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381-fix-hic #404

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merged 10 commits into from
May 31, 2024
Merged

381-fix-hic #404

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7557e19
Update HTAN.model.csv
aditigopalan May 9, 2024
f4889fd
Update HTAN.model.csv
aditigopalan May 9, 2024
45a9160
GitHub Action: convert *.model.csv to *.model.jsonld
github-actions[bot] May 9, 2024
cf893e4
Merge branch 'main' into fix-381-hic
adamjtaylor May 9, 2024
35b04be
Merge branch 'main' into fix-381-hic
adamjtaylor May 20, 2024
405cc74
Loop and stripe window update
aditigopalan May 28, 2024
9013ef9
Merge branch 'fix-381-hic' of https://github.com/ncihtan/data-models …
aditigopalan May 28, 2024
f900ba5
GitHub Action: convert *.model.csv to *.model.jsonld
github-actions[bot] May 28, 2024
17b62d2
Merge branch 'main' into fix-381-hic
adamjtaylor May 30, 2024
fac0b3a
Merge branch 'main' into fix-381-hic
aditigopalan May 30, 2024
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4 changes: 2 additions & 2 deletions HTAN.model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1,
Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organism,"Demographics, Family History, Exposure, Follow Up, Diagnosis, Therapy, Molecular Test",,
File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile,
Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$
File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf",,,TRUE,,,,
File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,,
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Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,,
HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning
HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning
Expand Down Expand Up @@ -155,7 +155,7 @@ Ligation Condition,Name of ligase and condition for proximity ligation,,,,TRUE,S
Biotin Enrichment,Whether biotin is used for enriching ligation product,"Yes, No",,,TRUE,Sequencing,,,
DNA Input Amount,"Amount of DNA for library construction, in nanograms.",,,,TRUE,Sequencing,,,int
Resolution,"Binning size used for generating contact matrix, in basepair.",,,,TRUE,Sequencing,,,
Stripe Calling,"Tool used for identifying architectural stripe-forming, interaction hotspots.","MACS2, Other",,,TRUE,Sequencing,,,
Stripe Calling,"Tool used for identifying architectural stripe-forming, interaction hotspots.","MACS2, Other",,,TRUE,Sequencing,,,list::-?\d+
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Loop Window,Binning size used for calling significant dot interactions (loops),,,,TRUE,Sequencing,,,int
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@adamjtaylor adamjtaylor May 10, 2024 •
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Validation rule for Loop Window should be list like :: regex search -?\d+

Stripe Window,"Binning size used for calling significant architectural stripes. Can be an integer or int/int, indicating bin size and sliding window size if different.","HiCCUPS, Cooltools, Other",,,TRUE,Sequencing,,,
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@adamjtaylor adamjtaylor May 10, 2024 •
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Change Stripe Window Description this to say

Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.

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@adamjtaylor adamjtaylor May 10, 2024 •
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The valid values here don't seem to be in the right attribute. Remove valid values from Stripe Window

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Valdation rule for Stripe Window should be list like :: regex search -?\d+

Loop Calling,Tool used for identifying loop interactions,,,,TRUE,Sequencing,,,
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Valid values for Loop Calling should be HiCCUPS, Cooltools, Other

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25 changes: 24 additions & 1 deletion HTAN.model.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -1294,6 +1294,9 @@
},
{
"@id": "bts:Sf"
},
{
"@id": "bts:Bedpe"
}
],
"sms:displayName": "File Format",
Expand Down Expand Up @@ -2856,6 +2859,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Bedpe",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "Bedpe",
"rdfs:subClassOf": [
{
"@id": "bts:FileFormat"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "bedpe",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Checksum",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -42299,7 +42319,10 @@
],
"sms:displayName": "Stripe Calling",
"sms:required": "sms:true",
"sms:validationRules": []
"sms:validationRules": [
"list",
"-?\\d+"
]
},
{
"@id": "bts:LoopWindow",
Expand Down
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