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Nextprot dataset and protein examples #423
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kwsamarasinghe
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43 changes: 43 additions & 0 deletions
43
Dataset/examples/0.1-0.2-DRAFT_examples/nextprot_jsonld.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| { | ||
| "@type": "Dataset", | ||
| "name": "neXtProt entries", | ||
| "description": "The collection of neXtProt entries for human proteins", | ||
| "url": "https://www.nextprot.org", | ||
| "keywords": "nextprot,Human,Proteins,Proteome,Proteomics,protein database,protein knowledgebase,protein resource,human protein,human proteome,function,medical,disease,expression,interactions,sequence,isoform,mutation,variant,phenotypes,proteomics,peptide,structure,3D,annotation,biocuration,chromosomes,protein validation,protein-coding genes,post-translational modifications,ptm,data integration,systems biology,genetic variations,UniProt", | ||
| "distribution": [ | ||
| { | ||
| "@type": "DataDownload", | ||
| "contentUrl": "ftp://ftp.nextprot.org/pub/current_release/xml/nextprot_all.xml.gz", | ||
| "fileFormat": "XML" | ||
| }, | ||
| { | ||
| "@type": "DataDownload", | ||
| "fileFormat": "RDF" | ||
| }, | ||
| { | ||
| "@type": "DataDownload", | ||
| "contentUrl": "ftp://ftp.nextprot.org/pub/current_release/peff/nextprot_all.peff.gz", | ||
| "fileFormat": "PEFF" | ||
| }, | ||
| { | ||
| "@type": "DataDownload", | ||
| "contentUrl": "ftp://ftp.nextprot.org/pub/current_release/md5/nextprot_sequence_md5.txt", | ||
| "fileFormat": "TXT" | ||
| }, | ||
| { | ||
| "@type": "DataDownload", | ||
| "contentUrl": "https://api.nextprot.org/export/entries/all.fasta", | ||
| "fileFormat": "FASTA" | ||
| } | ||
| ], | ||
| "potentialAction": { | ||
| "@type": "SearchAction", | ||
| "target": "https://www.nextprot.org/proteins/search?query={query}", | ||
| "query-input": "required name=query" | ||
| }, | ||
| "license": { | ||
| "@type": "CreativeWork", | ||
| "name": "Creative Commons CC BY 4.0 Attribution", | ||
| "url": "https://creativecommons.org/licenses/by/4.0/" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| { | ||
| "@context": "http://schema.org", | ||
| "@type": "DataRecord", | ||
| "@id": "https://www.nextprot.org/entry/NX_P52701", | ||
| "includedInDataset": "ftp://ftp.nextprot.org/pub/current_release/xml/nextprot_all.xml.gz", | ||
| "citation": { | ||
| "@id": "", | ||
| "@type": "" | ||
| }, | ||
| "mainEntity": { | ||
| "@id": "https://www.nextprot.org/entry/NX_P52701", | ||
| "@type": "Protein", | ||
| "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/specifications/Protein/0.9-DRAFT", | ||
| "identifier": "NX_P52701", | ||
| "name": "DNA mismatch repair protein Msh6", | ||
| "description": "", | ||
| "alternateName": ["G/T mismatch-binding protein", "GTBP", "GTMBP", "MutS protein homolog 6", "MutS-alpha 160 kDa subunit"], | ||
| "url": "https://www.nextprot.org/entry/NX_P52701", | ||
| "hasBioChemEntityPart": [ | ||
| { | ||
| "isEncodedByBioChemEntity": { | ||
| "@type": "Gene", | ||
| "name": "MSH6", | ||
| "identifier": "HGNC:7329", | ||
| "hasRepresentation": "2p16.3" | ||
| }, | ||
| "taxonomicRange": { | ||
| "@id": "https://identifiers.org/taxonomy:9606", | ||
| "@type": "Taxon", | ||
| "name": "Human" | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } | ||
|
|
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I guess the citations are not mandatory?