String db update to latest versions #360
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,15 +1,16 @@ | ||
| { | ||
| "@context": "http://schema.org", | ||
| "@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/", | ||
| "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" | ||
| }, | ||
|
|
@@ -22,7 +23,7 @@ | |
| "@type": "ImageObject", | ||
| "url": "https://string-db.org/images/string_logo_2015.png" | ||
| }, | ||
| "provider": { | ||
| "@type": "Organization", | ||
| "name": "STRING consortium", | ||
| "url": "https://string-db.org", | ||
|
|
@@ -54,10 +55,67 @@ | |
| } | ||
| ] | ||
| }, | ||
| "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", | ||
|
There was a problem hiding this comment. |
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| "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": [ | ||
| "[email protected]", | ||
| "[email protected]", | ||
| "[email protected]" | ||
| ], | ||
| "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/" | ||
|
There was a problem hiding this comment. Should not we use this URL as the "@id" as well? |
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| }, | ||
| "version": "11.0" | ||
| } | ||
| ] | ||
| } | ||
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@@ -8,23 +8,26 @@ | |
| "@base": "http://schema.org" | ||
| } | ||
| ], | ||
| "@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", | ||
|
There was a problem hiding this comment. |
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| "includedInDataset": "https://string-db.org/#string.v11", | ||
| "mainEntity": { | ||
| "@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", | ||
|
There was a problem hiding this comment. The currentProtein profile version is https://bioschemas.org/profiles/Protein/0.11-RELEASE/ should it not be better to update the example to the latest release rather than using an old DRAFT profile? |
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| "name": "GLI3", | ||
| "identifier": "9606.ENSP00000379258", | ||
| "taxonomicRange": [ | ||
| { | ||
| "@id": "http://identifiers.org/taxonomy:9606", | ||
| "identifier": "9606", | ||
| "@type": "bio:taxon", | ||
| "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.", | ||
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This link https://bioschemas.org/specifications/DataCatalog/0.3 does not work, the link should be https://bioschemas.org/profiles/DataCatalog/0.3-RELEASE-2019_07_01/