From 03e5f1d59e11a29387af776b4d3c6e43f9a3c012 Mon Sep 17 00:00:00 2001 From: Kasun Samarasinghe Date: Tue, 12 May 2020 15:00:06 +0200 Subject: [PATCH 1/2] Nextprot dataset and protein examples --- .../nextprot_jsonld.json | 43 +++++++++++++++++++ .../examples/0.9-DRAFT/nextprot-jsonld.json | 36 ++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 Dataset/examples/0.1-0.2-DRAFT_examples/nextprot_jsonld.json create mode 100644 Protein/examples/0.9-DRAFT/nextprot-jsonld.json diff --git a/Dataset/examples/0.1-0.2-DRAFT_examples/nextprot_jsonld.json b/Dataset/examples/0.1-0.2-DRAFT_examples/nextprot_jsonld.json new file mode 100644 index 00000000..709362f3 --- /dev/null +++ b/Dataset/examples/0.1-0.2-DRAFT_examples/nextprot_jsonld.json @@ -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/" + } +} \ No newline at end of file diff --git a/Protein/examples/0.9-DRAFT/nextprot-jsonld.json b/Protein/examples/0.9-DRAFT/nextprot-jsonld.json new file mode 100644 index 00000000..a8e5ac4a --- /dev/null +++ b/Protein/examples/0.9-DRAFT/nextprot-jsonld.json @@ -0,0 +1,36 @@ +{ + "@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" + } + } + ] + } + } + \ No newline at end of file From 6cd3a8f427075e032a32fe9c89e3a88645477a0d Mon Sep 17 00:00:00 2001 From: Alasdair Gray Date: Tue, 12 May 2020 14:54:43 +0100 Subject: [PATCH 2/2] Moved nextprot examples to appropriate folders --- .../nextprot_jsonld.json | 0 Protein/examples/{0.9-DRAFT => 0.11-RELEASE}/nextprot-jsonld.json | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename Dataset/examples/{0.1-0.2-DRAFT_examples => 0.3-RELEASE_examples}/nextprot_jsonld.json (100%) rename Protein/examples/{0.9-DRAFT => 0.11-RELEASE}/nextprot-jsonld.json (100%) diff --git a/Dataset/examples/0.1-0.2-DRAFT_examples/nextprot_jsonld.json b/Dataset/examples/0.3-RELEASE_examples/nextprot_jsonld.json similarity index 100% rename from Dataset/examples/0.1-0.2-DRAFT_examples/nextprot_jsonld.json rename to Dataset/examples/0.3-RELEASE_examples/nextprot_jsonld.json diff --git a/Protein/examples/0.9-DRAFT/nextprot-jsonld.json b/Protein/examples/0.11-RELEASE/nextprot-jsonld.json similarity index 100% rename from Protein/examples/0.9-DRAFT/nextprot-jsonld.json rename to Protein/examples/0.11-RELEASE/nextprot-jsonld.json