GeoMx Metadata Attributes
Fields that are collected for GeoMx data, available at dataset.metadata.<attribute>
* indicates a required field
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| dataset_type * | The specific type of dataset being produced. | ||
| analyte_class | Analytes are the target molecules being measured with the assay. | ||
| 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. | ||
| 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. | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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. | ||
| 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. | ||
| 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 | ||
| mapped_area_value | For Visium, this is the area of spots that was covered by tissue within the captured area, not the total possible captured area which is fixed. For GeoMx this would be the area of the AOI being captured. For HiFi this is the summed area of the ROIs in a single flowcell lane. For CosMx, Xenium and Resolve, this is the area of the FOV (aka ROI) region being captured. | ||
| mapped_area_unit | The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2. | ||
| 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. | ||
| number_of_channels | The number of distinct color channels in the image. | ||
| target_retrieval_incubation_temperature | Will normally be 100 degrees Celsius for RNA assays, and 80 degrees Celsius for protein assays. | ||
| target_retrieval_incubation_time_value | The duration for which a sample is exposed to a target retrieval solution. | ||
| target_retrieval_incubation_time_unit | The units for target retrieval incubation time value. | ||
| proteinasek_concentration | The amount or concentration of the enzyme Proteinase K within a sample (in ug/ml). | ||
| proteinasek_incubation_time_value | The duration for which a sample is exposed to Proteinase K. | ||
| proteinasek_incubation_time_unit | The units for proteinaseK incubation time value. | ||
| roi_label * | A label for the region of interest (ROI). For Xenium, Resolve and CosMx, this is the field of view (FOV) label. For GeoMx this can be found in the “Initial Dataset” spreadsheet (download from within Data Analysis Suite). | ||
| is_roi_segmentation_performed | Was the image segmented. For GeoMx this refers to whether segmentation was used to split ROIs (regions of interest) into AOIs (areas of interest). | ||
| roi_segmentation_strategy | The method of segmentation that was applied in a GeoMx assay. If an overlay was used the overlay image needs to be included in the dataset upload. | ||
| anatomical_structure_label | The overarching anatomical structure. | ||
| anatomical_structure_id | The ontology ID for the parent structure. Typically this would be an UBERON ID. | ||
| targeted_entity_label * | State what cell type(s) or functional tissue unit was targeted in this ROI/AOI. | ||
| targeted_entity_id | The ontology ID for the targeted entity. | ||
| segment_id * | This is the ID for the area of interest (AOI) in a GeoMx dataset. From “Initial Dataset” spreadsheet (download from within Data Analysis Suite), e.g. 9a828e39-43d8-4051-9bcc-581a520a85d4. | ||
| is_technical_replicate | Is the sequencing reaction run in replicate, “Yes” or “No”. If “Yes”, FASTQ files in dataset need to be merged. | ||
| 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 | ||
| non_global_files | A semicolon separated list of non-shared files to be included in the dataset. The path assumes the files are located in the “TOP/non-global/” directory. For example, for the file is TOP/non-global/lab_processed/images/1-tissue-boundary.geojson the value of this field would be “./lab_processed/images/1-tissue-boundary.geojson”. After ingest, these files will be copied to the appropriate locations within the respective dataset directory tree. This field is used 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 |
Deprecated Attributes
* indicates a field that was previously required
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| dataset_type | The specific type of dataset being produced. | ||
| analyte_class | Analytes are the target molecules being measured with the assay. | ||
| 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. | ||
| 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. | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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. | ||
| 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. | ||
| 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 | ||
| mapped_area_value | For Visium, this is the area of spots that was covered by tissue within the captured area, not the total possible captured area which is fixed. For GeoMx this would be the area of the AOI being captured. For HiFi this is the summed area of the ROIs in a single flowcell lane. For CosMx, Xenium and Resolve, this is the area of the FOV (aka ROI) region being captured. | ||
| mapped_area_unit | The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2. | ||
| 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. | ||
| number_of_channels | The number of distinct color channels in the image. | ||
| target_retrieval_incubation_temperature | Will normally be 100 degrees Celsius for RNA assays, and 80 degrees Celsius for protein assays. | ||
| target_retrieval_incubation_time_value | The duration for which a sample is exposed to a target retrieval solution. | ||
| target_retrieval_incubation_time_unit | The units for target retrieval incubation time value. | ||
| proteinasek_concentration | The amount or concentration of the enzyme Proteinase K within a sample (in ug/ml). | ||
| proteinasek_incubation_time_value | The duration for which a sample is exposed to Proteinase K. | ||
| proteinasek_incubation_time_unit | The units for proteinaseK incubation time value. | ||
| roi_label | A label for the region of interest (ROI). For Xenium, Resolve and CosMx, this is the field of view (FOV) label. For GeoMx this can be found in the “Initial Dataset” spreadsheet (download from within Data Analysis Suite). | ||
| is_roi_segmentation_performed | Was the image segmented. For GeoMx this refers to whether segmentation was used to split ROIs (regions of interest) into AOIs (areas of interest). | ||
| roi_segmentation_strategy | The method of segmentation that was applied in a GeoMx assay. If an overlay was used the overlay image needs to be included in the dataset upload. | ||
| anatomical_structure_label | The overarching anatomical structure. | ||
| anatomical_structure_id | The ontology ID for the parent structure. Typically this would be an UBERON ID. | ||
| targeted_entity_label | State what cell type(s) or functional tissue unit was targeted in this ROI/AOI. | ||
| targeted_entity_id | The ontology ID for the targeted entity. | ||
| segment_id | This is the ID for the area of interest (AOI) in a GeoMx dataset. From “Initial Dataset” spreadsheet (download from within Data Analysis Suite), e.g. 9a828e39-43d8-4051-9bcc-581a520a85d4. | ||
| is_technical_replicate | Is the sequencing reaction run in replicate, “Yes” or “No”. If “Yes”, FASTQ files in dataset need to be merged. | ||
| 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 | ||
| hybcode_pack_lot_number | Enter the lot number noted within the LabWorksheet.txt file (and used in downstream nCounter processing). | ||
| probe_hybridization_time_value | How many hours were the oligo-conjugated RNA or oligo-conjugated antibody probes hybridized with the sample? | ||
| probe_hybridization_time_unit | The units for probe hybridization time value. | ||
| oligo_probe_panel | This is the probe panel used to target genes and/or proteins. In cases where there is a core panel and add-on modules, the core panel should be selected here. If additional panels are used, then they must be included in the “additional_panels_used.csv” file that’s uploaded with the dataset. | ||
| is_custom_probes_used | State (“Yes” or “No”) whether custom RNA or antibody probes were used. If custom probes were used, they must be listed in the “custom_probe_set.csv” file. | ||
| non_global_files | A semicolon separated list of non-shared files to be included in the dataset. The path assumes the files are located in the “TOP/non-global/” directory. For example, for the file is TOP/non-global/lab_processed/images/1-tissue-boundary.geojson the value of this field would be “./lab_processed/images/1-tissue-boundary.geojson”. After ingest, these files will be copied to the appropriate locations within the respective dataset directory tree. This field is used 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 |