Bridge2AI Data Manifest
This page provides a comprehensive manifest of all data subsets, standards, substrates, topics, and relevant anatomy used across the Bridge2AI consortium.
Each data type is listed with its associated metadata and standards.
Table Features
- Click on any column header to sort the table
- Links are provided to standards, substrates, topics, and anatomy ontologies
- Icons indicate different types of metadata: 📋 Standards, 💾 Substrates, 🏷️ Topics, 🧬 Anatomy
Functional Genomics Grand Challenge
| Data Type | Description | 📋 Standards & Tools | 💾 Substrates | 🏷️ Topics | 🧬 Anatomy |
|---|---|---|---|---|---|
| Cell maps | Cell maps of cellular systems. | B2AI_STANDARD:372 (RO-CRATE) | B2AI_TOPIC:2 (Cell) | CLO:0000031 (cell line) | |
| Cell line metadata | Cell line metadata. | B2AI_STANDARD:372 (RO-CRATE) | B2AI_TOPIC:2 (Cell) | CLO:0000031 (cell line) | |
| AP-MS - Level 1 | AP-MS raw signal and metadata. | B2AI_STANDARD:372 (RO-CRATE) | B2AI_SUBSTRATE:58 (Mass Spectrometry Data) | B2AI_TOPIC:2 (Cell), B2AI_TOPIC:28 (Proteome) | CLO:0000031 (cell line) |
| AP-MS - Level 3 | AP-MS peptide counts. | B2AI_STANDARD:372 (RO-CRATE) | B2AI_SUBSTRATE:58 (Mass Spectrometry Data) | B2AI_TOPIC:2 (Cell), B2AI_TOPIC:28 (Proteome) | CLO:0000031 (cell line) |
| Confocal IF - Level 1 | Confocal immunofluorescence cell imaging raw signal (pixel intensity) and metadata. | B2AI_STANDARD:344 (JPEG), B2AI_STANDARD:372 (RO-CRATE) | B2AI_SUBSTRATE:56 (Immunofluorescence Image) | B2AI_TOPIC:2 (Cell), B2AI_TOPIC:19 (Microscale Imaging) | CLO:0000031 (cell line) |
| CROP-seq - Level 1 | CROP-seq raw signal (unaligned reads) and metadata. | B2AI_STANDARD:111 (FASTQ), B2AI_STANDARD:372 (RO-CRATE) | B2AI_SUBSTRATE:64 (Perturb-seq Data) | B2AI_TOPIC:34 (Transcriptome) | CLO:0000031 (cell line) |
| CROP-seq - Level 2 | CROP-seq aligned reads and metadata. | B2AI_STANDARD:21 (BAM/CRAM), B2AI_STANDARD:372 (RO-CRATE) | B2AI_SUBSTRATE:64 (Perturb-seq Data) | B2AI_TOPIC:34 (Transcriptome) | CLO:0000031 (cell line) |
| CROP-seq - Level 3 | CROP-seq gene counts and metadata. | B2AI_STANDARD:372 (RO-CRATE) | B2AI_SUBSTRATE:64 (Perturb-seq Data), B2AI_SUBSTRATE:43 (Text) | B2AI_TOPIC:34 (Transcriptome) | CLO:0000031 (cell line) |
| CROP-seq protocol | CROP-seq assay attributes. | B2AI_STANDARD:372 (RO-CRATE) | B2AI_TOPIC:34 (Transcriptome) | CLO:0000031 (cell line) | |
| CROP-seq sample metadata | CROP-seq sample attributes. | B2AI_STANDARD:372 (RO-CRATE) | B2AI_SUBSTRATE:64 (Perturb-seq Data), B2AI_SUBSTRATE:6 (Comma-separated values) | B2AI_TOPIC:34 (Transcriptome) | CLO:0000031 (cell line) |
| CROP-seq QC | CROP-seq quality control metrics. | B2AI_STANDARD:372 (RO-CRATE) | B2AI_SUBSTRATE:64 (Perturb-seq Data), B2AI_SUBSTRATE:43 (Text) | B2AI_TOPIC:34 (Transcriptome) | CLO:0000031 (cell line) |
| Evidence | Evidence supporting predictions, modeled as provenance graphs. | B2AI_STANDARD:372 (RO-CRATE), B2AI_STANDARD:444 (EVI) | B2AI_SUBSTRATE:20 (JSON) | B2AI_TOPIC:34 (Transcriptome) | CLO:0000031 (cell line) |
Salutogenesis Grand Challenge
| Data Type | Description | 📋 Standards & Tools | 💾 Substrates | 🏷️ Topics | 🧬 Anatomy |
|---|---|---|---|---|---|
| WGS - Level 1 | Whole genome sequencing raw reads and metadata. | B2AI_STANDARD:111 (FASTQ) | B2AI_SUBSTRATE:61 (DNA Sequence Data) | B2AI_TOPIC:13 (Genome) | |
| OCT | Optical coherence tomography (Retinal layer thickness measurements) and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:67 (Optical coherence tomography data) | B2AI_TOPIC:24 (Ophthalmic Imaging) | UBERON:0003951 (ocular fundus) |
| Near-IR ophthalmic imaging | Near-infrared ophthalmic imaging and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:65 (Retinal Image) | B2AI_TOPIC:24 (Ophthalmic Imaging) | UBERON:0003951 (ocular fundus) |
| Retinal fundus imaging | Retinal fundus imaging and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:65 (Retinal Image) | B2AI_TOPIC:24 (Ophthalmic Imaging) | UBERON:0003951 (ocular fundus) |
| OCTA | Optical coherence tomography angiography and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:68 (Optical coherence tomography angiography data) | B2AI_TOPIC:24 (Ophthalmic Imaging) | UBERON:0003951 (ocular fundus) |
| FLIO | Fluorescence lifetime imaging ophthalmoscopy and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:66 (Fluorescence Lifetime Imaging Ophthalmoscopy data) | B2AI_TOPIC:24 (Ophthalmic Imaging) | UBERON:0003951 (ocular fundus) |
| Clinical visit | Data produced during clinical visits, including results of vision assessments. | B2AI_STANDARD:243 (OMOP CDM) | B2AI_TOPIC:4 (Clinical Observations), B2AI_TOPIC:44 (Eye Diseases) | UBERON:0000468 (multicellular organism) | |
| Clinical labs | Clinical laboratory measurements. | B2AI_STANDARD:243 (OMOP CDM) | B2AI_TOPIC:9 (EHR) | UBERON:0000468 (multicellular organism) | |
| Survey data | Data from patient surveys, including social determinants of health (SDoH), diet, lifestyle, family history, and MoCA cognitive scores. | B2AI_STANDARD:243 (OMOP CDM), B2AI_STANDARD:821 (REDCap) | B2AI_SUBSTRATE:80 (Questionnaire response data) | B2AI_TOPIC:4 (Clinical Observations) B2AI_TOPIC:29 (SDoH) B2AI_TOPIC:40 (Governance) |
|
| Glucose levels | Patient glucose data from continuous monitoring over 10 days. | B2AI_STANDARD:246 (Open mHealth) | B2AI_SUBSTRATE:78 (Glucose monitoring data) | B2AI_TOPIC:38 (Glucose Monitoring) | UBERON:0000178 (blood) |
| Activity levels | Patient activity data from continuous monitoring over 10 days. | B2AI_STANDARD:246 (Open mHealth) | B2AI_SUBSTRATE:73 (Physical activity data), B2AI_SUBSTRATE:74 (Caloric burn data) | B2AI_TOPIC:39 (Activity Monitoring) | UBERON:0000468 (multicellular organism) |
| Heart rate | Patient heart rate data from continuous monitoring over 10 days. | B2AI_STANDARD:246 (Open mHealth) | B2AI_SUBSTRATE:71 (Heart rate) | B2AI_TOPIC:39 (Activity Monitoring) | UBERON:0000948 (heart) |
| SpO2 levels | Patient blood oxygen saturation levels from continuous monitoring over 10 days. | B2AI_STANDARD:246 (Open mHealth) | B2AI_SUBSTRATE:72 (Oxygen saturation) | B2AI_TOPIC:39 (Activity Monitoring), B2AI_TOPIC:46 (Respiration) | |
| ECG | Patient cardiac 12-lead electrocardiogram (waveform) data and metadata. | B2AI_STANDARD:202 (WFDB Format) | B2AI_SUBSTRATE:49 (Waveform Data) | B2AI_TOPIC:37 (Waveform) | UBERON:0000948 (heart) |
| Environmental data | Patient environment and air quality data. Includes temperature, humidity, oxygen, particle, and other measures of the environment. | B2AI_TOPIC:11 (Environment) | UBERON:0000468 (multicellular organism) |
Precision Public Health Grand Challenge
| Data Type | Description | 📋 Standards & Tools | 💾 Substrates | 🏷️ Topics | 🧬 Anatomy |
|---|---|---|---|---|---|
| WGS - Level 1 | Whole genome sequencing raw reads and metadata. Preserving/sharing unaligned reads (in same file as aligned reads) via CRAM. | B2AI_STANDARD:21 (BAM/CRAM) | B2AI_TOPIC:13 (Genome) | ||
| WGS - Level 2 | Whole genome sequencing aligned reads and metadata. Preserving/sharing unaligned reads (in same file as aligned reads) via CRAM. | B2AI_STANDARD:21 (BAM/CRAM) | B2AI_TOPIC:13 (Genome) | ||
| WGS - Level 3 | Whole genome sequencing variant calls (SNV/INDEL/CNV/SV) and metadata. Preserving/sharing unaligned reads (in same file as aligned reads) via CRAM. | B2AI_STANDARD:299 (VCF) | B2AI_TOPIC:13 (Genome) | ||
| WGS protocol | Whole genome sequencing protocol and metadata. | B2AI_TOPIC:13 (Genome) | |||
| WGS sample metadata | Whole genome sequencing sample attributes. | B2AI_TOPIC:13 (Genome) | |||
| WGS QC | Whole genome sequencing quality control metrics. | B2AI_TOPIC:13 (Genome) | |||
| CT | Computed tomography (CT) scans and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:11 (DICOM) | B2AI_TOPIC:22 (Neurologic Imaging) | |
| MR | Magnetic resonance (MR) imaging and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:11 (DICOM) | B2AI_TOPIC:22 (Neurologic Imaging) | |
| X-ray | X-ray imaging and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:11 (DICOM) | ||
| Voice | Voice recordings (spectrographs) and metadata. | B2AI_STANDARD:202 (WFDB Format) | B2AI_SUBSTRATE:49 (Waveform Data) | B2AI_TOPIC:36 (Voice) | UBERON:0000468 (multicellular organism) |
| Laryngoscopy | Laryngoscopy videos and metadata. | B2AI_STANDARD:98 (DICOM), B2AI_STANDARD:352 (MPEG-4) | B2AI_SUBSTRATE:19 (Image) | UBERON:0001737 (larynx) | |
| Speech test assessment | Speech test assessment results. | B2AI_SUBSTRATE:49 (Waveform Data) | B2AI_TOPIC:36 (Voice), B2AI_TOPIC:45 (Voice Disorders) | UBERON:0000468 (multicellular organism) | |
| Spontaneous speech assessment | Spontaneous speech assessment results. | B2AI_SUBSTRATE:49 (Waveform Data) | B2AI_TOPIC:36 (Voice), B2AI_TOPIC:45 (Voice Disorders) | UBERON:0000468 (multicellular organism) | |
| Forced cough assessment | Forced cough assessment results. | B2AI_SUBSTRATE:49 (Waveform Data) | B2AI_TOPIC:36 (Voice), B2AI_TOPIC:45 (Voice Disorders) | UBERON:0000468 (multicellular organism) | |
| Informed consent | Informed consent form responses. | B2AI_STANDARD:821 (REDCap) | |||
| Questionnaire | Questionnaire responses, including MoCA, GAD-7, VHI-10, PANAS, and DI. | B2AI_STANDARD:109 (FHIR) | B2AI_TOPIC:31 (Survey) | ||
| Demographics | Participant demographics information. | B2AI_STANDARD:109 (FHIR) | B2AI_TOPIC:29 (SDoH), B2AI_TOPIC:31 (Survey) | ||
| Treatment | Participant treatment history information. | B2AI_STANDARD:243 (OMOP CDM) | B2AI_TOPIC:4 (Clinical Observations) | UBERON:0000468 (multicellular organism) | |
| Diagnosis | Participant diagnosis history information and results of functional assessment. | B2AI_STANDARD:174 (ICD-10-CM) | B2AI_TOPIC:4 (Clinical Observations), B2AI_TOPIC:45 (Voice Disorders) | UBERON:0000468 (multicellular organism) | |
| Vital signs | Participant vital signs information. | B2AI_STANDARD:109 (FHIR) | B2AI_TOPIC:4 (Clinical Observations) | ||
| Social history | Participant social history information, including social history (e.g., smoking and alcohol use). | B2AI_TOPIC:29 (SDoH) |
AI/ML for Clinical Care Grand Challenge
| Data Type | Description | 📋 Standards & Tools | 💾 Substrates | 🏷️ Topics | 🧬 Anatomy |
|---|---|---|---|---|---|
| Clinical labs | Clinical laboratory measurements. | B2AI_TOPIC:4 (Clinical Observations), B2AI_TOPIC:9 (EHR) | |||
| Clinical treatments | Clinical treatment information, including details of medications administered. | B2AI_TOPIC:4 (Clinical Observations) | |||
| Physiologic telemetry | Physiologic telemetry data. | B2AI_SUBSTRATE:49 (Waveform Data) | B2AI_TOPIC:4 (Clinical Observations), B2AI_TOPIC:9 (EHR) | ||
| Physiologic EEG | Physiologic electroencephalogram data. | B2AI_SUBSTRATE:49 (Waveform Data) | B2AI_TOPIC:4 (Clinical Observations), B2AI_TOPIC:9 (EHR) | UBERON:0000955 (brain) | |
| ECG | Patient cardiac 5-lead electrocardiogram (waveform) data and metadata. | B2AI_STANDARD:202 (WFDB Format) | B2AI_SUBSTRATE:49 (Waveform Data) | B2AI_TOPIC:37 (Waveform) | UBERON:0000948 (heart) |
| Heart rate | Patient heart rate data. | B2AI_SUBSTRATE:71 (Heart rate) | B2AI_TOPIC:39 (Activity Monitoring) | UBERON:0000948 (heart) | |
| SpO2 levels | Patient blood oxygen saturation levels. | B2AI_SUBSTRATE:72 (Oxygen saturation) | B2AI_TOPIC:46 (Respiration) | ||
| X-ray | X-ray imaging and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:11 (DICOM) | ||
| CT | Computed tomography (CT) scans and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:11 (DICOM) | B2AI_TOPIC:22 (Neurologic Imaging) | |
| MR | Magnetic resonance (MR) imaging and metadata. | B2AI_STANDARD:98 (DICOM) | B2AI_SUBSTRATE:11 (DICOM) | B2AI_TOPIC:22 (Neurologic Imaging) | |
| Social determinants of health | Social determinants of health data based on Area Deprivation Index (ADI). | B2AI_TOPIC:29 (SDoH) | |||
| Practice metadata | Metadata about clinical practice. |