From c919e7b8abf70560de73ca22814ee9ca0402ad76 Mon Sep 17 00:00:00 2001 From: Alasdair Gray Date: Fri, 29 Nov 2019 14:34:04 +0000 Subject: [PATCH 1/2] Use DataRecord and conform to Protein-v0.9 --- .../0.9-DRAFT/STRING_9606.ENSP00000379258.json | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/Protein/examples/0.9-DRAFT/STRING_9606.ENSP00000379258.json b/Protein/examples/0.9-DRAFT/STRING_9606.ENSP00000379258.json index d5e22c3d..5a4b542f 100644 --- a/Protein/examples/0.9-DRAFT/STRING_9606.ENSP00000379258.json +++ b/Protein/examples/0.9-DRAFT/STRING_9606.ENSP00000379258.json @@ -8,15 +8,17 @@ "@base": "http://schema.org" } ], - "@type": "Dataset", + "@type": "bio:DataRecord", "@id": "https://string-db.org/network/9606.ENSP00000379258", + "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/specifications/DataRecord/0.2-DRAFT", + "includedInDataset": "https://string-db.org/#string.v11", "mainEntity": { - "@type": [ - "bio:Protein" - ], + "@type": "bio:Protein", + "@id": "https://string-db.org/network/9606.ENSP00000379258", + "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/specifications/Protein/0.9-DRAFT", "name": "GLI3", "identifier": "9606.ENSP00000379258", - "additionalproperty": [ + "taxonomicRange": [ { "@id": "http://identifiers.org/taxonomy:9606", "identifier": "9606", @@ -24,7 +26,8 @@ "name": "Homo sapiens", "taxonRank": "species" } - ] + ], + "url": "https://string-db.org/network/9606.ENSP00000379258", }, "name": "STRING GLI3 interaction network (Homo sapiens)", "description": "Homo sapiens STRING functional association network of GLI3 protein.", From 2bc166610199f93e2f9207a4f0eacd0420b1f646 Mon Sep 17 00:00:00 2001 From: Alasdair Gray Date: Fri, 29 Nov 2019 14:58:12 +0000 Subject: [PATCH 2/2] Suggesting changes to string-db markup for main page --- DataCatalog/examples/0.3/string-db.json | 76 ++++++++++++++++++++++--- 1 file changed, 67 insertions(+), 9 deletions(-) diff --git a/DataCatalog/examples/0.3/string-db.json b/DataCatalog/examples/0.3/string-db.json index 6df9c788..140bdcd8 100644 --- a/DataCatalog/examples/0.3/string-db.json +++ b/DataCatalog/examples/0.3/string-db.json @@ -1,15 +1,16 @@ { "@context": "http://schema.org", - "@type": "WebPage", - "@id": "https://string-db.org", - "identifier": "stringdb", + "@type": "DataCatalog", + "@id": "https://string-db.org/", + "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/specifications/DataCatalog/0.3", "name": "STRING protein-protein interaction networks", "description": "STRING is a database of known and predicted protein-protein interactions and a functional enrichment tool covering more than 5000 genomes", - "url": "https://string-db.org", + "url": "https://string-db.org/", "keywords": "protein, protein interactions, string, functional annotation, functional associations, interaction network, enrichment", "dateModified": "2019.01.13", - "publication": { - "@type": "PublicationEvent", + "citation": { + "@type": "ScholarlyArticle", + "@id": "https://doi.org/10.1093/nar/gky1131", "name": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.", "url": "http://identifiers.org/pubmed:30476243" }, @@ -22,7 +23,7 @@ "@type": "ImageObject", "url": "https://string-db.org/images/string_logo_2015.png" }, - "creator": { + "provider": { "@type": "Organization", "name": "STRING consortium", "url": "https://string-db.org", @@ -54,10 +55,67 @@ } ] }, - "version": "11.0", "potentialAction": { "target": "https://string-db.org/cgi/network.pl?identifier={query_string}", "@type": "SearchAction", "query-input": "required name=query_string" - } + }, + "dataset": [ + { + "@type": "Dataset", + "@id": "https://string-db.org/#string.v11", + "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/specifications/Dataset/0.3", + "identifier": "stringdb", + "name": "STRING protein-protein interaction networks", + "description": "STRING is a database of known and predicted protein-protein interactions and a functional enrichment tool covering more than 5000 genomes", + "url": "https://string-db.org/", + "keywords": "protein, protein interactions, string, functional annotation, functional associations, interaction network, enrichment", + "dateModified": "2019.01.13", + "citation": { + "@type": "ScholarlyArticle", + "@id": "https://doi.org/10.1093/nar/gky1131", + "name": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.", + "url": "http://identifiers.org/pubmed:30476243" + }, + "creator": { + "@type": "Organization", + "name": "STRING consortium", + "url": "https://string-db.org", + "email": [ + "mering@imls.uzh.ch", + "bork@embl.de", + "lars.juhl.jensen@cpr.ku.dk" + ], + "memberOf": [ + { + "@type": "Organization", + "name": "SIB Swiss bioinformatics institute", + "url": "https://www.sib.swiss/" + }, + { + "@type": "Organization", + "name": "European Molecular Biology Laboratory", + "url": "https://embl.org/" + }, + { + "@type": "Organization", + "name": "University of Zurich", + "url": "https://www.uzh.ch/" + }, + { + "@type": "Organization", + "name": "University of Copenhagen", + "url": "https://www.ku.dk/" + } + ] + }, + "distribution": "https://string-db.org/cgi/download.pl", + "license": { + "@type": "CreativeWork", + "name": "Creative Commons Attribution 4.0 International", + "url": "https://creativecommons.org/licenses/by/4.0/" + }, + "version": "11.0" + } + ] }