Nextprot dataset and protein examples #423
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| "@id": "https://www.nextprot.org/entry/NX_P52701", | ||
| "includedInDataset": "ftp://ftp.nextprot.org/pub/current_release/xml/nextprot_all.xml.gz", | ||
| "citation": { | ||
| "@id": "", |
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I guess the citations are not mandatory?
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| { | |||
| "@type": "Dataset", | |||
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Should have an @id property to identify the dataset
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I agree, @id is important for Dataset
| "name": "Creative Commons CC BY 4.0 Attribution", | ||
| "url": "https://creativecommons.org/licenses/by/4.0/" | ||
| } | ||
| } |
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identifier property is missing
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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.
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| { | |||
| "@type": "Dataset", | |||
| "name": "neXtProt entries", | |||
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Is 'entries' part of the dataset name?
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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": [ |
| { | ||
| "@context": "http://schema.org", | ||
| "@type": "DataRecord", | ||
| "@id": "https://www.nextprot.org/entry/NX_P52701", |
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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.
| "@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", |
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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.
| "@type": "DataRecord", | ||
| "@id": "https://www.nextprot.org/entry/NX_P52701", | ||
| "includedInDataset": "ftp://ftp.nextprot.org/pub/current_release/xml/nextprot_all.xml.gz", | ||
| "citation": { |
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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
| "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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Please update to 0.11-RELEASE
| "http://purl.org/dc/terms/conformsTo": "https://bioschemas.org/specifications/Protein/0.9-DRAFT", | ||
| "identifier": "NX_P52701", | ||
| "name": "DNA mismatch repair protein Msh6", | ||
| "description": "", |
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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
| "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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Do you intend that these are embedded within the hasBioChemEntityPart rather than properties of the protein directly?
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According to the profile, these two properties can be used directly for a Protein.
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I agree with @AlasdairGray comments. I have added a couple more, please have a look. Thanks.
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| { | |||
| "@type": "Dataset", | |||
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I agree, @id is important for Dataset
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| { | |||
| "@type": "Dataset", | |||
| "name": "neXtProt entries", | |||
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It does not seem it is from what I saw on their website
| }, | ||
| { | ||
| "@type": "DataDownload", | ||
| "fileFormat": "RDF" |
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Are not you missing the download URL here?
| "name": "Creative Commons CC BY 4.0 Attribution", | ||
| "url": "https://creativecommons.org/licenses/by/4.0/" | ||
| } | ||
| } |
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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.
| "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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According to the profile, these two properties can be used directly for a Protein.
Examples