diff --git a/docs/assays/metadata/DNA-Methylation.md b/docs/assays/metadata/DNA-Methylation.md new file mode 100644 index 0000000..f87faab --- /dev/null +++ b/docs/assays/metadata/DNA-Methylation.md @@ -0,0 +1,28 @@ +--- +layout: page +--- +# DNA Methylation + +
Version 2 (current) + +## Version 2 (current) + +| Attribute Name | Type | Description | Allowable Values | Required | +|---------------|------|-------------|------------------|----------| +| lab_id | Textfield | 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 | | False | +| dataset_type | Assigned Value | The specific type of dataset being produced. Example: RNAseq | ```Visium HD```, ```4i```, ```Illumina Spatial ver0```, ```LC-MS```, ```Thick section Multiphoton MxIF```, ```Light Sheet```, ```ATACseq```, ```Resolve```, ```HiFi-Slide```, ```COMET```, ```DNA Methylation```, ```MPLEx```, ```10X Multiome```, ```MALDI```, ```MACSima```, ```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``` | True | +| analyte_class | Assigned Value | 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``` | True | +| acquisition_instrument_vendor | Assigned Value | 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```, ```Miltenyi Biotec```, ```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``` | True | +| acquisition_instrument_model | Assigned Value | 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```, ```LSM 710 Confocal Microscope```, ```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```, ```MACSima System```, ```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 HF-X``` | True | +| source_storage_duration_value | Numeric | 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 | | True | +| source_storage_duration_unit | Assigned Value | The unit of measurement used to specify the source storage duration value. Example: hour | ```hour```, ```month```, ```day```, ```minute```, ```year``` | True | +| time_since_acquisition_instrument_calibration_value | Numeric | 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 | | False | +| time_since_acquisition_instrument_calibration_unit | Assigned Value | The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month | ```month```, ```day```, ```year``` | False | +| preparation_protocol_doi | Link | 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 | | True | +| is_targeted | Radio | Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes | ```Yes```, ```No``` | True | +| contributors_path | Textfield | The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv | | True | +| data_path | Textfield | 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 | | True | +| parent_sample_id | Textfield | 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 | | True | +| metadata_schema_id | Textfield | The unique string identifier for the metadata specification version, which is easily interpretable by computers for purposes of data validation and processing. Example: d70bfe24-e82a-46cb-9369-28ae03660d97 | | True | + +
\ No newline at end of file diff --git a/docs/assays/metadata/index.md b/docs/assays/metadata/index.md index db8c27f..59b9f05 100644 --- a/docs/assays/metadata/index.md +++ b/docs/assays/metadata/index.md @@ -15,6 +15,7 @@ A list of available dataset types (data types from multiple supported assays), w | COMET [](COMET "Attribute description") | COMET is a technique used to measure DNA damage in individual cells. The name comes from the shape that damaged DNA fragments form when they migrate out of a cell's nucleus under an electric field, resembling a comet with a head and a tail. This assay is widely used in genetics research to study DNA damage from factors like radiation, chemicals, and environmental exposure. | | [CosMx Proteomics](https://hubmapconsortium.github.io/ingest-validation-tools/cosmx-proteomics/current/) [](CosMx Proteomics "Attribute description")| CosMx Proteomics is a technology that enables the high-resolution, spatial analysis of proteins within their native tissue environment. It is part of the CosMx Spatial Molecular Imager (SMI) platform, which provides single-cell and subcellular resolution to map protein expression, cell states, and cell-cell interactions in FFPE and fresh frozen tissue samples. | | [DESI](https://pmc.ncbi.nlm.nih.gov/articles/PMC6053038/) [](DESI "Attribute description")| Desorption Electrospray Ionization (DESI), an ambient ionization technique that can be coupled to mass spectrometry (MS) for chemical analysis of samples at atmospheric conditions. Link to [DESI directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/desi/current/). | +| DNA-Methylation [](DNA-Methylation "Attribute description") | DNA methylation is a critical, reversible epigenetic mechanism in biomedical research involving the addition of a methyl group to DNA (usually cytosine in CpG islands), altering gene expression without changing the underlying sequence. | | [Enhanced SRS](https://www.nature.com/articles/s41467-019-13230-1) [](EnhancedSRS "Attribute description")| Refers to improvements made to Stimulated Raman Scattering (SRS), a technique used in microscopy and spectroscopy for chemical imaging and analysis. These enhancements aim to improve sensitivity, spatial resolution, and other capabilities of SRS. Link to [Enhanced SRS directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/enhanced-srs/current/). | | [GeoMx](https://nanostring.com/products/geomx-digital-spatial-profiler/spatial-multiomics-enabled-with-geomx-dsp/) [](GeoMx "Attribute description")| A platform for spatial biology that analyzes RNA and protein expression within tissue sections which allows for non-destructive, in situ profiling of gene expression and protein levels from specific regions of interest (ROIs) within a tissue. Link to [GeoMx directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/geomx-ngs/current/). | | [HiFi](https://www.researchgate.net/publication/370676672_HiFi-Slide_spatial_RNA-Sequencing_v2) [](HiFi "Attribute description")| High-Fidelity Spatial Transcriptomic Slide (HiFi-Slide) sequencing, a super-resolution spatial transcriptomics sequencing technology, captures and spatially resolves genome-wide RNA expression in a submicron resolution for fresh-frozen tissue. Link to [HiFi directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/hifi-slide/current/). |