iCLAP Metadata Attributes
Fields that are collected for iCLAP 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| number_of_antibodies | The number of antibodies used in the assay. If no antibodies were utilized, enter 0. Example: 5 | ||
| number_of_biomarker_imaging_rounds | The number of imaging rounds required to capture the tagged biomarkers. For CODEX, a biomarker imaging round includes steps such as (1) oligo application, (2) fluor application, and (3) washes. For Cell DIVE, it involves (1) the staining of a biomarker via secondary detection or direct conjugate, followed by (2) dye inactivation. Example: 3 | ||
| number_of_total_imaging_rounds | The total number of imaging rounds performed using a microscope to collect either autofluorescence/background or stained signals, such as those used in histological analysis. Example: 5 | ||
| slide_id | 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 | ||
| 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 iCLAP CyCIF SNARE-seq2 nanoSPLITS STARmap Stereo-seq Visium (with probes) SIMS Auto-fluorescence CyTOF CosMx Proteomics Virtual Histology DBiT-seq |
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| 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 Lipid + metabolite + protein RNA + protein Peptide Protein Unsaturated lipid Endogenous fluorophore Chromatin Polysaccharide |
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| 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 |
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| 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 |
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| source_storage_duration_unit | The unit of measurement used to specify the source storage duration value. Example: hour | hour month day minute year |
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| 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 |
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| 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 | ||
| 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 | ||
| antibodies_path | The path to the antibodies.tsv file relative to the root directory of the upload structure. This path should start with “.” and is typically formatted as “./extras/antibodies.tsv”. Example: ./extras/antibodies.tsv | ||
| 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 | ||
| number_of_channels | The number of fluorescent channels that are imaged during each cycle. Example: 3 |