| lab_id |
Textfield |
A locally assigned identifier provided by the data provider for the dataset. It is used to reference an external metadata record that may be maintained independently, enabling traceability and supporting provenance tracking. Example: Visium_9OLC_A4_S1 |
|
False |
| dataset_type |
Assigned Value |
The specific type of dataset being produced. Example: RNAseq |
Visium HD, 4i, LC-MS, Thick section Multiphoton MxIF, Light Sheet, ATACseq, Resolve, HiFi-Slide, COMET, MPLEx, 10X Multiome, MALDI, Histology, Cell DIVE, FACS, MS Lipidomics, Visium (no probes), MUSIC, RNAseq, GeoMx (NGS), GeoMx (nCounter), RNAseq (with probes), Singular Genomics G4X, Molecular Cartography, CosMx Transcriptomics, MERFISH, Pixel-seqV2, 2D Imaging Mass Cytometry, Confocal, seqFISH, DART-FISH, MIBI, Olink, Enhanced Stimulated Raman Spectroscopy (SRS), DESI, Xenium, CyCIF, SNARE-seq2, nanoSPLITS, Stereo-seq, Visium (with probes), SIMS, Auto-fluorescence, CyTOF, CosMx Proteomics, DBiT-seq, PhenoCycler, CODEX, Second Harmonic Generation (SHG), Seq-Scope |
True |
| analyte_class |
Assigned Value |
The analyte class which is the target molecule that the assay is measuring. Example: DNA |
Nucleic acid + protein, Lipid + metabolite, Collagen, RNA, Fluorochrome, DNA, Metabolite, DNA + RNA, Saturated lipid, Lipid, Peptide, Protein, Unsaturated lipid, Endogenous fluorophore, Chromatin, Polysaccharide |
True |
| acquisition_instrument_vendor |
Assigned Value |
The company that manufactures or supplies the acquisition instrument. An acquisition instrument is a device equipped with signal detection hardware and signal processing software. It captures signals produced by assays, such as variations in light intensity or color, or signals corresponding to molecular mass. If the instrument was custom-built or developed internally, enter “In-House”. Example: Illumina |
Complete Genomics, Cytek Biosciences, Thermo Fisher Scientific, Sciex, Vizgen, Leica Microsystems, Akoya Biosciences, Keyence, Andor, Standard BioTools (Fluidigm), Leica Biosystems, Zeiss Microscopy, Ionpath, Motic, In-House, Evident Scientific (Olympus), GE Healthcare, Element Biosciences, Hamamatsu, Bruker, Illumina, 3DHISTECH, Singular Genomics, Huron Digital Pathology, Resolve Biosciences, NanoString, Cytiva, 10x Genomics, Microscopes International, BGI Genomics |
True |
| acquisition_instrument_model |
Assigned Value |
The specific model of the acquisition instrument, as manufacturers often offer various versions with differing features or sensitivities. These differences may be relevant to the processing or interpretation of the data. If the instrument was custom-built or developed internally, enter “In-House”. If the model is unknown, enter “Unknown”. Example: HiSeq 4000 |
NovaSeq X, NovaSeq X Plus, Cytek Northern Lights, Lightsheet 7, Resolve Biosciences Molecular Cartography, timsTOF HT, timsTOF Pro 2, timsTOF Pro, timsTOF Ultra, timsTOF Ultra 2, timsTOF SCP, Axio Scan.Z1, MALDI timsTOF Flex Prototype, CosMx Spatial Molecular Imager, Unknown, MERSCOPE Ultra, Juno System, timsTOF FleX, Custom: Multiphoton, CyTOF XT, Helios, EVOS M7000, Aperio AT2, Phenocycler-Fusion 2.0, Axio Observer 5, Axio Observer 7, Axio Observer 3, NanoZoomer-SQ, NanoZoomer S210, NanoZoomer S60, NanoZoomer S360, DM6 B, MoticEasyScan One, In-House, NextSeq 500, BZ-X710, QTRAP 5500, NextSeq 550, HiSeq 2500, HiSeq 4000, NovaSeq 6000, Q Exactive HF, Orbitrap Fusion Lumos Tribrid, Q Exactive, VS200 Slide Scanner, Not applicable, Orbitrap Eclipse Tribrid, MIBIscope, IN Cell Analyzer 2200, timsTOF FleX MALDI-2 |
True |
| source_storage_duration_value |
Numeric |
The length of time the sample was stored prior to processing it. For assays performed on tissue sections, this refers to how long the tissue section (e.g., slide) was stored before the assay began (e.g., imaging). For assays performed on suspensions, such as sequencing, it refers to how long the suspension was stored before library construction started. Example: 12 |
|
True |
| source_storage_duration_unit |
Assigned Value |
The unit of measurement used to specify the source storage duration value. Example: hour |
hour, month, day, minute, year |
True |
| time_since_acquisition_instrument_calibration_value |
Numeric |
The length of time since the acquisition instrument was last serviced or calibrated. This provides a metric for assessing drift in data capture. Example: 10 |
|
False |
| time_since_acquisition_instrument_calibration_unit |
Assigned Value |
The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month |
month, day, year |
False |
| preparation_protocol_doi |
Link |
The DOI for the protocols.io page that details the assay or the procedures used for sample procurement and preparation. For example, in the case of an imaging assay, the protocol may start with tissue section staining and end with the generation of an OME-TIFF file. The documented protocol should also include any image processing steps involved in producing the final OME-TIFF. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 |
|
True |
| is_targeted |
Radio |
Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes |
Yes, No |
True |
| contributors_path |
Textfield |
The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv |
|
True |
| data_path |
Textfield |
The top-level directory containing the raw and/or processed data. For a single dataset upload, this might be represented as “.”, whereas for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For example, if the data is within a directory named “TEST001-RK”, use the syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2”, where “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field used solely for data ingestion. Example: ./TEST001-RK |
|
True |
| parent_sample_id |
Textfield |
The unique identifier from HuBMAP or SenNet for the sample (such as a block, section, or suspension) used to perform the assay. For instance, in an RNAseq assay, the parent sample would be the suspension, while in imaging assays, it would be the tissue section. If the assay is derived from multiple parent samples, this field should contain a comma-separated list of identifiers. Example: HBM386.ZGKG.235, HBM672.MKPK.442 |
|
True |
| mapped_area_value |
Numeric |
The mapped area value, which refers to the specific area covered or captured in various assays. For Visium, it is the area of spots covered by tissue within the captured area, excluding the total possible captured area. For GeoMx, it refers to the area of the AOI being captured. In HiFi, it is the summed area of the ROIs in a single flowcell lane. For CosMx and Resolve, it indicates the area of the FOV (also known as ROI) region being captured. For Xenium, it is the total area of the FOV regions (also known as ROI) being captured. For Stereo-Seq, this value represents the number of beads. Example: 42.25 |
|
False |
| mapped_area_unit |
Assigned Value |
The unit of measurement for the mapped area value. If mapping area is not specified, this field may be left blank. Example: um^2 |
um^2, mm^2 |
False |
| slide_id |
Textfield |
The unique identifier assigned to each slide, enabling users to determine which tissue sections were processed together on the same slide. It is recommended that data providers prefix the ID with the center name to prevent overlapping values across different centers. Example: VAN0071-PA-1-1_AF |
|
True |
| target_retrieval_incubation_temperature |
Numeric |
The incubation temperature required for target retrieval, which is typically 100 degrees Celsius for RNA assays and 80 degrees Celsius for protein assays. Example: 100 |
|
False |
| target_retrieval_incubation_time_value |
Numeric |
The duration for which a sample is exposed to a target retrieval solution. Example: 15 |
|
False |
| target_retrieval_incubation_time_unit |
Assigned Value |
The unit of measurement for the target retrieval incubation time value. If no incubation time is specified, this field may be left blank. Example: minute |
minute |
False |
| probe_hybridization_time_value |
Numeric |
The duration for which the oligo-conjugated RNA or oligo-conjugated antibody probes were hybridized with the sample. Example: 30 |
|
False |
| probe_hybridization_time_unit |
Assigned Value |
The unit of measurement for the probe hybridization time value. If the hybridization time is not specified, this field may be left blank. Example: minute |
hour, minute |
False |
| oligo_probe_panel |
Assigned Value |
The oligo probe panel used to target genes and/or proteins. If there is a core panel along with add-on modules, the core panel should be selected in this field. Any additional panels utilized should be documented in the “additional_panels_used.csv” file, which must be uploaded alongside the dataset. Example: 10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363 |
NanoString Technologies; GeoMx Mouse Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-MsWTA-4, NanoString Technologies; CosMx Mouse Neuroscience Panel (RNA, 1000 Plex); PN CMX-M-NEUP-R, 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 16 rxns; PN 1000420, 10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363, 10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 4 rxns x 4 BC; PN 1000475, NanoString Technologies; CosMx Human 6K Discovery Panel (RNA, 6175 Plex); PN 121500041, 10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome, 4 rxns x 1 BC; PN 1000474, 10x Genomics; Xenium Human Multi-Tissue and Cancer Panel v1; PN 1000626, NanoString Technologies; CosMx Human Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-H-USCP-1KP-R, 10x Genomics; Xenium Custom Gene Expression Panel (up to 50 genes); PN 1000464, NanoString Technologies; CosMx Hs Univ Cell (RNA, 1000 Plex); PN 121500002, 10x Genomics; Visium Human Transcriptome Probe Kit-Large; PN 1000364, 10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365, 10x Genomics; Xenium Mouse Multi-Tissue Atlassing Panel; PN 1000627, 10x Genomics; Xenium Custom Gene Expression Panel (51-100 genes); PN 1000561, 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 64 rxns; PN 1000456, NanoString Technologies; GeoMx Human Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-HuWTA-4, 10x Genomics; Visium Mouse Transcriptome Probe Kit v2.0 - Small; PN 1000667, NanoString Technologies; CosMx Mouse Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-M-USCP-1KP-R, NanoString Technologies; CosMx Human Immuno-Oncology Panel (Protein, 64 Plex); PN CMX-H-IOP-64P-P, Custom, 10x Genomics; Visium Human Transcriptome Probe Kit v2 - Small; PN 1000466, 10x Genomics; Xenium Human Colon Gene Expression Panel; PN 1000642, 10x Genomics; Chromium Next GEM Single Cell Fixed RNA Mouse Transcriptome Probe Kit, 64 rxns; PN 1000492, NanoString Technologies; CosMx Mouse Neuroscience Panel (Protein, 64 Plex); PN CMX-M-Neuro-64P-P, NanoString Technologies; CosMx Hs WTX RNA Panel Kit, 2 slides: PN 121500047, 10x Genomics; Xenium Human Lung Gene Expression Panel; PN 1000601, 10x Genomics; Xenium Prime 5K Human Pan Tissue & Pathways Panel; PN 1000724 |
False |
| is_custom_probes_used |
Radio |
Indicates whether custom RNA or antibody probes were utilized in the assay. If custom probes were employed, they should be documented in the “custom_probe_set.csv” file. Example: No |
Yes, No |
True |
| number_of_panel_targets |
Numeric |
The number of panel targets, which refers to the total count of genes, RNA isoforms, or RNA regions that are targeted by probes. Example: 1000 |
|
True |
| roi_label |
Textfield |
The label for the region of interest (ROI). For Resolve and CosMx, this corresponds to the field of view (FOV) label. In the case of Xenium, it refers to the ID of the region containing the analysis. For GeoMx, this information can be located in the “Initial Dataset” spreadsheet, which can be downloaded from within the Data Analysis Suite. Example: Decidua |
|
False |
| anatomical_structure_label |
Textfield |
The label for the overarching anatomical structure. If the anatomical structure is not applicable or not specified, this field may be left blank. Example: Kidney |
|
False |
| anatomical_structure_id |
Textfield |
The ontology ID associated with the anatomical structure, typically represented by an UBERON ID. Example: UBERON:0002113 |
|
False |
| metadata_schema_id |
Textfield |
The unique string identifier for the metadata specification version, which is easily interpretable by computers for purposes of data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9 |
|
True |
| non_global_files |
Textfield |
Specifies a semicolon-separated list of non-global files that are to be included in the dataset. The file paths assume that the files are located in the “TOP/non-global/” directory. For instance, if the file is located at TOP/non-global/lab_processed/images/1-tissue-boundary.geojson, the value for this field would be “./lab_processed/images/1-tissue-boundary.geojson”. Once ingested, these files will be copied to their appropriate locations within the respective dataset directory tree. This field is intended for internal HuBMAP processing. Examples for GeoMx and PhenoCycler are provided in the File Locations documentation: https://docs.google.com/document/d/1n2McSs9geA9Eli4QWQaB3c9R3wo5d5U1Xd57DWQfN5Q/edit#heading=h.1u82i4axggee Example: ./lab_processed/images/1-tissue-boundary.geojson |
|
False |
