover/stare/ doi:10.1109/TMI.2003.815900 B2AI_STANDARD:672 ReferenceDataOrDataset STARE STructured Analysis of the REtina dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
eyedata B2AI_TOPIC:24 Subbasal nerve plexus Mosaic images acquired in vivo using laser-scanning confocal microscopy of the cornea in healthy subjects and type 2 diabetes mellitus subjects of the same age. Mosaics represent wide-field images of the plexus incorporating 3D nerve path data projected onto a 2D plane. True False https://figshare.com/collections/SBP_Mosaic_Dataset/3950197 doi:10.1038/s41598-018-32410-5 B2AI_STANDARD:673 ReferenceDataOrDataset SBP Mosiac Subbasal nerve plexus Mosaic Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_TOPIC:26 A database of structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 3,200 completely sequenced genomes against the hidden Markov models. True False https://supfam.org/ doi:10.1093/nar/gky1130 B2AI_STANDARD:674 ReferenceDataOrDataset SUPERFAMILY SUPERFAMILY database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 4 male actors in 7 different emotions, 480 British English utterances in total, including video of speaker faces. True True http://kahlan.eps.surrey.ac.uk/savee/ B2AI_STANDARD:675 ReferenceDataOrDataset SAVEE Surrey Audio-Visual Expressed Emotion Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 A database of sentences, translations, and spoken audio for use in language learning. This download contains spoken English recorded by their community. True False https://tatoeba.org/eng/downloads B2AI_STANDARD:676 ReferenceDataOrDataset Tatoeba Tatoeba dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Audio talks and their transcriptions available on the TED website. True False https://www.openslr.org/51/ B2AI_STANDARD:677 ReferenceDataOrDataset Ted-LIUM Ted-LIUM corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 The Cancer Genome Atlas (TCGA), a landmark cancer genomics program, molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. True True https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga doi:10.1038/ng.2764 B2AI_STANDARD:678 ReferenceDataOrDataset TCGA The Cancer Genome Atlas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Speech dataset. 7356 files; 24 professional actors vocalizing lexically-matched statements and songs in a neutral North American accent. True False https://zenodo.org/record/1188976#.XrC7a5NKjOR doi:10.1371/journal.pone.0196391 B2AI_STANDARD:679 ReferenceDataOrDataset RAVDESS The Ryerson Audio-Visual Database of Emotional Speech and Song Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Recordings of 630 speakers of eight major dialects of American English, each reading ten phonetically rich sentences. It includes time-aligned orthographic, phonetic and word transcriptions as well as a speech waveform file for each utterance. False True https://catalog.ldc.upenn.edu/LDC93S1 B2AI_STANDARD:680 ReferenceDataOrDataset TIMIT TIMIT Acoustic-Phonetic Continuous Speech Corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Speech dataset. 2800 recordings by 2 actresses. True False https://tspace.library.utoronto.ca/handle/1807/24487 https://borealisdata.ca/dataset.xhtml?persistentId=doi:10.5683/SP2/E8H2MF B2AI_STANDARD:681 ReferenceDataOrDataset TESS Toronto emotional speech set Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 Human non-speech emotion vocalizations. True False https://zenodo.org/record/4066235 B2AI_STANDARD:682 ReferenceDataOrDataset VIVAE Variably Intense Vocalizations of Affect and Emotion Corpus Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 A speech dataset targeting acoustically challenging and reverberant environments with robust labels and truth data for transcription, denoising, and speaker identification. True False https://iqtlabs.github.io/voices/ B2AI_STANDARD:683 ReferenceDataOrDataset VOiCES Voices Obscured in Complex Environmental Settings Dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
speechdata B2AI_TOPIC:36 100K hours of unlabelled speech data for 23 languages, 1.8K hours of transcribed speech data for 16 languages, and 17.3K hours of speech-to-speech interpretation data for 16x15 directions. True False doi:10.18653/v1/2021.acl-long.80 https://github.com/facebookresearch/voxpopuli B2AI_STANDARD:684 ReferenceDataOrDataset VoxPopuli VoxPopuli Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
drugdata B2AI_TOPIC:8 WHODrug contains individual trade names, active ingredients and additional information such as marketing authorisation holder, country of sale, pharmaceutical form and strength. All related medications are linked using a structured WHODrug alphanumeric code, connecting trade names and variation of the ingredient with the active moiety of the ingredient. True True https://who-umc.org/whodrug/whodrug-global/ doi:10.1007/s43441-020-00130-6 https://who-umc.org/whodrug/whodrug-global/applications/download-area/ B2AI_STANDARD:685 ReferenceDataOrDataset WHODrug WHODrug medicinal information dictionary Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:21 WikiPathways is a database of biological pathways maintained by and for the scientific community. True False https://www.wikipathways.org/index.php/WikiPathways doi:10.1093/nar/gkaa1024 B2AI_STANDARD:686 ReferenceDataOrDataset WikiPathways WikiPathways database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:19 B2AI_ORG:25 This paper proposed a pipeline for the integration of multiple microscopy imaging modalities into the PACS-DICOM universe, including the numerous metadata elements. A proof-of-concept system was developed, for validation purposes, and integrated with the Dicoogle open-source PACS, providing image storage, metadata indexing and visualization. False True doi:10.1109/ISCC53001.2021.9631529 B2AI_STANDARD:687 ReferenceImplementation Gupta2021 A DICOM Standard Pipeline for Microscope Imaging Modalities Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:40 ...we offer an architecture that utilizes a resource server based on GraphQL and HL7 FHIR that establishes communication between two heterogeneous EHRs. This paper describes how the proposed architecture is implemented to achieve interoperability between two heterogeneous EHRs, HL7 FHIR and OpenMRS. The presented approach establishes secure communication between the EHRs and provides accurate mappings that enable timely health information exchange between EHRs. True False doi:10.1177/14604582211043920 B2AI_STANDARD:688 ReferenceImplementation MukhiyaLamo2021 An HL7 FHIR and GraphQL approach for interoperability between heterogeneous Electronic Health Record systems Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_TOPIC:9 B2AI_ORG:15 B2AI_ORG:79 This work investigates the mapping and data interoperability between healthcare and research standards - EN13606 used for the EHRs and the Clinical Data Interchange Standards Consortium Operational Data Model (CDISC ODM) used for clinical research. True False doi:10.1177/2055207618777676 B2AI_STANDARD:689 ReferenceImplementation Tapuria2018 Comparison and transformation between CDISC ODM and EN13606 EHR standards in connecting EHR data with clinical trial research data Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datasheets B2AI_TOPIC:32 This datasheet describes the Pile, a 825 GiB dataset of human-authored text compiled by EleutherAI for use in large-scale language modeling. The Pile is comprised of 22 different text sources, ranging from original scrapes done for this project, to text data made available by the data owners, to third-party scrapes available online. True False doi:0.48550/arXiv.2201.07311 B2AI_STANDARD:690 ReferenceImplementation Biderman2022 Datasheet for the Pile Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 B2AI_ORG:25 The small animal imaging Digital Imaging and Communications in Medicine (DICOM) acquisition context structured report (SR) was developed to incorporate pre-clinical data in an established DICOM format for rapid queries and comparison of clinical and non-clinical datasets. Established terminologies (i.e., anesthesia, mouse model nomenclature, veterinary definitions, NCI Metathesaurus) were utilized to assist in defining terms implemented in pre-clinical imaging and new codes were added to integrate the specific small animal procedures and handling processes, such as housing, biosafety level, and pre-imaging rodent preparation. True False doi:10.3390/tomography7010001 B2AI_STANDARD:691 ReferenceImplementation Kalen2021 Design and Implementation of the Pre-Clinical DICOM Standard in Multi-Cohort Murine Studies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
multimodal B2AI_ORG:40 B2AI_ORG:76 We developed a system called FHIR-Ontop-OMOP to generate virtual clinical KGs from the OMOP relational databases. We leveraged an OMOP CDM-based Medical Information Mart for Intensive Care (MIMIC-III) data repository to evaluate the FHIR-Ontop-OMOP system in terms of the faithfulness of data transformation and the conformance of the generated CKGs to the FHIR RDF specification. True False doi:10.1016/j.jbi.2022.104201 https://github.com/fhircat/FHIROntopOMOP B2AI_STANDARD:692 ReferenceImplementation Xiao2022 FHIR-Ontop-OMOP - Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_TOPIC:13 B2AI_ORG:40 The Electronic Medical Records and Genomics (eMERGE) Network’s Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7® FHIR®), to represent clinical genomics results. These new standards improve the utility of HL7® FHIR® as an international healthcare interoperability standard for management of genetic data from patients. True False doi:10.1016/j.jbi.2021.103795 B2AI_STANDARD:693 ReferenceImplementation Murugan2021 Genomic considerations for FHIR; eMERGE implementation lessons Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 A complete implementation of the HL7 FHIR standard for healthcare interoperability in Java. True False https://hapifhir.io/ B2AI_STANDARD:694 ReferenceImplementation HAPI FHIR HAPI FHIR Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:76 The National COVID Cohort Collaborative (N3C) table of laboratory measurement data—over 3.1 billion patient records and over 19 000 unique measurement concepts in the Observational Medical Outcomes Partnership (OMOP) common-data-model format from 55 data partners. We grouped ontologically similar OMOP concepts together for 52 variables relevant to COVID-19 research, and developed a unit-harmonization pipeline comprised of (1) selecting a canonical unit for each measurement variable, (2) arriving at a formula for conversion, (3) obtaining clinical review of each formula, (4) applying the formula to convert data values in each unit into the target canonical unit, and (5) removing any harmonized value that fell outside of accepted value ranges for the variable. True False doi:10.1093/jamia/ocac054 B2AI_STANDARD:695 ReferenceImplementation Bradwell2022 Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:15 B2AI_ORG:40 B2AI_ORG:76 B2AI_ORG:79 To overcome the hurdle of disparate data sources and repositories with heterogeneous data formats a metadata crosswalk was initiated, based on existing standards. FAIR Principles were included, as well as data format specifications. The metadata crosswalk is the foundation of data provision between a Medical Data Integration Center (MeDIC) and researchers, providing a selection of metadata information for research design and requests. Based on the crosswalk, metadata items were prioritized and categorized to demonstrate that not one single predefined standard meets all requirements of a MeDIC and only a maximum data set of metadata is suitable for use. The development of a convergence format including the maximum data set is the anticipated solution for an automated transformation of metadata in a MeDIC. True False doi:10.1038/s41597-022-01792-7 B2AI_STANDARD:696 ReferenceImplementation Bönisch2022 Harvesting metadata in clinical care - a crosswalk between FHIR, OMOP, CDISC and openEHR metadata Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:40 This paper provides insights into how mHealth4Afrika is leveraging HL7 FHIR to support standards-based data exchange and interoperability between Electronic Medical Records and DHIS2. This work is currently being validated in the field. True False doi:10.3233/SHTI190175 B2AI_STANDARD:697 ReferenceImplementation Baskaya2019 Health4Afrika - Implementing HL7 FHIR Based Interoperability Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:76 COVID-19 data from 2 large countries in the Global South were harmonized and analyzed using a standardized health informatics framework developed by an international community of health informaticians. True False doi:10.1093/jamia/ocac180 https://github.com/ohdsi-studies/EhdenCovidUseCase B2AI_STANDARD:698 ReferenceImplementation PereiraPintoJunior2022 Integrating real-world data from Brazil and Pakistan into the OMOP common data model and standardized health analytics framework to characterize COVID-19 in the Global South Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_TOPIC:15 B2AI_ORG:25 Using a single tool, i) biomedical images can be imported and inspected, ii) the target can be identified and segmented, iii) features can be extracted from the target, iv) reduced and selected, and v) used to build a predictive model using machine learning algorithms. As result, two different feature extractors can be chosen, a Matlab-based extractor, and the Pyradiomics extractor naturally integrated into matRadiomics. True False doi:10.3390/jimaging8080221 B2AI_STANDARD:699 ReferenceImplementation Pasini2022 matRadiomics - A Novel and Complete Radiomics Framework, from Image Visualization to Predictive Model Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
multimodal We propose a solution to model patient trajectories that combines different types of information (e.g. clinical text, standard codes) and considers the temporal aspect of clinical data. This solution leverages two different architectures - one supporting flexible sets of input features, to convert patient admissions into dense representations; and a second exploring extracted admission representations in a recurrent-based architecture, where patient trajectories are processed in sub-sequences using a sliding window mechanism. True False doi:10.1016/j.jbi.2022.104195 https://github.com/bioinformatics-ua/PatientTM B2AI_STANDARD:700 ReferenceImplementation PatientTM Modelling patient trajectories using multimodal information Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datasheets B2AI_TOPIC:15 Following the structured format of Datasheets for Datasets, this paper expands on the original CheXpert paper and other sources to show the critical role played by radiologists in the creation of reliable labels and to describe the different aspects of the dataset composition in detail. Such structured documentation intends to increase the awareness in the machine learning and medical communities of the strengths, applications, and evolution of CheXpert, thereby advancing the field of medical image analysis. True False doi:10.48550/arXiv.2105.03020 B2AI_STANDARD:701 ReferenceImplementation Garbin2021 Structured dataset documentation - a datasheet for CheXpert Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:25 One of the critical tools for early detection and subsequent evaluation of the incidence of lung diseases is chest radiography. This study presents a real-world implementation of a convolutional neural network (CNN) based Carebot Covid app to detect COVID-19 from chest X-ray (CXR) images. Our proposed model takes the form of a simple and intuitive application. Used CNN can be deployed as a STOW-RS prediction endpoint for direct implementation into DICOM viewers. True False doi:10.48550/arXiv.2203.10596 B2AI_STANDARD:702 ReferenceImplementation Kvak2022 Towards Clinical Practice - Design and Implementation of Convolutional Neural Network-Based Assistive Diagnosis System for COVID-19 Case Detection from Chest X-Ray Images Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:76 We converted UK Biobank data to OMOP CDM v. 5.3. We transformed participant research data on diseases collected at recruitment and electronic health records (EHR) from primary care, hospitalizations, cancer registrations, and mortality from providers in England, Scotland, and Wales. We performed syntactic and semantic validations and compared comorbidities and risk factors between source and transformed data. True False doi:10.1093/jamia/ocac203 B2AI_STANDARD:703 ReferenceImplementation Papez2022 Transforming and evaluating the UK Biobank to the OMOP Common Data Model for COVID-19 research and beyond Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
dataregistry softwareregistry B2AI_TOPIC:1 Registry of software tools, databases and services for bioinformatics and the life sciences. True False https://bio.tools/ https://github.com/bio-tools/biotoolsregistry/ B2AI_STANDARD:704 Registry bio.tools bio.tools Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
softwareregistry B2AI_TOPIC:5 The mission of the Bioconductor project is to develop, support, and disseminate free open source software that facilitates rigorous and reproducible analysis of data from current and emerging biological assays. We are dedicated to building a diverse, collaborative, and welcoming community of developers and data scientists. True False https://www.bioconductor.org/ https://github.com/Bioconductor/BiocManager B2AI_STANDARD:705 Registry Bioconductor Bioconductor Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
ontologyregistry B2AI_TOPIC:1 An ontology registry. True False https://bioportal.bioontology.org/ https://github.com/ncbo B2AI_STANDARD:706 Registry BioPortal BioPortal Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
standardsregistry B2AI_TOPIC:5 A registry of prefixes and identifier formats used in biomedical data sets, knowledge bases, and ontologies. True False https://bioregistry.io/ doi:10.1101/2022.07.08.499378 https://github.com/biopragmatics/bioregistry B2AI_STANDARD:707 Registry Bioregistry Bioregistry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
standardsregistry B2AI_TOPIC:5 Standards, tools, reference implementations, and related resources. True False https://github.com/bridge2ai/b2ai-standards-registry B2AI_STANDARD:708 Registry Bridge2AI registry Bridge to Artificial Intelligence Registry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:15 CDISC launched the CDISC Shared Health And Research Electronic library (SHARE) to provide the standards metadata in machine-readable formats to facilitate the automated management and implementation of the standards. True True https://www.cdisc.org/faq/share/what-cdisc-share PUBMED:29888049 B2AI_STANDARD:709 Registry CDISC SHARE CDISC Shared Health And Research Electronic library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A catalog of worldwide biological databases maintained by the China National Center for Bioinformation, True False https://ngdc.cncb.ac.cn/databasecommons/ doi:10.1016/j.gpb.2022.12.004 B2AI_STANDARD:710 Registry Database Commons Database Commons Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
softwareregistry B2AI_TOPIC:5 B2AI_ORG:34 A free and open source platform for sharing reusable and scalable analytical tools and workflows. True False https://dockstore.org/ https://github.com/dockstore/dockstore B2AI_STANDARD:711 Registry Dockstore Dockstore Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
standardsregistry B2AI_TOPIC:5 standards and databases True False https://fairsharing.org/ https://github.com/FAIRsharing B2AI_STANDARD:712 Registry Fairsharing Fairsharing Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
standardsregistry B2AI_TOPIC:5 schemas and machine-actionable standards True False https://linkml.io/linkml-registry/registry/ https://github.com/linkml/linkml-registry/ B2AI_STANDARD:713 DataStandardOrTool LinkML registry LinkML schema registry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
standardsregistry B2AI_TOPIC:4 B2AI_TOPIC:7 B2AI_ORG:71 Registry and repository for oncology research common data elements and forms. True False https://datascience.cancer.gov/resources/metadata https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search B2AI_STANDARD:714 Registry NCI caDSR National Cancer Institute Cancer Data Standards Repository Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
dataregistry The primary purpose of NRDR is to aid facilities with their quality improvement programs and efforts to improve patient care by comparing facility data to that of their region and the nation. A practice or facility may choose to participate in any or all registries as appropriate for their practice. When a facility joins more than one registry, the warehouse allows information to be shared across registries within the facility. False True https://nrdr.acr.org/Portal/Nrdr/Main/page.aspx doi:10.1016/j.jacr.2011.05.014 B2AI_STANDARD:715 Registry NRDR National Radiology Data Registry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
ontologyregistry B2AI_TOPIC:5 B2AI_ORG:75 Ontologies. True False https://obofoundry.org/ doi:10.1093/database/baab069 B2AI_STANDARD:716 Registry OBO Foundry Open Biological and Biomedical Ontology Foundry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A free and open resource with Machine Learning papers, code, datasets, methods and evaluation tables. True False https://paperswithcode.com/ https://github.com/paperswithcode B2AI_STANDARD:717 Registry PwC Papers With Code Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
dataregistry re3data is a global registry of research data repositories. The registry covers research data repositories from different academic disciplines. re3data presents repositories for the permanent storage and access of data sets to researchers, funding bodies, publishers and scholarly institutions. re3data aims to promote a culture of sharing, increased access and better visibility of research data. True False https://www.re3data.org/ doi:10.5281/zenodo.6697943 B2AI_STANDARD:718 DataStandardOrTool r3data Registry of Research Data Repositories Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
dataregistry B2AI_ORG:85 The joint RSNA and American College of Radiology (ACR) 3D printing clinical data registry collects 3D printing data at the point of clinical care. With the goal of improving both patient care and characterizing resource utilization, the brand-new registry collects anonymized 3D printing case information, clinical indications and intended uses for printed models, source imaging, model construction techniques and effort, 3D printing techniques and effort, and the clinical impact of the models. False True https://www.rsna.org/practice-tools/RSNA-ACR-3D-printing-registry B2AI_STANDARD:719 Registry 3DP Registry RSNA-ACR 3D Printing Registry Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:40 A framework for transforming free-text problem descriptions into standardized Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) models. True False doi:10.1016/j.jbi.2020.103541 https://github.com/OHNLP/clinical-problem-standardization B2AI_STANDARD:720 SoftwareOrTool clinical-problem-standardization A corpus-driven standardization framework for encoding clinical problems with HL7 FHIR Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:76 A Research Exploration System designed to improved the transparency of observational data research. ARES is an opinionated framework that delineates three levels of observational data assessment. True False https://github.com/OHDSI/Ares B2AI_STANDARD:721 SoftwareOrTool ARES A Research Exploration System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 Aesara is a Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays. True False https://github.com/aesara-devs/aesara B2AI_STANDARD:722 SoftwareOrTool Aesara Aesara Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudservice B2AI_TOPIC:5 Cloud computing platform. False True https://aws.amazon.com/ B2AI_STANDARD:723 SoftwareOrTool AWS Amazon Web Services Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Amundsen is a data discovery and metadata engine for improving the productivity of data analysts, data scientists and engineers when interacting with data. It does that today by indexing data resources (tables, dashboards, streams, etc.) and powering a page-rank style search based on usage patterns (e.g. highly queried tables show up earlier than less queried tables). True False https://www.amundsen.io/ https://github.com/amundsen-io/amundsen B2AI_STANDARD:724 SoftwareOrTool Amundsen Amundsen Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
toolkit B2AI_TOPIC:20 Anduril is a workflow platform for analyzing large data sets. Anduril provides facilities for analyzing high-thoughput data in biomedical research, and the platform is fully extensible by third parties. True False https://anduril.org/site/ doi:10.1093/bioinformatics/btz133 https://bitbucket.org/anduril-dev/anduril/src/stable/ B2AI_STANDARD:725 SoftwareOrTool Anduril Anduril Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:5 Apache Atlas provides open metadata management and governance capabilities for organizations to build a catalog of their data assets, classify and govern these assets and provide collaboration capabilities around these data assets for data scientists, analysts and the data governance team. True False https://atlas.apache.org/ https://github.com/apache/atlas B2AI_STANDARD:726 SoftwareOrTool Apache Atlas Apache Atlas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:5 Apache Spark is a unified analytics engine for large-scale data processing. It provides high-level APIs in Java, Scala, Python and R, and an optimized engine that supports general execution graphs. True False https://spark.apache.org/docs/latest/index.html https://github.com/apache/spark B2AI_STANDARD:727 SoftwareOrTool Spark Apache Spark Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
deprecated workflowlanguage B2AI_TOPIC:5 Taverna is a domain-independent suite of tools used to design and execute data-driven workflows. True False https://incubator.apache.org/projects/taverna.html B2AI_STANDARD:728 SoftwareOrTool Taverna Apache Taverna Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datavisualization notebookplatform B2AI_TOPIC:5 Appyters extend the Jupyter Notebook language to support external, end-user configurable variables. Appyters can be considered a meta Jupyter Notebook language that is compatible with standard Jupyter Notebook execution. True False https://appyters.maayanlab.cloud/ doi:10.1016/j.patter.2021.100213 https://github.com/MaayanLab/appyter-catalog B2AI_STANDARD:729 SoftwareOrTool Appyters Appyters Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:76 A resource of searchable and loadable standardized vocabularies. True False https://athena.ohdsi.org/search-terms/terms https://github.com/OHDSI/Athena B2AI_STANDARD:730 SoftwareOrTool ATHENA ATHENA Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:76 An open source software tool for researchers to conduct scientific analyses on standardized observational data converted to the OMOP Common Data Model V5. Researchers can create cohorts by defining groups of people based on an exposure to a drug or diagnosis of a particular condition using healthcare claims data. True False https://atlas-demo.ohdsi.org/#/home https://github.com/OHDSI/Atlas B2AI_STANDARD:731 SoftwareOrTool ATLAS ATLAS Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_TOPIC:37 A database of continuously-recorded physiological waveform data and other associated clinical and medical device data. Also the platform for storage and retrieval of clinical waveform data. False True https://laussenlabs.ca/atriumdb/ doi:10.1088/1361-6579/ab7cb5 B2AI_STANDARD:732 SoftwareOrTool AtriumDB AtriumDB Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:76 Provides descriptive statistics on an OMOP CDM database. True False https://ohdsi.github.io/TheBookOfOhdsi/DataQuality.html#data-quality-checks https://github.com/OHDSI/Achilles B2AI_STANDARD:733 SoftwareOrTool ACHILLES Automated Characterization of Health Information at Large-scale Longitudinal Evidence System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:55 A Python package for balancing biased data samples. True False https://import-balance.org/ https://github.com/facebookresearch/balance B2AI_STANDARD:734 SoftwareOrTool balance balance package Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:37 A fully managed, serverless data warehouse that enables scalable analysis over petabytes of data. It is a Platform as a Service (PaaS) that supports querying using ANSI SQL. False True https://cloud.google.com/bigquery B2AI_STANDARD:735 SoftwareOrTool BigQuery BigQuery Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
toolkit B2AI_TOPIC:1 Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. True False https://biopython.org/ https://github.com/biopython/biopython B2AI_STANDARD:736 SoftwareOrTool Biopython Biopython Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
toolkit B2AI_TOPIC:20 This package bundles popular tasks in computational molecular biology into a uniform Python library. True False https://www.biotite-python.org/ https://github.com/biotite-dev/biotite B2AI_STANDARD:737 SoftwareOrTool Biotite Biotite Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:22 A toolbox for the statistical analysis and context decoding of neuroimaging data. It implements both univariate and multivariate linear models and interfaces with the BigBrain Atlas, Allen Human Brain Atlas and Nimare databases. True False https://brainstat.readthedocs.io/ doi:10.1016/j.neuroimage.2022.119807 https://github.com/MICA-MNI/BrainStat B2AI_STANDARD:738 SoftwareOrTool BrainStat BrainStat Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:1 A data analysis and sharing platform designed to accelerate discovery in a scalable, cloud-based compute environment where data, results, and workflows are shared among the world's research community. Developed by Seven Bridges and funded in-part by a grant from the National Institutes of Health (NIH) Common Fund, CAVATICA is continuously updated with new tools and datasets. False True https://www.cavatica.org/ B2AI_STANDARD:739 SoftwareOrTool Cavatica Cavatica data analysis platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Celery is a simple, flexible, and reliable distributed system to process vast amounts of messages, while providing operations with the tools required to maintain such a system. It’s a task queue with focus on real-time processing, while also supporting task scheduling. True False https://docs.celeryq.dev/en/latest/ https://github.com/celery/celery B2AI_STANDARD:740 SoftwareOrTool Celery Celery - Distributed Task Queue Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:12 B2AI_TOPIC:21 An updated version of the CliXO (Clique eXtracted Ontology) algorithm for inferring gene ontology terms from pairwise gene similarity data. True False doi:10.1126/science.abf3067 https://github.com/fanzheng10/CliXO-1.0 B2AI_STANDARD:741 SoftwareOrTool CLiXO Clique eXtracted Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Platform for managing machine learning models. False True https://www.comet.com/ https://github.com/comet-ml B2AI_STANDARD:742 SoftwareOrTool Comet Comet Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:12 B2AI_TOPIC:21 Performs multiscale community detection and functional enrichment for network analysis through a service-oriented architecture. These features are provided by integrating popular community detection algorithms and enrichment tools. All the algorithms and tools run remotely on a dedicated server. True False https://cdaps.readthedocs.io/ doi:10.1371/journal.pcbi.1008239 https://github.com/cytoscape/cy-community-detection B2AI_STANDARD:743 SoftwareOrTool CDAPS Community Detection APplication and Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:12 B2AI_TOPIC:21 Builds a CDAPS compatible community detection Docker image using CliXO. True False https://github.com/idekerlab/cdclixo B2AI_STANDARD:744 SoftwareOrTool CD-CLiXO Community Detection CliXO Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datamodel B2AI_TOPIC:5 A framework for rigorous self-validated data modeling and integrative, reproducible data analysis True False doi:10.1093/gigascience/giac089 https://github.com/jmchandonia/CORAL B2AI_STANDARD:745 SoftwareOrTool CORAL Contextual Ontology-based Repository Analysis Library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Continuous Machine Learning (CML) is an open-source library for implementing continuous integration & delivery (CI/CD) in machine learning projects. Use it to automate parts of your development workflow, including model training and evaluation, comparing ML experiments across your project history, and monitoring changing datasets. True False https://cml.dev/ https://github.com/iterative/cml B2AI_STANDARD:746 SoftwareOrTool CML library Continuous Machine Learning Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Cromwell is an open-source Workflow Management System for bioinformatics. True False https://cromwell.readthedocs.io/en/stable/ doi:10.7490/f1000research.1114634.1 https://github.com/broadinstitute/cromwell B2AI_STANDARD:747 SoftwareOrTool Cromwell Cromwell Workflow Management System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:21 An open source software platform for visualizing complex networks and integrating these with any type of attribute data. True False https://cytoscape.org/ https://github.com/cytoscape/cytoscape B2AI_STANDARD:748 SoftwareOrTool Cytoscape Cytoscape software Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Open source orchestration platform for the development, production, and observation of data assets. False True https://dagster.io/ https://github.com/dagster-io/dagster B2AI_STANDARD:749 SoftwareOrTool Dagster Dagster Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 A Python toolkit to support deep learning models for analyzing single-cell gene expression at scale. True False https://omicsml.ai/ https://github.com/OmicsML/dance B2AI_STANDARD:750 SoftwareOrTool DANCE DANCE platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:34 generic interface to data repositories True False https://ga4gh.github.io/data-repository-service-schemas/preview/release/drs-1.2.0/docs/ B2AI_STANDARD:751 SoftwareOrTool DRS Data Repository Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Open-source version control system for machine learning and data set management. True False https://dvc.org/ https://github.com/iterative/dvc B2AI_STANDARD:752 SoftwareOrTool DVC Data Version Control Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 An open-source metadata platform. True False https://datahubproject.io/ https://github.com/linkedin/datahub B2AI_STANDARD:753 SoftwareOrTool DataHub DataHub Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A tool for exploring and publishing data. It helps people take data of any shape, analyze and explore it, and publish it as an interactive website and accompanying API. True False https://datasette.io/ https://github.com/simonw/datasette B2AI_STANDARD:754 SoftwareOrTool Datasette Datasette Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 An analysis method for scRNA-seq data that clusters single cells into genetically distinct subclones and reconstructs the phylogenetic tree relating the subclones. True False doi:10.1186/s13059-019-1922-x https://github.com/zhouzilu/DENDRO B2AI_STANDARD:755 SoftwareOrTool DENDRO DENDRO Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 Determined is an open-source deep learning training platform. True False https://www.determined.ai/ https://github.com/determined-ai/determined B2AI_STANDARD:756 SoftwareOrTool Determined Determined Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 Dicoogle is an open source Picture Archiving and Communications System (PACS) archive. Its modular architecture allows the quick development of new functionalities, due the availability of a Software Development Kit (SDK). True False https://dicoogle.com/ doi:10.1109/ISCC50000.2020.9219545 https://github.com/bioinformatics-ua/dicoogle B2AI_STANDARD:757 SoftwareOrTool Dicoogle Dicoogle Picture Archiving and Communications System Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudservice B2AI_TOPIC:5 Cloud computing platform. False True https://www.digitalocean.com/ B2AI_STANDARD:758 SoftwareOrTool DigitalOcean DigitalOcean Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 An approach that detects doublet cell capture artifacts in scRNA-seq data with a combination of deconvolution analyses and the identification of unique cell-state gene expression. True False doi:10.1016/j.celrep.2019.09.082 https://github.com/EDePasquale/DoubletDecon B2AI_STANDARD:759 SoftwareOrTool DoubletDecon DoubletDecon Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Open metadata and governance for enterprises - automatically capturing, managing and exchanging metadata between tools and platforms, no matter the vendor. True False https://egeria-project.org/ https://github.com/odpi/egeria B2AI_STANDARD:760 SoftwareOrTool Egeria Egeria Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Eido is used to 1) validate or 2) convert format of sample metadata. Sample metadata is stored according to the standard PEP specification. For validation, eido is based on JSON Schema and extends it with new features, like required input files. True False http://eido.databio.org/ doi:10.1093/gigascience/giab077 https://github.com/pepkit/eido B2AI_STANDARD:761 SoftwareOrTool Eido Eido Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 A simple denoising strategy for scRNA-seq data based on principal component analysis (PCA). True False doi:10.1101/655365 https://github.com/yanailab/enhance B2AI_STANDARD:762 SoftwareOrTool ENHANCE Expression denoising heuristic using aggregation of neighbors and principal component extraction Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 FAIR Data Point (FDP) is a REST API for creating, storing, and serving FAIR metadata. This FDP implementation also presents a Web-based graphical user interface (GUI). The metadata contents are generated semi-automatically according to the FAIR Data Point software specification document. True False doi:10.1162/dint_a_00160 https://github.com/FAIRDataTeam/FAIRDataPoint B2AI_STANDARD:763 SoftwareOrTool FDP FAIR Data Point Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A reusable computational framework, enabling simplified access to modern scalable cloud-based components. FAIRSCAPE fully implements the FAIR data principles and extends them to provide fully FAIR Evidence, including machine-interpretable provenance of datasets, software and computations, as metadata for all computed results. True False https://fairscape.github.io/ doi:10.1007/s12021-021-09529-4 https://github.com/fairscape/fairscape B2AI_STANDARD:764 SoftwareOrTool FAIRSCAPE FAIRSCAPE digital commons framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 fastai is a deep learning library which provides practitioners with high-level components that can quickly and easily provide state-of-the-art results in standard deep learning domains, and provides researchers with low-level components that can be mixed and matched to build new approaches. It aims to do both things without substantial compromises in ease of use, flexibility, or performance. This is possible thanks to a carefully layered architecture, which expresses common underlying patterns of many deep learning and data processing techniques in terms of decoupled abstractions. These abstractions can be expressed concisely and clearly by leveraging the dynamism of the underlying Python language and the flexibility of the PyTorch library. True False https://github.com/fastai/fastai B2AI_STANDARD:765 SoftwareOrTool FastAI FastAI Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
toolkit B2AI_TOPIC:20 Galaxy is an open source, web-based platform for data intensive biomedical research. True False https://usegalaxy.org/ doi:10.1093/nar/gky379 https://github.com/galaxyproject/galaxy B2AI_STANDARD:766 SoftwareOrTool Galaxy Galaxy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudservice B2AI_TOPIC:5 B2AI_ORG:37 Cloud computing platform. False True https://cloud.google.com/ B2AI_STANDARD:767 SoftwareOrTool GCP Google Cloud Platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
graphdataplatform machinelearningframework B2AI_TOPIC:21 A fast graph processing and embedding library, designed to scale with big graphs and to run on both off-the-shelf laptop and desktop computers and High Performance Computing clusters of workstations. True False doi:10.48550/arXiv.2110.06196 https://github.com/AnacletoLAB/grape B2AI_STANDARD:768 SoftwareOrTool GrAPE Graph Representation leArning, Predictions and Evaluation library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:32 B2AI_TOPIC:16 HESML is an efficient, scalable and large Java software library of ontology-based semantic similarity measures and Information Content (IC) models based on WordNet, SNOMED-CT, MeSH or any other OBO-based ontology. True False http://hesml.lsi.uned.es/ doi:10.1186/S12859-021-04539-0 https://github.com/jjlastra/HESML B2AI_STANDARD:769 SoftwareOrTool HESML Half-Edge Semantic Measures Library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Version control for tensor data. True False https://hangar-py.readthedocs.io/en/stable/ https://github.com/tensorwerk/hangar-py B2AI_STANDARD:770 SoftwareOrTool Hangar Hangar Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_ORG:76 HADES (formally known as the OHDSI Methods Library) is a set of open source R packages for large scale analytics, including population characterization, population-level causal effect estimation, and patient-level prediction. True False https://ohdsi.github.io/Hades/ https://github.com/OHDSI/Hades B2AI_STANDARD:771 SoftwareOrTool HADES Health Analytics Data-to-Evidence Suite Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
multimodal A unified Holistic AI in Medicine (HAIM) framework to facilitate the generation and testing of AI systems that leverage multimodal inputs. True False doi:10.1038/s41746-022-00689-4 https://github.com/lrsoenksen/HAIM B2AI_STANDARD:772 SoftwareOrTool HAIM Holistic AI in Medicine framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 A Python library to facilitate the rapid development of high throughput sequencing data analysis scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. True False doi:10.1093/bioinformatics/btu638 https://github.com/htseq/htseq B2AI_STANDARD:773 SoftwareOrTool HTSeq HTSeq Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 A plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. ImJoy runs on mobile and desktop environment cross different operating systems, plugins can run in the browser, localhost, remote and cloud servers. True False https://imjoy.io/ doi:10.1038/s41592-019-0627-0 https://github.com/imjoy-team/ImJoy B2AI_STANDARD:774 SoftwareOrTool ImJoy ImJoy Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_ORG:42 A system for searching and exchanging clinical data. True False https://www.i2b2.org/software/index.html doi:10.1093/jamia/ocv188 https://github.com/i2b2 B2AI_STANDARD:775 SoftwareOrTool i2b2 Informatics for Integrating Biology and the Bedside platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:15 The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. True False https://itk.org/ https://github.com/InsightSoftwareConsortium/ITK B2AI_STANDARD:776 SoftwareOrTool ITK Insight Segmentation and Registration Toolkit Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 B2AI_TOPIC:15 A free and open-source web application to digitize, process and explore multimodal patient data. IMPatienT has a modular architecture, including four components to (i) create a standard vocabulary for a domain, (ii) digitize and process free-text data by mapping it to a set of standard terms, (iii) annotate images and perform image segmentation, and (iv) generate an automatic visualization dashboard to provide insight on the data and perform automatic diagnosis suggestions. True False https://impatient.lbgi.fr https://github.com/lambda-science/IMPatienT B2AI_STANDARD:777 SoftwareOrTool IMPatienT Integrated digital Multimodal PATIENt daTa framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:27 An open source C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way. IMP can also be used from the Chimera molecular modeling system, or via one of several web applications. True False https://integrativemodeling.org/ https://github.com/salilab/imp B2AI_STANDARD:778 SoftwareOrTool IMP Integrative Modeling Platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
notebookplatform B2AI_TOPIC:5 A web-based notebook environment for interactive computing. True False https://jupyter.org/ https://github.com/jupyter/notebook B2AI_STANDARD:779 SoftwareOrTool Jupyter Jupyter Notebook Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:37 Toolkit for speech recognition. True False https://kaldi-asr.org/ https://github.com/kaldi-asr/kaldi B2AI_STANDARD:780 SoftwareOrTool Kaldi Kaldi Speech Recognition Toolkit Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Version control for machine learning. A Python library that uploads files and metadata (like hyperparameters) to Amazon S3 or Google Cloud Storage. True False https://keepsake.ai/ https://github.com/replicate/keepsake B2AI_STANDARD:781 SoftwareOrTool Keepsake Keepsake Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
A freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. True False https://khmer.readthedocs.io/ doi:10.12688/f1000research.6924.1 https://github.com/dib-lab/khmer/ B2AI_STANDARD:782 SoftwareOrTool khmer khmer Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:58 Transform csv, json, yaml, jsonl, and xml and converting them to a target csv, json, or jsonl format based on your dataclass model. Koza also can output data in the KGX format. Write data transforms in semi-declarative Python. Configure source files, expected columns/json properties and path filters, field filters, and metadata in yaml. Create or import mapping files to be used in ingests (eg id mapping, type mappings). Create and use translation tables to map between source and target vocabularies. True False https://github.com/monarch-initiative/koza B2AI_STANDARD:783 SoftwareOrTool Koza Koza data transformation framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:7 B2AI_TOPIC:25 B2AI_TOPIC:35 B2AI_ORG:58 Performs phenotype-driven prioritization of candidate diseases and genes in the setting of genomic diagnostics (exome or genome) in which the phenotypic abnormalities are described as Human Phenotype Ontology (HPO) terms. True False https://lirical.readthedocs.io/ doi:10.1016/j.ajhg.2020.06.021 https://github.com/TheJacksonLaboratory/LIRICAL B2AI_STANDARD:784 SoftwareOrTool LIRICAL LIkelihood Ratio Interpretation of Clinical AbnormaLities Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudservice B2AI_TOPIC:5 Cloud computing platform. False True https://www.linode.com/ B2AI_STANDARD:785 SoftwareOrTool Linode Linode Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 A method for imputing missing values in scRNA-seq data. True False https://www.krishnaswamylab.org/projects/magic doi:10.1016/j.cell.2018.05.061 https://github.com/KrishnaswamyLab/MAGIC B2AI_STANDARD:786 SoftwareOrTool MAGIC Markov Affinity-based Graph Imputation of Cells Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Marquez is an open source metadata service for the collection, aggregation, and visualization of a data ecosystem's metadata. It maintains the provenance of how datasets are consumed and produced, provides global visibility into job runtime and frequency of dataset access, centralization of dataset lifecycle management, and much more. Marquez was released and open sourced by WeWork. True False https://lfaidata.foundation/projects/marquez/ https://github.com/MarquezProject/marquez B2AI_STANDARD:787 SoftwareOrTool Marquez Marquez Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem. True False https://monai.io/ https://github.com/Project-MONAI/MONAI B2AI_STANDARD:788 SoftwareOrTool MONAI Medical Open Network for AI Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:65 Metacat is a unified metadata exploration API service. You can explore Hive, RDS, Teradata, Redshift, S3 and Cassandra. Metacat provides you information about what data you have, where it resides and how to process it. True False https://github.com/Netflix/metacat B2AI_STANDARD:789 SoftwareOrTool Metacat Metacat Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudservice B2AI_TOPIC:5 B2AI_ORG:56 Cloud computing platform. False True https://azure.microsoft.com/ B2AI_STANDARD:790 SoftwareOrTool Azure Microsoft Azure Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudservice B2AI_TOPIC:5 S3 compatible object storage. Native to Kubernetes, MinIO is the only object storage suite available on every public cloud, every Kubernetes distribution, the private cloud and the edge. MinIO is software-defined and is 100% open source under GNU AGPL v3. True False https://min.io/ https://github.com/minio/ B2AI_STANDARD:791 SoftwareOrTool MinIO MinIO Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:37 ML Metadata (MLMD) is a library for recording and retrieving metadata associated with ML developer and data scientist workflows. True False https://www.tensorflow.org/tfx/guide/mlmd https://github.com/google/ml-metadata B2AI_STANDARD:792 SoftwareOrTool MLMD ML Metadata Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 MLflow is an open source platform to manage the ML lifecycle, including experimentation, reproducibility, deployment, and a central model registry True False https://mlflow.org/ https://github.com/mlflow/mlflow/ B2AI_STANDARD:793 SoftwareOrTool MLflow MLflow platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 Embeds flexible and recombinable ML models into standardized processes for training and real operations. In addition, it integrates numerous common open source frameworks and thus standardizes their use. True False https://mlpro.readthedocs.io/ doi:10.1016/j.simpa.2022.100421 https://github.com/fhswf/MLPro B2AI_STANDARD:794 SoftwareOrTool MLPro MLPro framework Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:23 A novel joint clustering framework that can be applied to several types of single-cell multi-omics data. A selective automatic doublet detection module that can identify and filter out doublets is introduced in the pretraining stage to improve data quality. Omics-specific autoencoders are introduced to characterize the multi-omics data. True False https://zenodo.org/record/7306504 doi:10.1093/bioinformatics/btac736 B2AI_STANDARD:795 SoftwareOrTool MoClust MoClust Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
modelcards B2AI_TOPIC:5 B2AI_ORG:37 The Model Card Toolkit (MCT) streamlines and automates generation of Model Cards, machine learning documents that provide context and transparency into a model's development and performance. True False doi:10.48550/arXiv.1810.03993 https://github.com/tensorflow/model-card-toolkit B2AI_STANDARD:796 SoftwareOrTool MCT Model Card Toolkit Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A non-relational document database that provides support for JSON-like storage. True False https://www.mongodb.com/ https://github.com/mongodb/mongo B2AI_STANDARD:797 SoftwareOrTool MongoDB MongoDB Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:21 An algorithm that uses reversed graph embedding to describe multiple fate decisions in a fully unsupervised manner. True False doi:10.1038/nmeth.4402 https://github.com/cole-trapnell-lab/monocle-release B2AI_STANDARD:798 SoftwareOrTool Monocle2 Monocle 2 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
multimodal B2AI_TOPIC:23 MIMaL is a new method for integrating multiomic data using SHAP model explanations. True False https://mimal.app/ doi:10.1093/bioinformatics/btac631 https://github.com/jessegmeyerlab/MIMaL B2AI_STANDARD:799 SoftwareOrTool MIMaL Multi-Omic Integration by Machine Learning Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
multimodal B2AI_TOPIC:26 B2AI_TOPIC:28 MuSIC is a hierarchical map of human cell architecture created from integrating immunofluorescence images in the Human Protein Atlas with affinity purification experiments from the BioPlex resource. Integration involves configuring each approach to produce a general measure of protein distance, then calibrating the two measures using machine learning. True False https://nrnb.org/music/ doi:10.1038/s41586-021-04115-9 https://github.com/idekerlab/MuSIC B2AI_STANDARD:800 SoftwareOrTool MuSIC Multi-Scale Integrated Cell pipeline Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A relational database management system developed by Oracle that is based on structured query language (SQL). True False https://www.mysql.com/ https://github.com/mysql/mysql-server B2AI_STANDARD:801 SoftwareOrTool MySQL MySQL Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
graphdataplatform B2AI_TOPIC:21 A popular graph database platform. True False https://neo4j.com/ https://github.com/neo4j/neo4j B2AI_STANDARD:802 SoftwareOrTool Neo4j Neo4j Graph Data Platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:16 Starting from a set of fulltext obtained from PubMed, through an easy-to-use web interface, interactively extracts a group of biological elements stored into a selected list of ontological databases and then synthesizes a network with inferred relations among such elements. True False https://netme.click/#/ doi:10.1007/S41109-021-00435-X B2AI_STANDARD:803 SoftwareOrTool NETME NETME Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 A network analysis pipeline for RNA-Seq time series data. True False doi:10.1186/S12859-021-04554-1 https://github.com/igbb-popescu-lab/NetSeekR B2AI_STANDARD:804 SoftwareOrTool NetSeekR NetSeekR network analysis R package Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
graphdataplatform B2AI_TOPIC:21 The NDEx Project provides an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge. True True https://www.ndexbio.org/ B2AI_STANDARD:805 SoftwareOrTool NDEx Network Data Exchange Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 A R/Bioconductor tool for cell type annotation using single-cell RNA-seq data. It is a supervised cell label assignment method that uses existing scRNA-seq data with known labels to train a neural network-based classifier, and then predict cell labels in single-cell RNA-seq data of interest. True False doi:10.1038/s41598-021-04473-4 https://github.com/haoharryfeng/NeuCA B2AI_STANDARD:806 SoftwareOrTool NeuCA NeuCA - Neural-network based Cell Annotation tool Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:20 B2AI_ORG:90 Enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. True False https://www.nextflow.io/ https://github.com/nextflow-io/nextflow B2AI_STANDARD:807 SoftwareOrTool Nextflow Nextflow Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudplatform B2AI_TOPIC:13 B2AI_ORG:73 AnVIL is NHGRI's Genomic Data Science Analysis, Visualization, and Informatics Lab-Space. True True https://anvilproject.org/ https://github.com/anvilproject B2AI_STANDARD:808 SoftwareOrTool AnVIL NHGRI Analysis Visualization and Informatics Lab-space Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:23 An R package for quality evaluation of omics data tables. For each data table, OmicsEV uses a series of methods to evaluate data depth, data normalization, batch effect, biological signal, platform reproducibility, and multi-omics concordance, producing comprehensive visual and quantitative evaluation results that help assess data quality of individual data tables and facilitate the identification of the optimal data processing method and parameters for the omics study under investigation. True False doi:10.1093/bioinformatics/btac698 https://github.com/bzhanglab/OmicsEV B2AI_STANDARD:809 SoftwareOrTool OmicsEV OmicsEV Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:58 OAK provides a collection of interfaces for various ontology operations. True False https://incatools.github.io/ontology-access-kit/ https://github.com/INCATools/ontology-access-kit B2AI_STANDARD:810 SoftwareOrTool OAK Ontology Access Kit Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:58 A toolkit and workflow system for managing the ontology life-cycle. True False doi:10.1093/database/baac087 https://github.com/INCATools/ontology-development-kit B2AI_STANDARD:811 SoftwareOrTool ODK Ontology Development Kit Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:18 An open-source platform for wearable health monitoring. It aims to design a standard set of hardware/software and wearable devices that can enable autonomous collection of clinically relevant data. True False https://sites.google.com/view/openhealth-wearable-health/home doi:10.1109/MDAT.2019.2906110 B2AI_STANDARD:812 SoftwareOrTool OpenHealth OpenHealth Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 An open source data analysis and manipulation tool built on top of the Python programming language. True False https://pandas.pydata.org/ B2AI_STANDARD:813 SoftwareOrTool pandas pandas Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
datavisualization B2AI_TOPIC:5 An open-source Python library that lets you create custom interactive web apps and dashboards by connecting user-defined widgets to plots, images, tables, or text. True False https://panel.holoviz.org/ https://github.com/holoviz/panel B2AI_STANDARD:814 SoftwareOrTool Panel Panel Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 An open source object-relational database system. True False https://www.postgresql.org/ https://github.com/postgres/postgres B2AI_STANDARD:815 SoftwareOrTool PostgreSQL PostgreSQL Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 A popular machine learning platform. True False https://pytorch.org/ https://github.com/pytorch/pytorch B2AI_STANDARD:816 SoftwareOrTool PyTorch PyTorch Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
notebookplatform B2AI_TOPIC:5 An open-source scientific and technical publishing system built on Pandoc. True False https://quarto.org/ https://github.com/quarto-dev/quarto-cli B2AI_STANDARD:817 SoftwareOrTool Quarto Quarto publishing system Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudplatform B2AI_TOPIC:4 B2AI_ORG:31 The Rare Disease Cures Accelerator-Data and Analytics Platform (RDCA-DAP®) is an FDA-funded initiative that provides a centralized and standardized infrastructure to support and accelerate rare disease characterization, with the goal of accelerating therapy development across rare diseases. False True https://c-path.org/programs/rdca-dap/ B2AI_STANDARD:818 SoftwareOrTool RDCA-DAP Rare Disease Cures Accelerator-Data and Analytics Platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:13 B2AI_ORG:34 Enables access to reference genomic sequences without ambiguity from different databases and servers using a checksum identifier based on the sequence content itself. True False https://samtools.github.io/hts-specs/refget.html B2AI_STANDARD:819 SoftwareOrTool refget refget API Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 Relexi is an open source reinforcement learning (RL) framework written in Python and based on TensorFlow’s RL library TF-Agents. Relexi allows to employ RL for environments that require computationally intensive simulations like applications in computational fluid dynamics. For this, Relexi couples legacy simulation codes with the RL library TF-Agents at scale on modern high-performance computing (HPC) hardware using the SmartSim library. Relexi thus provides an easy way to explore the potential of RL for HPC applications. True False doi:10.1016/j.simpa.2022.100422 https://github.com/flexi-framework/relexi B2AI_STANDARD:820 SoftwareOrTool Relexi Relexi Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:31 Electronic data capture software and workflow methodology for designing clinical and translational research databases. True True https://www.project-redcap.org/ doi:10.1016/j.jbi.2008.08.010 B2AI_STANDARD:821 SoftwareOrTool REDCap Research Electronic Data Capture Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:86 Synapse is a set of web services and tools that make it easier for researchers to aggregate, organize, analyze, and share scientific data, code, and insights. True True https://www.synapse.org/ doi:10.2139/ssrn.3502410 https://github.com/Sage-Bionetworks/Synapse-Repository-Services B2AI_STANDARD:822 SoftwareOrTool Synapse Sage Synapse Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:9 An open source semantic search and analytics tool for EHRs. True False doi:10.1093/jamia/ocx160 https://github.com/CogStack/CogStack-SemEHR B2AI_STANDARD:823 SoftwareOrTool SemEHR SemEHR Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 A regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse scRNA-seq data. True False https://mohuangx.github.io/SAVER/ doi:10.1038/s41592-018-0033-z https://github.com/mohuangx/SAVER B2AI_STANDARD:824 SoftwareOrTool SAVER Single-cell Analysis Via Expression Recovery Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Platform for automated data labeling. False True https://www.snorkel.org/ https://github.com/snorkel-team/snorkel B2AI_STANDARD:825 SoftwareOrTool Snorkel Snorkel Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:25 B2AI_TOPIC:35 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). True False https://pcingola.github.io/SnpEff/se_introduction/ doi:10.4161/fly.19695 https://github.com/pcingola/SnpEff B2AI_STANDARD:826 SoftwareOrTool SnpEff SnpEff Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
scrnaseqanalysis B2AI_TOPIC:34 A method to cluster cells using the genetic variants detected within the scRNA-seq reads. True False doi:10.1038/s41592-020-0820-1 https://github.com/wheaton5/souporcell B2AI_STANDARD:827 SoftwareOrTool Souporcell Souporcell Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:33 Software based on an RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. True False doi:10.1093/bioinformatics/bts635 https://github.com/alexdobin/STAR B2AI_STANDARD:828 SoftwareOrTool STAR Spliced Transcripts Alignment to a Reference Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A web service for automatic layout of biological data in various standard formats as well as construction of customized images in both raster image and scalable vector formats of these maps. Some of the supported standards are more generic such as GraphML and JSON, whereas others are specialized to biology such as SBGNML (The Systems Biology Graphical Notation Markup Language) and SBML (The Systems Biology Markup Language). True False http://syblars.cs.bilkent.edu.tr/ doi:10.1371/journal.pcbi.1010635 https://github.com/iVis-at-Bilkent/syblars B2AI_STANDARD:829 SoftwareOrTool SyBLaRS Systems Biology Layout and Rendering Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:34 standardized schema and API for describing and executing batch execution tasks True False https://ga4gh.github.io/task-execution-schemas/docs/ B2AI_STANDARD:830 SoftwareOrTool TES Task Execution Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 B2AI_ORG:37 A popular machine learning platform. True False https://www.tensorflow.org/ https://github.com/tensorflow/tensorflow B2AI_STANDARD:831 SoftwareOrTool TF Tensorflow Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudplatform B2AI_TOPIC:20 B2AI_ORG:71 Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate. True True https://app.terra.bio/ https://github.com/DataBiosphere/terra-ui B2AI_STANDARD:832 SoftwareOrTool Terra Terra Community Workbench Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 A free software environment for statistical computing and graphics. True False https://www.r-project.org/ B2AI_STANDARD:833 SoftwareOrTool R The R Project for Statistical Computing Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
deprecated machinelearningframework B2AI_TOPIC:5 A Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It is being continued as aesara. True False https://github.com/Theano/Theano B2AI_STANDARD:834 SoftwareOrTool Theano Theano Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:34 common API for describing tools in registries True False https://ga4gh.github.io/tool-registry-service-schemas/ B2AI_STANDARD:835 SoftwareOrTool TRS Tool Registry Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:4 B2AI_TOPIC:13 B2AI_ORG:94 U-BRITE (UAB Biomedical Research Information Technology Enhancement) assembles new and existing HIPAA-compliant, high-performance informatics tools to provide researchers with a means to better manage and analyze clinical and genomic data sets and implements a “translational research commons” to facilitate and enable interdisciplinary team science across geographical locations. False True https://ubrite.org/ B2AI_STANDARD:836 SoftwareOrTool U-BRITE UAB Biomedical Research Information Technology Enhancement Commons Program Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:76 An application to help create mappings between coding systems and the Vocabulary standard concepts. True False https://github.com/OHDSI/Usagi B2AI_STANDARD:837 SoftwareOrTool Usagi Usagi Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:34 A computationally efficient Bayesian model to demultiplex single-cell data from pooled experimental designs. True False doi:10.1186/s13059-019-1865-2 https://github.com/single-cell-genetics/vireo B2AI_STANDARD:838 SoftwareOrTool Vireo Vireo Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
cloudservice B2AI_TOPIC:5 Cloud storage platform. False True https://wasabi.com/ B2AI_STANDARD:839 SoftwareOrTool Wasabi Wasabi Cloud Storage Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Platform for tracking, comparing, and visualizing machine learning experiments. True True https://wandb.ai/ B2AI_STANDARD:840 SoftwareOrTool W&B Weights and Balances platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 B2AI_ORG:34 Standard for submitting workflow requests to workflow execution systems. True False https://ga4gh.github.io/workflow-execution-service-schemas/docs/ B2AI_STANDARD:841 SoftwareOrTool WES Workflow Execution Service Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_TOPIC:5 Git-based collaboration to large scale repositories of data, code, or any combination of files. True True https://xethub.com/assets/docs/ B2AI_STANDARD:842 SoftwareOrTool Xethub Xethub Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
machinelearningframework B2AI_TOPIC:5 ZenML is an extensible, open-source MLOps framework for creating portable, production-ready MLOps pipelines. True False https://zenml.io/ https://github.com/zenml-io/zenml B2AI_STANDARD:843 SoftwareOrTool ZenML ZenML Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:76 This workshop is for data holders who want to apply OHDSI’s data standards to their own observational datasets and researchers who want to be aware of OHDSI’s data standards, so they can leverage data in OMOP CDM format for their own research purposes. True False https://www.ohdsi.org/2019-tutorials-omop-common-data-model-and-standardized-vocabularies/ https://github.com/OHDSI/Tutorial-CDM B2AI_STANDARD:844 TrainingProgram OHDSI Tutorials 2019 OHDSI Tutorials - OMOP Common Data Model and Standardized Vocabularies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 A series of HL7 FAIR training lecture recordings made available through YouTube. True False https://www.cdc.gov/nchs/data/nvss/modernization/Introductory-Training-FHIR.pdf B2AI_STANDARD:845 DataStandardOrTool CDC Introduction to FHIR CDC Introduction to FHIR - Training Recordings Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 This set of pages contains a series of FHIR tutorials for those just beginning to learn the new specification. The tutorials require no prior knowledge of FHIR or REST. At present these tutorials are in their beta stage of development and we would appreciate any feedback you may have as we plan to build upon these in time to create a full set of tutorials from the very basic to the more complex. True False https://fhir-drills.github.io/ B2AI_STANDARD:846 TrainingProgram FHIR Drills FHIR Drills Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 This is an asynchronous, instructor-led online course that allows you to work at your own pace. Learning takes place through discussions with the instructor, tutors and peers. Assessments are in the form of weekly assignments, quizzes, exams and projects. Plan on spending 5 to 7 hours per week. There are no live lectures to attend. False True https://www.hl7.org/training/fhir-fundamentals.cfm https://courses.hl7fundamentals.org/campus/ B2AI_STANDARD:847 TrainingProgram FHIR Fundamentals HL7 FHIR Fundamentals Course Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:53 Welcome to the LOINC Library. This is our A to Z collection of resources that we've collected to help you learn about LOINC and get connected to the community. True False https://loinc.org/learn/ B2AI_STANDARD:848 TrainingProgram Learn LOINC Learn LOINC Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:25 B2AI_ORG:56 Learn why DICOM standards are important. Explore the DICOM standards and DICOM service. Review the use case for radiology data in cancer treatment with examples. True False https://learn.microsoft.com/en-us/training/modules/medical-imaging-data/ B2AI_STANDARD:849 TrainingProgram Microsoft Medical Imaging Microsoft Learn - Work with medical imaging data and DICOM Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 This course will help you understand the basics of FHIR. It is a FREE sample of a comprehensive hands-on introductory course (details inside). The full course includes direct access to the course creator via a private members-only Slack room. True True https://www.udemy.com/course/introduction-to-fhir/ B2AI_STANDARD:850 TrainingProgram Udemy FHIR Udemy - Introduction to FHIR Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 B2AI_ORG:103 This is subset of all FHIR profiles for the US Realm, i.e., those supporting the minimum requirements for clinical data exchange in the United States. True False https://build.fhir.org/ig/HL7/US-Core/index.html B2AI_STANDARD:851 BiomedicalStandard FHIR US Core Fast Healthcare Interoperability Resources - US Core B2AI_STANDARD:109 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 B2AI_ORG:103 USCDI is the set of basic healthcare data types expected to supported by other systems. This is the FHIR US Core profile with all elements required by USCDI. True False https://build.fhir.org/ig/HL7/US-Core/uscdi.html B2AI_STANDARD:852 BiomedicalStandard FHIR USCDI Fast Healthcare Interoperability Resources - US Core Data for Interoperability B2AI_STANDARD:851 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 B2AI_ORG:103 USCDI is the set of basic healthcare data types expected to supported by other systems. This is the FHIR US Core profile with all elements required by USCDI v1. True False https://build.fhir.org/ig/HL7/US-Core/uscdi.html B2AI_STANDARD:853 BiomedicalStandard FHIR USCDI v1 Fast Healthcare Interoperability Resources - US Core Data for Interoperability, version 1 B2AI_STANDARD:852 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
B2AI_ORG:40 B2AI_ORG:103 USCDI is the set of basic healthcare data types expected to supported by other systems. This is the FHIR US Core profile with all elements required by USCDI v4. True False https://build.fhir.org/ig/HL7/US-Core/uscdi.html B2AI_STANDARD:854 BiomedicalStandard FHIR USCDI v4 Fast Healthcare Interoperability Resources - US Core Data for Interoperability, version 4 B2AI_STANDARD:852 Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
multimodal A cross-platform app for analyzing qualitative and mixed methods research False True https://www.dedoose.com/ B2AI_STANDARD:855 SoftwareOrTool Dedoose Dedoose app Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-10
A lightweight application written in Java, that aims to support researchers in managing research metadata according to the FAIR principles. True False https://fairbydesign.nl/ doi:10.1093/gigascience/giad014 B2AI_STANDARD:856 SoftwareOrTool FAIR Data Station FAIR Data Station Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-13
guidelines The Council of Medical Specialty Societies (CMSS) and Patient-Led Research Collaborative (PLRC) have developed a sustainable collaborative model of CER based on information from and the expertise of patient communities, researchers, funders, and clinical research organizations. This model takes the form of scorecards which serve to evaluate how effective a patient group and research partner collaboration will be at conducting truly patient-led research. True False https://patientresearchcovid19.com/storage/2023/02/Patient-Led-Research-Scorecards.pdf B2AI_STANDARD:857 BiomedicalStandard Patient-Led Research Scorecards Patient-Led Research Scorecards Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-14
B2AI_TOPIC:32 B2AI_ORG:104 A framework for performing Zero and Few shot named entity recognition. True False https://ibm.github.io/zshot/ https://github.com/IBM/zshot B2AI_STANDARD:858 SoftwareOrTool Zshot Zshot Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-16
B2AI_TOPIC:5 B2AI_ORG:74 A registry of standardized, precisely defined questions, paired with sets of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. True False https://cde.nlm.nih.gov/ https://cde.nlm.nih.gov/api B2AI_STANDARD:859 Registry NIH CDE NIH Common Data Elements Repository Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-21
B2AI_TOPIC:5 A database of Knowledge Organization Systems and KOS related registries. True False https://bartoc.org/ B2AI_STANDARD:860 Registry BARTOC Basic Register of Thesauri, Ontologies & Classifications Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-24
B2AI_TOPIC:5 A database platform designed for working with tabular data. True False https://duckdb.org/ https://github.com/neo4j/neo4j B2AI_STANDARD:861 SoftwareOrTool DuckDB DuckDB Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-24
B2AI_TOPIC:5 A DataFrame library for Rust, Python, and Node.js. Intended to be very fast. True False https://www.pola.rs/ https://github.com/pola-rs/polars/ B2AI_STANDARD:862 SoftwareOrTool Polars Polars library Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-27
B2AI_TOPIC:5 A collection of searchable ontologies and vocabularies, spanning multiple fields. True False https://lov.linkeddata.es/ https://github.com/pyvandenbussche/lov B2AI_STANDARD:863 Registry LOV Linked Open Vocabularies Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-27
B2AI_TOPIC:4 A catalog of recommended measurement protocols for biomedical research. True False https://www.phenxtoolkit.org/ B2AI_STANDARD:864 Registry PhenX Toolkit PhenX Toolkit Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-03-27
B2AI_TOPIC:22 An archive for cellular neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments. True False https://www.dandiarchive.org/ B2AI_STANDARD:865 ReferenceDataOrDataset DANDI Distributed Archives for Neurophysiology Data Integration Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-04-10
B2AI_TOPIC:23 An OWL2 ontology for representing and semantically annotating pairwise and multiple sequence alignments. True False https://benhid.com/SALON/ doi:10.1186/s12859-023-05190-7 B2AI_STANDARD:866 OntologyOrVocabulary SALON Sequence Alignment Ontology Harry Caufield caufieldjh ORCID:0000-0001-5705-7831
diagnosticinstrument B2AI_TOPIC:4 A neurological assessment tool used to evaluate level of consciousness based on patient responses in three categories: eye-opening, verbal response, and motor response, with a higher score indicating a more favorable neurological status. True False https://www.glasgowcomascale.org/ doi:10.1016/s0140-6736(74)91639-0 B2AI_STANDARD:867 BiomedicalStandard GCS Glasgow Coma Scale Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-05-23
datamodel B2AI_TOPIC:5 A set of patterns for describing data, including Table Schema (for tables), Data Resource (for files), and Data Package (for datasets). True False https://specs.frictionlessdata.io/ https://github.com/frictionlessdata/specs B2AI_STANDARD:868 DataStandard Frictionless Frictionless data standards Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-05-23
B2AI_TOPIC:29 B2AI_ORG:105 Care coordination module focused on social determinant of health factors. Part of the Epic EHR platform. False True https://www.epic.com/software/population-health B2AI_STANDARD:869 SoftwareOrTool Compass Rose Epic Compass Rose module Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-06-20
B2AI_TOPIC:5 A platform for organizing, testing, and validating data. True False https://greatexpectations.io/ https://github.com/great-expectations/great_expectations B2AI_STANDARD:870 SoftwareOrTool GX Great Expectations platform Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-06-20
B2AI_TOPIC:5 A database platform built around creating vector representations of data. The basic implementation is a managed, cloud-native product, though there is a free tier. False True https://www.pinecone.io/ B2AI_STANDARD:871 SoftwareOrTool Pinecone Pinecone vector database Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-06-20
guidelines B2AI_TOPIC:5 An open-source guide to help with writing command-line programs, based on UNIX principles. True False https://clig.dev/ B2AI_STANDARD:872 DataStandard CLIG Command Line Interface Guidelines Harry Caufield caufieldjh ORCID:0000-0001-5705-7831 2023-06-20