Skip to content

Commit

Permalink
Add ExSeq minimal clone from OtherAssay
Browse files Browse the repository at this point in the history
  • Loading branch information
adamjtaylor committed Mar 13, 2024
1 parent dd3dc0e commit 0775840
Show file tree
Hide file tree
Showing 2 changed files with 7 additions and 1 deletion.
3 changes: 2 additions & 1 deletion HTAN.model.csv
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ Biospecimen,"HTAN biological entity; this can be tissue, blood, analyte and subs
SRRS Biospecimen,"SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen",,"Component, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Adjacent Biospecimen IDs, Biospecimen Type, Timepoint Label, Collection Days from Index, Acquisition Method Type, Ischemic Time, Ischemic Temperature, Collection Media, Topography Code, Additional Topography, Fixative Type, Storage Method, Preinvasive Morphology, Histologic Morphology Code, Preservation Method, Processing Days from Index, Protocol Link",,FALSE,Biosample,Patient,,
Source HTAN Biospecimen ID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,,,,FALSE,Biosample,,,
Other Assay,Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay Type",,FALSE,Assay,Biospecimen,,
ExSeq Minimal,Minimal metadata for the ExSeq assay,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay Type",,FALSE,Assay,Biospecimen,,
Assay Type,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",,,,TRUE,Assay,,,
scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Days from Index, Single Cell Dissociation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index, Protocol Link, Technical Replicate Group",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913,
scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Sequencing,scRNA-seq Level 1,,
Expand Down Expand Up @@ -1011,4 +1012,4 @@ Tile overlap Y,Percentage of image overlap to allow tile stitching in x directio
Barretts Esophagus Goblet Cells Present,Presence or absennce of Barretts esophagus goblet cells.,"Yes, No",,,FALSE,Follow Up,,,
Pancreatitis Onset Year,Date of onset of pancreatitis.,,,,FALSE,Follow Up,,,num
HTAN Parent Channel Metadata ID,HTAN ID for a level 3 channels table.,,,,TRUE, Imaging Level 4,,,
Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,,
Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,,
5 changes: 5 additions & 0 deletions dca-template-config.json
Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,11 @@
"schema_name": "ElectronMicroscopyLevel4",
"type": "file"
},
{
"display_name": "ExSeq Minimal",
"schema_name": "ExSeq Minimal",
"type": "file"
},
{
"display_name": "HI-C-seq Level 1",
"schema_name": "HI-C-seqLevel1",
Expand Down

0 comments on commit 0775840

Please sign in to comment.