From 3070cc96774e2ddc356558a10828b39446be530b Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Wed, 10 Apr 2024 08:03:41 +0100 Subject: [PATCH 1/3] Add data types --- HTAN.model.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index ff302cdd..271a976a 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -896,7 +896,7 @@ Location of Publication,"The name of the preprint server, journal, or conference Publication Abstract,The abstract or short description of the content presented/published.,,,,TRUE,Publication,,, License,The type of license applicable to the content.,"0BSD, AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement, Proprietary, Other, Not licensed, Freeware",,,FALSE,Publication,,,list like PMID,The PubMed identifier associated with the publication (applicable to published manuscripts). Provide as a URL of the form https://pubmed.ncbi.nlm.nih.gov/{pmid},,,,FALSE,Publication,,,url -Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10X Visium, Bulk DNA, Bulk RNA-seq, LC-MS-MS, LC-MS3, Shotgun MS (lipidomics), scATAC-seq, scRNA-seq, Publication Demographics, H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI, MERFISH, ExSeq, Other Data Type Specified",,,TRUE,Publication,,,list like +Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10X Visium, Bulk DNA, Bulk RNA-seq, LC-MS-MS, LC-MS3, Shotgun MS (lipidomics), scATAC-seq, scRNA-seq, Publication Demographics, H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI, MERFISH, ExSeq, RPPA, Electron Microscopy, Other Data Type Specified",,,TRUE,Publication,,,list like Other Data Type Specified,Other types of data associated with the content.,,,,FALSE,Publication,,,list like Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url Supporting Link Description,Description of relevant external links associated with the publication (e.g An external mouse dataset used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and-or any other applicable agreement(s).,,,,FALSE,Publication,,, @@ -1011,4 +1011,4 @@ 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,,, \ No newline at end of file +Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,, From 0cbb969dbb80714b142a234e5859a1afb7c2ebdf Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Wed, 10 Apr 2024 09:17:14 +0100 Subject: [PATCH 2/3] url warning for supporting link --- HTAN.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index 271a976a..571b7a08 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -898,7 +898,7 @@ License,The type of license applicable to the content.,"0BSD, AAL, ADSL, AFL-1.1 PMID,The PubMed identifier associated with the publication (applicable to published manuscripts). Provide as a URL of the form https://pubmed.ncbi.nlm.nih.gov/{pmid},,,,FALSE,Publication,,,url Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10X Visium, Bulk DNA, Bulk RNA-seq, LC-MS-MS, LC-MS3, Shotgun MS (lipidomics), scATAC-seq, scRNA-seq, Publication Demographics, H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI, MERFISH, ExSeq, RPPA, Electron Microscopy, Other Data Type Specified",,,TRUE,Publication,,,list like Other Data Type Specified,Other types of data associated with the content.,,,,FALSE,Publication,,,list like -Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url +Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url warning Supporting Link Description,Description of relevant external links associated with the publication (e.g An external mouse dataset used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and-or any other applicable agreement(s).,,,,FALSE,Publication,,, Tool,Were any software or computational tools generated for this content,"Yes, No",,,TRUE,Publication,,, Accessory,An empty parent attribute for accessory ,,,,FALSE,,,, From a9e575a364af6b8e536b8696d954ba90504bcc26 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 11 Apr 2024 19:23:42 +0000 Subject: [PATCH 3/3] GitHub Action: convert *.model.csv to *.model.jsonld --- HTAN.model.jsonld | 42 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index 252e2b45..8a7f0c35 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -142214,6 +142214,12 @@ { "@id": "bts:ExSeq" }, + { + "@id": "bts:RPPA" + }, + { + "@id": "bts:ElectronMicroscopy" + }, { "@id": "bts:OtherDataTypeSpecified" } @@ -142240,7 +142246,7 @@ "sms:displayName": "Supporting Link", "sms:required": "sms:false", "sms:validationRules": [ - "url" + "url warning" ] }, { @@ -148261,6 +148267,40 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:RPPA", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "RPPA", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "RPPA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ElectronMicroscopy", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ElectronMicroscopy", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Electron Microscopy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:OtherDataTypeSpecified", "@type": "rdfs:Class",