STARmap Metadata Attributes

Fields that are collected for STARmap data, available at dataset.metadata.<attribute>  

* indicates a required field

Attribute Type Description Allowable Values
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  
dataset_type * 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 Raman Imaging 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 STARmap Stereo-seq Visium (with probes) SIMS Auto-fluorescence CyTOF CosMx Proteomics Virtual Histology DBiT-seq PhenoCycler
analyte_class 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 RNA + protein Peptide Protein Unsaturated lipid Endogenous fluorophore Chromatin Polysaccharide
acquisition_instrument_vendor 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 Revvity Evident Scientific (Olympus) GE Healthcare Element Biosciences Hamamatsu Waters Bruker Illumina 3DHISTECH Singular Genomics Huron Digital Pathology Resolve Biosciences NanoString Cytiva 10x Genomics Microscopes International BGI Genomics
acquisition_instrument_model 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 DMi8 NextSeq 550 HiSeq 2500 HiSeq 4000 NovaSeq 6000 Opera Phenix Plus HCS SYNAPT G2-Si Q Exactive HF Orbitrap Fusion Tribrid Orbitrap Fusion Lumos Tribrid Q Exactive VS200 Slide Scanner Not applicable
source_storage_duration_value 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  
source_storage_duration_unit The unit of measurement used to specify the source storage duration value. Example: hour hour month day minute year
time_since_acquisition_instrument_calibration_value 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  
time_since_acquisition_instrument_calibration_unit The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month month day year
preparation_protocol_doi * 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  
is_targeted Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes  
contributors_path The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv  
data_path 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  
parent_sample_id 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  
mapped_area_value 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  
mapped_area_unit 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
target_retrieval_incubation_temperature 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  
target_retrieval_incubation_time_value The duration for which a sample is exposed to a target retrieval solution. Example: 15  
target_retrieval_incubation_time_unit 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
proteinasek_concentration The concentration of the enzyme Proteinase K within a sample, measured in micrograms per milliliter (ug/ml). Example: 10  
proteinasek_incubation_time_value The duration for which a sample is incubated with Proteinase K. Example: 15  
proteinasek_incubation_time_unit The unit of measurement for the proteinaseK incubation time value. If no incubation time is specified, this field may be left blank. Example: minute minute
probe_hybridization_time_value The duration for which the oligo-conjugated RNA or oligo-conjugated antibody probes were hybridized with the sample. Example: 30  
probe_hybridization_time_unit 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
is_custom_probes_used * 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  
number_of_panel_targets 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  
anatomical_structure_label 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  
anatomical_structure_id The ontology ID associated with the anatomical structure, typically represented by an UBERON ID. Example: UBERON:0002113  
non_global_files 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  
metadata_schema_id * 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