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Nextprot dataset and protein examples #423

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Nextprot dataset and protein examples
kwsamarasinghe May 12, 2020
6cd3a8f
Moved nextprot examples to appropriate folders
May 12, 2020
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43 changes: 43 additions & 0 deletions Dataset/examples/0.3-RELEASE_examples/nextprot_jsonld.json
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{
"@type": "Dataset",
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@AlasdairGray AlasdairGray May 12, 2020

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Should have an @id property to identify the dataset

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@ljgarcia ljgarcia May 12, 2020

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I agree, @id is important for Dataset

"name": "neXtProt entries",
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@AlasdairGray AlasdairGray May 12, 2020

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Is 'entries' part of the dataset name?

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@ljgarcia ljgarcia May 12, 2020

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It does not seem it is from what I saw on their website

"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": [
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@AlasdairGray AlasdairGray May 12, 2020

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This looks to be correct

{
"@type": "DataDownload",
"contentUrl": "ftp://ftp.nextprot.org/pub/current_release/xml/nextprot_all.xml.gz",
"fileFormat": "XML"
},
{
"@type": "DataDownload",
"fileFormat": "RDF"
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@ljgarcia ljgarcia May 12, 2020

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Are not you missing the download URL here?

},
{
"@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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@AlasdairGray AlasdairGray May 12, 2020

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identifier property is missing

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@ljgarcia ljgarcia May 12, 2020

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And it is minimum according to https://bioschemas.org/profiles/Dataset/0.3-RELEASE-2019_06_14/.
By the way, I did not see a dct:conformsTo linking to the corresponding Bioschemas profile version, you should add it if you do not have it yet.

36 changes: 36 additions & 0 deletions Protein/examples/0.11-RELEASE/nextprot-jsonld.json
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{
"@context": "http://schema.org",
"@type": "DataRecord",
"@id": "https://www.nextprot.org/entry/NX_P52701",
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@AlasdairGray AlasdairGray May 12, 2020

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This @id should be different from the value for the main entity. You may just want to add #DR onto the end of this one.

"includedInDataset": "ftp://ftp.nextprot.org/pub/current_release/xml/nextprot_all.xml.gz",
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@AlasdairGray AlasdairGray May 12, 2020

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The value of this should be the value of the @id in your Dataset markup. It should point to the description of the dataset rather than the download file.

"citation": {
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@AlasdairGray AlasdairGray May 12, 2020

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Omit this property if there isn't a value for it.

You may also want to add a citation property into your dataset markup

"@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",
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@AlasdairGray AlasdairGray May 12, 2020

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Please update to 0.11-RELEASE

"identifier": "NX_P52701",
"name": "DNA mismatch repair protein Msh6",
"description": "",
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@AlasdairGray AlasdairGray May 12, 2020

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Omit properties for which there is no data. However in this case you probably want to include the text in your overview section of the webpage

"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"
}
Comment on lines +21 to +31
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@AlasdairGray AlasdairGray May 12, 2020

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Do you intend that these are embedded within the hasBioChemEntityPart rather than properties of the protein directly?

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@ljgarcia ljgarcia May 12, 2020

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According to the profile, these two properties can be used directly for a Protein.

}
]
}
}