CODEX
NOTE: Several versions of this metadata schema have been created over time. The (Latest) version contains most attributes, but there may be some deprecated attributes in the older versions for which data has been collected. HuBMAP is in the process of creating a reference which combines all of these versions into a single view. That reference will be available here once completed.
Version 2 (Latest)
Version 2
| Attribute | Type | Description | Allowable Values | Required |
|---|---|---|---|---|
| source_storage_duration_value | Numeric | How long was the source material (parent) stored, prior to this sample being processed. | 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 | |
| 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 | |
| number_of_antibodies | Numeric | Number of antibodies | True | |
| number_of_channels | Numeric | Number of fluorescent channels imaged during each cycle. | True | |
| number_of_biomarker_imaging_rounds | Numeric | 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. | True | |
| number_of_total_imaging_rounds | Numeric | The total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal (e.g., histology). | True | |
| slide_id | Textfield | 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. | False | |
| total_run_time_value | Numeric | How long the tissue was on the acquisition instrument. | False | |
| 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_unit | Allowable Value | The time duration unit of measurement | hour month day minute year |
True |
| 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 |
| total_run_time_unit | Allowable Value | The units for the total run time unit field. | Hour Minute |
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 | |
| 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 |
| antibodies_path | Textfield | 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”. | True | |
| 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 |
True |
| 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 |
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 |
Version 1
Version 1
| Attribute | Type | Description | Allowable Values | Required |
|---|---|---|---|---|
| version | Allowable Value | Version of the schema to use when validating this metadata. | [‘1’] | True |
| description | Textfield | Free-text description of this assay. | True | |
| donor_id | Textfield | HuBMAP Display ID of the donor of the assayed tissue. | True | |
| tissue_id | Textfield | HuBMAP Display ID of the assayed tissue. | True | |
| execution_datetime | Datetime | Start date and time of assay, typically a date-time stamped foldergenerated 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 thehour with leading zeros, mm are the minutes with leading zeros. | True | |
| protocols_io_doi | Textfield | DOI for protocols.io referring to the protocol for this assay. | True | |
| operator | Textfield | Name of the person responsible for executing the assay. | True | |
| operator_email | Textfield | Email address for the operator. | True | |
| pi | Textfield | Name of the principal investigator responsible for the data. | True | |
| pi_email | Textfield | Email address for the principal investigator. | True | |
| assay_category | Allowable Value | Each assay is placed into one of the following 4 general categories:generation of images of microscopic entities, identification & quantitation ofmolecules by mass spectrometry, imaging mass spectrometry, and determination ofnucleotide sequence. | [‘imaging’] | True |
| assay_type | Allowable Value | The specific type of assay being executed. | [‘CODEX’, ‘CODEX2’] | True |
| analyte_class | Allowable Value | Analytes are the target molecules being measured with the assay. | [‘protein’] | True |
| is_targeted | Allowable Value | Specifies whether or not a specific molecule(s) is/are targeted fordetection/measurement by the assay. | [‘Yes’, ‘No’] | True |
| acquisition_instrument_vendor | Allowable Value | An acquisition_instrument is the device that contains the signal detectionhardware and signal processing software. Assays generate signals such as lightof various intensities or color or signals representing molecular mass. | [‘Keyence’, ‘Zeiss’] | True |
| acquisition_instrument_model | Allowable Value | Manufacturers of an acquisition instrument may offer various versions(models) of that instrument with different features or sensitivities. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data. | [‘BZ-X800’, ‘BZ-X710’, ‘Axio Observer Z1’] | True |
| resolution_x_value | Numeric | The width of a pixel. (Akoya pixel is 377nm square) | True | |
| resolution_x_unit | Allowable Value | The unit of measurement of width of a pixel.(nm) | [‘mm’, ‘um’, ‘nm’] | False |
| resolution_y_value | Numeric | The height of a pixel. (Akoya pixel is 377nm square) | True | |
| resolution_y_unit | Allowable Value | The unit of measurement of height of a pixel. (nm) | [‘mm’, ‘um’, ‘nm’] | False |
| resolution_z_value | Numeric | Optional if assay does not have multiple z-levels. Note that thisis resolution within a given sample: z-pitch (resolution_z_value) is the incrementdistance between image slices (for Akoya, z-pitch=1.5um) ie. the microscope stageis moved up or down in increments of 1.5um to capture images of several focalplanes. The best one will be used & the rest discarded. The thickness of the sampleitself is sample metadata. | False | |
| resolution_z_unit | Allowable Value | The unit of incremental distance between image slices. | [‘mm’, ‘um’, ‘nm’] | False |
| preparation_instrument_vendor | Allowable Value | The manufacturer of the instrument used to prepare the sample for theassay. | [‘CODEX’] | True |
| preparation_instrument_model | Allowable Value | The model number/name of the instrument used to prepare the samplefor the assay | [‘version 1 robot’, ‘prototype robot - Stanford/Nolan Lab’] | True |
| number_of_antibodies | Numeric | Number of antibodies | True | |
| number_of_channels | Numeric | Number of fluorescent channels imaged during each cycle. | True | |
| number_of_cycles | Numeric | Number of cycles of 1. oligo application, 2. fluor application, 3.washes | True | |
| section_prep_protocols_io_doi | Textfield | DOI for protocols.io referring to the protocol for preparing tissuesections for the assay. | True | |
| reagent_prep_protocols_io_doi | Textfield | DOI for protocols.io referring to the protocol for preparing reagentsfor the assay. | True | |
| antibodies_path | Textfield | Relative path to file with antibody information for this dataset. | True | |
| contributors_path | Textfield | Relative path to file with ORCID IDs for contributors for this dataset. | True | |
| data_path | Textfield | Relative path to file or directory with instrument data. Downstreamprocessing will depend on filename extension conventions. | True |
Version 0
Version 0
| Attribute | Type | Description | Allowable Values | Required |
|---|---|---|---|---|
| donor_id | Textfield | HuBMAP Display ID of the donor of the assayed tissue. | True | |
| tissue_id | Textfield | HuBMAP Display ID of the assayed tissue. | True | |
| execution_datetime | Datetime | Start date and time of assay, typically a date-time stamped foldergenerated 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 thehour with leading zeros, mm are the minutes with leading zeros. | True | |
| protocols_io_doi | Textfield | DOI for protocols.io referring to the protocol for this assay. | True | |
| operator | Textfield | Name of the person responsible for executing the assay. | True | |
| operator_email | Textfield | Email address for the operator. | True | |
| pi | Textfield | Name of the principal investigator responsible for the data. | True | |
| pi_email | Textfield | Email address for the principal investigator. | True | |
| assay_category | Allowable Value | Each assay is placed into one of the following 4 general categories:generation of images of microscopic entities, identification & quantitation ofmolecules by mass spectrometry, imaging mass spectrometry, and determination ofnucleotide sequence. | [‘imaging’] | True |
| assay_type | Allowable Value | The specific type of assay being executed. | [‘CODEX’] | True |
| analyte_class | Allowable Value | Analytes are the target molecules being measured with the assay. | [‘protein’] | True |
| is_targeted | Allowable Value | Specifies whether or not a specific molecule(s) is/are targeted fordetection/measurement by the assay. | [‘Yes’, ‘No’] | True |
| acquisition_instrument_vendor | Allowable Value | An acquisition_instrument is the device that contains the signal detectionhardware and signal processing software. Assays generate signals such as lightof various intensities or color or signals representing molecular mass. | [‘Keyence’, ‘Zeiss’] | True |
| acquisition_instrument_model | Allowable Value | Manufacturers of an acquisition instrument may offer various versions(models) of that instrument with different features or sensitivities. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data. | [‘BZ-X800’, ‘BZ-X710’, ‘Axio Observer Z1’] | True |
| resolution_x_value | Numeric | The width of a pixel. (Akoya pixel is 377nm square) | True | |
| resolution_x_unit | Allowable Value | The unit of measurement of width of a pixel.(nm) | [‘mm’, ‘um’, ‘nm’] | False |
| resolution_y_value | Numeric | The height of a pixel. (Akoya pixel is 377nm square) | True | |
| resolution_y_unit | Allowable Value | The unit of measurement of height of a pixel. (nm) | [‘mm’, ‘um’, ‘nm’] | False |
| resolution_z_value | Numeric | Optional if assay does not have multiple z-levels. Note that thisis resolution within a given sample: z-pitch (resolution_z_value) is the incrementdistance between image slices (for Akoya, z-pitch=1.5um) ie. the microscope stageis moved up or down in increments of 1.5um to capture images of several focalplanes. The best one will be used & the rest discarded. The thickness of the sampleitself is sample metadata. | False | |
| resolution_z_unit | Allowable Value | The unit of incremental distance between image slices. | [‘mm’, ‘um’, ‘nm’] | False |
| Textfield | ||||
| preparation_instrument_vendor | Allowable Value | The manufacturer of the instrument used to prepare the sample for theassay. | [‘CODEX’] | True |
| preparation_instrument_model | Allowable Value | The model number/name of the instrument used to prepare the samplefor the assay | [‘version 1 robot’, ‘prototype robot - Stanford/Nolan Lab’] | True |
| number_of_antibodies | Numeric | Number of antibodies | True | |
| number_of_channels | Numeric | Number of fluorescent channels imaged during each cycle. | True | |
| number_of_cycles | Numeric | Number of cycles of 1. oligo application, 2. fluor application, 3.washes | True | |
| section_prep_protocols_io_doi | Textfield | DOI for protocols.io referring to the protocol for preparing tissuesections for the assay. | True | |
| reagent_prep_protocols_io_doi | Textfield | DOI for protocols.io referring to the protocol for preparing reagentsfor the assay. | True | |
| antibodies_path | Textfield | Relative path to file with antibody information for this dataset. | True | |
| contributors_path | Textfield | Relative path to file with ORCID IDs for contributors for this dataset. | True | |
| data_path | Textfield | Relative path to file or directory with instrument data. Downstreamprocessing will depend on filename extension conventions. | True |