Cell DIVE Metadata Attributes
The attributes shown here have been colleced for STARmap data, available from the HuBMAP Search and Entity APIs at Dataset.metadata.<attribute>.
These attributes are harmonized across all versions of the Cell DIVE metadata specifications. See the latest version of the Cell DIVE Metadata Specifications for the schema and directory structure needed when ingesting Segmentation Mask metadata.
* indicates a required field
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| parent_sample_id | Unique HuBMAP or SenNet identifier of the sample (i.e., block, section or suspension) used to perform this assay. For example, for a RNAseq assay, the parent would be the suspension, whereas, for one of the imaging assays, the parent would be the tissue section. If an assay comes from multiple parent samples then this should be a comma separated list. Example: HBM386.ZGKG.235, HBM672.MKPK.442 or SNT232.UBHJ.322, SNT329.ALSK.102 | ||
| lab_id | 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 | ||
| preparation_protocol_doi | DOI for the protocols.io page that describes the assay or sample procurment and preparation. For example for an imaging assay, the protocol might include staining of a section through the creation of an OME-TIFF file. In this case the protocol would include any image processing steps required to create the OME-TIFF file. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 | ||
| dataset_type | The specific type of dataset being produced. | 10X Multiome 2D Imaging Mass Cytometry ATACseq Auto-fluorescence Cell DIVE CODEX Confocal CosMx CyCIF DBiT DESI Enhanced Stimulated Raman Spectroscopy (SRS) GeoMx (nCounter) GeoMx (NGS) HiFi-Slide Histology LC-MS Light Sheet MALDI MERFISH MIBI Molecular Cartography MUSIC nanoSPLITS PhenoCycler Resolve RNAseq RNAseq (with probes) Second Harmonic Generation (SHG) SIMS SNARE-seq2 Stereo-seq Thick section Multiphoton MxIF Visium (no probes) Visium (with probes) Xenium |
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| analyte_class | Analytes are the target molecules being measured with the assay. | Chromatin DNA DNA + RNA Endogenous fluorophores Fluorochrome Lipid Metabolite Nucleic acid and protein Peptide Polysaccharide Protein RNA |
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| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay (“Yes” or “No”). The CODEX analyte is protein. | ||
| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Akoya Biosciences Andor BGI Genomics Bruker Cytiva Evident Scientific (Olympus) GE Healthcare Hamamatsu Huron Digital Pathology Illumina In-House Ionpath Keyence Leica Biosystems Leica Microsystems Motic NanoString Resolve Biosciences Sciex Standard BioTools (Fluidigm) Thermo Fisher Scientific Zeiss Microscopy |
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| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Aperio AT2 Aperio CS2 Axio Observer 3 Axio Observer 5 Axio Observer 7 Axio Scan.Z1 BZ-X710 BZ-X800 BZ-X810 CosMx Spatial Molecular Imager Custom: Multiphoton Digital Spatial Profiler DM6 B DNBSEQ-T7 EVOS M7000 HiSeq 2500 HiSeq 4000 Hyperion Imaging System IN Cell Analyzer 2200 Lightsheet 7 MALDI timsTOF Flex Prototype MIBIscope MoticEasyScan One NanoZoomer 2.0-HT NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 NanoZoomer-SQ NextSeq 2000 NextSeq 500 NextSeq 550 NovaSeq 6000 NovaSeq X NovaSeq X Plus Orbitrap Eclipse Tribrid Orbitrap Fusion Lumos Tribrid Phenocycler-Fusion 1.0 Phenocycler-Fusion 2.0 PhenoImager Fusion Q Exactive Q Exactive HF Q Exactive UHMR QTRAP 5500 Resolve Biosciences Molecular Cartography SCN400 STELLARIS 5 TissueScope LE Slide Scanner Unknown VS200 Slide Scanner Xenium Analyzer Zyla 4.2 sCMOS |
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| source_storage_duration_value | How long was the source material stored, prior to this sample being processed? For assays applied to tissue sections, this would be how long the tissue section (e.g., slide) was stored, prior to the assay beginning (e.g., imaging). For assays applied to suspensions such as sequencing, this would be how long the suspension was stored before library construction began. | ||
| source_storage_duration_unit | The time duration unit of measurement | hour month day minute year |
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| time_since_acquisition_instrument_calibration_value | The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture. | ||
| time_since_acquisition_instrument_calibration_unit | The time unit of measurement | Column-by-column Not applicable Row-by-row Snake-by-columns Snake-by-rows |
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| contributors_path | The path to the file with the ORCID IDs for all contributors of this dataset (e.g., “./extras/contributors.tsv” or “./contributors.tsv”). This is an internal metadata field that is just used for ingest. | ||
| data_path | The top level directory containing the raw and/or processed data. For a single dataset upload this might be “.” where as for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For instance, if the data is within a directory called “TEST001-RK” use syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2” in which “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field that is just used for ingest. | ||
| antibodies_path | This is the location of the antibodies.tsv file relative to the root of the top level of the upload directory structure. This path should begin with “.” and would likely be something like “./extras/antibodies.tsv”. | ||
| number_of_antibodies | Number of antibodies | ||
| number_of_channels | Number of fluorescent channels imaged during each cycle. | ||
| number_of_biomarker_imaging_rounds | Number of imaging rounds to capture the tagged biomarkers. For CODEX a biomarker imaging round consists of 1. oligo application, 2. fluor application, 3. washes. For Cell DIVE a biomarker imaging round consists of 1. staining of a biomarker via secondary detection or direct conjugate and 2. dye inactivation. | ||
| number_of_total_imaging_rounds | The total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal (e.g., histology). | ||
| slide_id | A unique ID denoting the slide used. This allows users the ability 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 values overlapping across centers. | ||
| cell_boundary_marker_or_stain | If a marker or stain was used to identify all cell boundaries in the tissue, then the name of the marker or stain should be included here. The name of the antibody-targeted molecule marker or non-antibody targeted molecule stain included here must be identical to what is found in the imaging data. For example, with the PhenoCycler, this name must match the value found in the XPD output file. If multiple marker or stains are used to identify all cell boundaries, then a comma separated list should be used here. | NAKATPASE CD298 Not applicable |
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| nuclear_marker_or_stain | For markers, an antibody-targetted molecule present in or around the cell nucleus, the protein or gene symbol that identifies the antibody target that is used as the nuclear marker. This symbol must match the antibody target that is either generated from the panel used or entered with custom panels. Preferably, if using a custom antibody marker, this symbol should be the HGNC symbol (https://www.genenames.org/). For non-protein targets this is the stain name (e.g., DAPI) and, when appropriate, associated staining kit and vendor. For the PhenoCycler, this symbol must match the value found in the XPD output file. | DAPI Not applicable |
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| metadata_schema_id | The string that serves as the definitive identifier for the metadata schema version and is readily interpretable by computers for data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9 |
Deprecated Attributes
These attributes were supported by older metadata version specifications. They are no longer collected but there may be some older datasets that contain data for these attributes.
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | sequence |
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| description | Free-text description of this assay. | ||
| donor_id | HuBMAP Display ID of the donor of the assayed tissue. | ||
| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | ||
| operator | Name of the person responsible for executing the assay. | ||
| operator_email | Email address for the operator. | ||
| overall_protocols_io_doi | DOI for protocols.io referring to the overall protocol for the assay. | ||
| pi | Name of the principal investigator responsible for the data. | ||
| pi_email | Email address for the principal investigator. | ||
| processing_protocols_io_doi | DOI for analysis protocols.io for this assay. | ||
| resolution_x_unit | The unit of measurement of width of a pixel.(nm) | mm um nm |
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| resolution_x_value | The width of a pixel. (Akoya pixel is 377nm square) | ||
| resolution_y_unit | The unit of measurement of height of a pixel. (nm) | mm um nm |
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| resolution_y_value | The height of a pixel. (Akoya pixel is 377nm square) | ||
| version | Version of the schema to use when validating this metadata. | 1 |