| dataset_type |
Allowable Value |
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 |
True |
| analyte_class |
Allowable Value |
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 |
True |
| acquisition_instrument_vendor |
Allowable Value |
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 |
True |
| acquisition_instrument_model |
Allowable Value |
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 |
True |
| source_storage_duration_value |
Numeric |
How long was the source material (parent) stored, prior to this sample being processed. |
|
True |
| source_storage_duration_unit |
Allowable Value |
The time duration unit of measurement |
hour month day minute year |
True |
| time_since_acquisition_instrument_calibration_value |
Numeric |
The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture. |
|
False |
| time_since_acquisition_instrument_calibration_unit |
Allowable Value |
The time unit of measurement |
Column-by-column Not applicable Row-by-row Snake-by-columns Snake-by-rows |
False |
| preparation_protocol_doi |
Textfield |
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 |
|
True |
| is_targeted |
Allowable Value |
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. |
Yes No |
True |
| contributors_path |
Textfield |
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. |
|
True |
| data_path |
Textfield |
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. |
|
True |
| mass_analysis_polarity |
Allowable Value |
The polarity of the mass analysis (positive or negative ion modes). |
Negative and positive ion mode Negative ion mode Positive ion mode |
True |
| mass_resolving_power |
Numeric |
The mass resolving power m/∆m, where ∆m is defined as the full width at half-maximum (FWHM) for a given peak with a specified mass-to-charge (m/z). (unitless) |
|
True |
| mass-to-charge_resolving_power |
Numeric |
The peak (m/z) used to calculate the resolving power. |
|
True |
| matrix_deposition_method |
Allowable Value |
Common methods of depositing matrix for assisting in desorption and ionization in imaging mass spectrometry include robotic spotting, electrospray deposition, and sublimation. |
Electrospray deposition Not applicable Robotic spotting Robotic spraying Sublimation |
False |
| preparation_instrument_vendor |
Allowable Value |
The manufacturer of the instrument used to prepare (staining/processing) the sample for the assay. If an automatic slide staining method was indicated this field should list the manufacturer of the instrument. |
10x Genomics Hamamatsu HTX Technologies In-House Leica Biosystems Not applicable Roche Diagnostics SunChrom Thermo Fisher Scientific |
False |
| preparation_instrument_model |
Allowable Value |
Manufacturers of a staining system instrument may offer various versions (models) of that instrument with different features. Differences in features or sensitivities may be relevant to processing or interpretation of the data. |
AutoStainer XL Chromium Connect Chromium Controller Chromium iX Chromium X Discovery Ultra EVOS M7000 M3+ Sprayer M5 Sprayer NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 Not applicable ST5020 Multistainer Sublimator SunCollect Sprayer TM-Sprayer Visium CytAssist |
False |
| preparation_matrix |
Allowable Value |
The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the ionizing probe. It also helps ionize the sample, carrying it along the flight tube so it can be detected. |
2,5-DHA (2,5-dihydroxyacetophenone) 2,5-DHB (2,5-Dihydroxybenzoic acid) 9-AA (9-aminoacridine) CHCA (alpha-cyano-4-hydroxy-cinnamic acid) DAN (1,5-diaminonapthalene) DMACA (4-(dimethylamino)cinnamic acid) NEDC (N-(1-naphthyl) ethylenediamine dihydrochloride) SA (sinapic acid) |
False |
| metadata_schema_id |
Textfield |
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 |
|
True |
| mass-to-charge_range_low_value |
Numeric |
The low value of the scanned mass-to-charge range, for MS1. (unitless) |
|
False |
| mass-to-charge_range_high_value |
Numeric |
The high value of the scanned mass-to-charge range, for MS1. (unitless) |
|
False |
| analysis_protocol_doi |
Textfield |
A DOI to a protocols.io protocol describing the software and database(s) used to process the raw data. Example: https://dx.doi.org/10.17504/protocols.io.bsu5ney6 |
|
True |
| ms_ionization_technique |
Allowable Value |
The ionization approach (i.e., sample probing method) for performing imaging mass spectrometry. |
DESI ESI HESI LA LDI MALDI MALDI-2 nanoDESI SIMS-C60 SIMS-H20 |
True |
| ms_scan_mode |
Allowable Value |
MS (mass spectrometry) scan mode refers to the number of steps in the separation of fragments. |
MS1 MS2 MS3 |
True |
| parent_sample_id |
Textfield |
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 |
|
True |
