7299050865

Committed 22 Dec 2023 10:51AM UTC coverage: 23.647% (+0.05%) from 23.594%

Build # 7299050865

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github

Committed by

gustavo-salazar

Commit Message

Merge branch 'new-description' into future

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32.0

/src/schema_org/processors.js

import config from 'config';
import descriptionToPath from 'utils/processDescription/descriptionToPath';
import { getDescriptionText } from 'components/Description';

const INTERPRO_DESCRIPTION =
  'InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites';

export const schemaProcessDataInterpro = ({ description = null }) => ({
  '@type': 'Dataset',
  '@id': '@mainEntity',
  name: 'InterPro',
  description,
  url: 'https://www.ebi.ac.uk/interpro/',
  keywords: ['InterPro', 'Domain', 'Family', 'Annotation', 'Protein'],
  provider: {
    '@type': 'Organization',
    name: 'European Bioinformatics Institute',
    url: 'https://www.ebi.ac.uk/',
  },
  citation: '@citation',
  hasPart: '@dataset',
  license: 'https://creativecommons.org/licenses/by/4.0/',
});
export const schemaProcessDataForDB = ({
  name,
  releaseDate = null,
  version = null,
  description = null,
}) => ({
  '@type': 'Dataset',
  '@id': '@dataset',
  name,
  identifier: name,
  version,
  description,
  license: 'https://creativecommons.org/licenses/by/4.0/',
  datePublished: releaseDate,
  url: `https://www.ebi.ac.uk/interpro/entry/${name}`,
});

export const schemaProcessDataTable = ({ data: { db }, location }) => ({
  '@type': 'Dataset',
  '@id': '@mainEntity',
  identifier: db.canonical,
  name: db.name,
  version: db.version,
  url: location.href,
  hasPart: '@TableRow',
  isPartOf: {
    '@type': 'Dataset',
    '@id': config.root.website.protocol + config.root.website.href,
  },
  description: `Dataset of the type ${db.type || '?'} from the database ${
    db.name
  } - version ${db.version}`,
  license: 'https://creativecommons.org/licenses/by/4.0/',
});

export const schemaProcessDataTableRow = ({ data: { row, endpoint } }) => ({
  '@type': 'Dataset',
  '@id': '@TableRow',
  identifier: row.accession,
  name: row.name || row.db || row.source_database,
  description: `Data item of the type ${row.type || '?'} from the database ${
    row.db || row.source_database
  } with accession ${row.accession} and name ${row.name}`,
  license: 'https://creativecommons.org/licenses/by/4.0/',
  url:
    config.root.website.protocol +
    config.root.website.href +
    descriptionToPath({
      main: { key: endpoint },
      [endpoint]: {
        db: row.db || row.source_database,
        accession: row.accession.toString(),
      },
    }),
});

export const isPartOf = (main, db, version, description = undefined) => ({
  '@type': 'Dataset',
  '@id':
    config.root.website.protocol +
    config.root.website.href +
    descriptionToPath({
      main: { key: main },
      [main]: { db },
    }),
  version,
  name: db,
  description,
  license: 'https://creativecommons.org/licenses/by/4.0/',
});
export const schemaProcessIntegrated = ({ name, version }) => ({
  '@type': ['Dataset'],
  // '@type': ['Entry', 'BioChemEntity', 'CreativeWork'],
  '@id': '@isBasisFor',
  isPartOf: isPartOf('entry', 'InterPro', version, INTERPRO_DESCRIPTION),
  name,
  url:
    config.root.website.protocol +
    config.root.website.href +
    descriptionToPath({
      main: { key: 'entry' },
      entry: { db: 'InterPro', accession: name },
    }),
});

export const isContainedInOrganism = ({ taxId, fullName = null }) => ({
  '@id': '@additionalProperty',
  '@type': 'PropertyValue',
  name: 'isContainedIn',
  value: {
    '@type': 'StructuredValue',
    additionalType: [
      'bio:Taxon',
      'bio:BioChemEntity',
      'http://semanticscience.org/resource/SIO_010000',
    ],
    identifier: taxId,
    name: fullName,
    url: `http://purl.bioontology.org/ontology/NCBITAXON/${taxId}`,
    sameAs: `http://purl.uniprot.org/taxonomy/${taxId}`,
  },
});

export const isTranscribedFrom = ({ gene }) => ({
  '@id': '@additionalProperty',
  '@type': 'PropertyValue',
  additionalType: 'http://semanticscience.org/resource/SIO_010081',
  name: 'gene',
  value: {
    '@type': 'StructuredValue',
    additionalType: [
      'bio:Gene',
      'bio:BioChemEntity',
      'http://semanticscience.org/resource/SIO_010035',
    ],
    identifier: gene,
    name: gene,
  },
});
// const mapTypeToOntology = new Map([
//   ['Domain', 'DomainAnnotation'],
//   ['Family', 'FamilyAnnotation'],
//   ['Repeat', 'RepeatAnnotation'],
//   ['Unknown', 'UnknownAnnotation'],
//   ['Conserved_site', 'ConservedSiteAnnotation'],
//   ['Binding_site', 'BindingSiteAnnotation'],
//   ['Active_site', 'ActiveSiteAnnotation'],
//   ['PTM', 'PTMAnnotation'],
// ]);

// export const schemaProcessDataRecord = ({ data, endpoint, version }) => ({
//   '@type': 'Dataset',
//   '@id': '@mainEntityOfPage',
//   identifier: data.metadata.source_database,
//   name: data.metadata.source_database,
//   description: data.metadata.description,
//   url: `https://www.ebi.ac.uk/interpro/${endpoint}/${data.metadata.source_database}/${data.metadata.accession}`,
//   mainEntity: '@mainEntity',
//   seeAlso: '@seeAlso',
//   isBasedOn: '@isBasedOn',
//   isBasisFor: '@isBasisFor',
//   citation: '@citation',
//   license: 'https://creativecommons.org/licenses/by/4.0/',
// });

export const endpoint2type = {
  entry: 'bio:ProteinAnnotation',
  protein: 'bio:Protein',
  taxonomy: 'bio:Taxon',
  proteome: 'bio:DataRecord',
  structure: 'bio:ProteinStructure',
  set: 'bio:DataRecord',
};

const cleanUpDescription = (description /*: string */) =>
  getDescriptionText(
    (Array.isArray(description) ? description[0] : description) || '',
  )
    .replace(/\r/g, '')
    .replace(/\n/g, '')
    .replace(/<\/?[a-zA-Z]+>/g, '')
    .replace(/\[(\[cite:[a-zA-Z0-9]+\](, )?)+\]/g, '')
    .replace(/\[(PMID: [0-9]+(, )?)+\]/g, '');

export const schemaProcessMainEntity = ({ data, type }) => {
  const schema = {
    // '@type': [type, 'StructuredValue', 'BioChemEntity', 'CreativeWork'],
    '@type': ['Dataset'],
    '@id': '@mainEntity',
    additionalType: endpoint2type[type],
    identifier: data.accession,
    url: `https://www.ebi.ac.uk/interpro/${type}/${data.source_database}/${data.accession}`,
    name: data.name.name || data.accession,
    alternateName: data.name.long || null,
    additionalProperty: '@additionalProperty',
    hasPart: '@hasPart',
    isContainedIn: '@isContainedIn',
    isPartOf: `https://www.ebi.ac.uk/interpro/${type}/${data.source_database}/`,
    license: 'https://creativecommons.org/licenses/by/4.0/',
  };
  if (data.description) {
    schema.description = cleanUpDescription(data.description);
  } else
    schema.description = `The main entity of this document is a ${type} with accession number ${data.accession}`;
  // if (type === 'Entry') {
  //   schema['@type'].push(
  //     mapTypeToOntology.get(data.type) || mapTypeToOntology.get('Unknown'),
  //   );
  // }
  return schema;
};

export const schemaProcessCitations = ({ identifier, author, name }) => ({
  '@type': 'CreativeWork',
  '@id': '@citation',
  identifier,
  name,
  author,
});

export const schemaProcessDataWebPage = ({ name, description, location }) => ({
  '@type': 'WebPage',
  '@id': '@mainEntityOfPage',
  name,
  description,
  url: location.href,
  keywords: ['InterPro', 'Domain', 'Family', 'Annotation', 'Protein'],
  provider: {
    '@type': 'Organization',
    name: 'European Bioinformatics Institute',
    url: 'https://www.ebi.ac.uk/',
  },
  hasPart: '@hasPart',
});

export const schemaProcessDataPageSection = ({ name, description }) => ({
  '@type': 'WebPageElement',
  '@id': '@mainEntity',
  name,
  description,
});

export const schemaProcessInterProCitation = () => ({
  '@type': 'CreativeWork',
  '@id': '@mainCitation',
  mainEntityOfPage: 'https://www.ebi.ac.uk/interpro/',
  name: 'The InterPro protein families and domains database: 20 years on',
  headline: 'The InterPro protein families and domains database: 20 years on',
  url: 'https://doi.org/10.1093/nar/gkaa977',
  datePublished: '2020-11',
  dateModified: '2020-11',
  publisher: {
    '@type': 'Organization',
    '@id': 'https://academic.oup.com/nar',
    name: 'Nucleic Acids Research',
    url: 'https://academic.oup.com/nar',
    logo: {
      '@type': 'imageObject',
      url: 'https://example.com/logo.png',
    },
  },
  image:
    'https://proteinswebteam.github.io/interpro-blog/assets/media/images/logo_medium.png',
  author: [
    'Blum M',
    'Chang H',
    'Chuguransky S',
    'Grego T',
    'Kandasaamy S',
    'Mitchell A',
    'Nuka G',
    'Paysan-Lafosse T',
    'Qureshi M',
    'Raj S',
    'RichardsonL',
    'Salazar GA',
    'Williams L',
    'Bork P',
    'Bridge A',
    'Gough J',
    'Haft DH',
    'Letunic I',
    'Marchler-Bauer A',
    'Mi H',
    'Natale DA',
    'Necci M',
    'Orengo CA',
    'Pandurangan AP',
    'Rivoire C',
    'Sigrist CJA',
    'Sillitoe I',
    'Thanki N',
    'Thomas PD',
    'Tosatto SCE',
    'Wu CH',
    'Bateman A',
    'Finn RD',
  ],
  sameAs: [
    'https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa977/5958491',
    'https://pubmed.ncbi.nlm.nih.gov/33156333/',
  ],
});

1	import config from 'config';
2	import descriptionToPath from 'utils/processDescription/descriptionToPath';
3	import { getDescriptionText } from 'components/Description';
4
5	const INTERPRO_DESCRIPTION =
6	'InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites';	16✔
7
8	export const schemaProcessDataInterpro = ({ description = null }) => ({	16!
9	'@type': 'Dataset',
10	'@id': '@mainEntity',
11	name: 'InterPro',
12	description,
13	url: 'https://www.ebi.ac.uk/interpro/',
14	keywords: ['InterPro', 'Domain', 'Family', 'Annotation', 'Protein'],
15	provider: {
16	'@type': 'Organization',
17	name: 'European Bioinformatics Institute',
18	url: 'https://www.ebi.ac.uk/',
19	},
20	citation: '@citation',
21	hasPart: '@dataset',
22	license: 'https://creativecommons.org/licenses/by/4.0/',
23	});
24	export const schemaProcessDataForDB = ({	16✔
25	name,
26	releaseDate = null,	×
27	version = null,	×
28	description = null,	×
29	}) => ({	×
30	'@type': 'Dataset',
31	'@id': '@dataset',
32	name,
33	identifier: name,
34	version,
35	description,
36	license: 'https://creativecommons.org/licenses/by/4.0/',
37	datePublished: releaseDate,
38	url: `https://www.ebi.ac.uk/interpro/entry/${name}`,
39	});
40
41	export const schemaProcessDataTable = ({ data: { db }, location }) => ({	16✔
42	'@type': 'Dataset',
43	'@id': '@mainEntity',
44	identifier: db.canonical,
45	name: db.name,
46	version: db.version,
47	url: location.href,
48	hasPart: '@TableRow',
49	isPartOf: {
50	'@type': 'Dataset',
51	'@id': config.root.website.protocol + config.root.website.href,
52	},
53	description: `Dataset of the type ${db.type \|\| '?'} from the database ${	×
54	db.name
55	} - version ${db.version}`,
56	license: 'https://creativecommons.org/licenses/by/4.0/',
57	});
58
59	export const schemaProcessDataTableRow = ({ data: { row, endpoint } }) => ({	16✔
60	'@type': 'Dataset',
61	'@id': '@TableRow',
62	identifier: row.accession,
63	name: row.name \|\| row.db \|\| row.source_database,	×
64	description: `Data item of the type ${row.type \|\| '?'} from the database ${	×
65	row.db \|\| row.source_database	×
66	} with accession ${row.accession} and name ${row.name}`,
67	license: 'https://creativecommons.org/licenses/by/4.0/',
68	url:
69	config.root.website.protocol +
70	config.root.website.href +
71	descriptionToPath({
72	main: { key: endpoint },
73	[endpoint]: {
74	db: row.db \|\| row.source_database,	×
75	accession: row.accession.toString(),
76	},
77	}),
78	});
79
80	export const isPartOf = (main, db, version, description = undefined) => ({	16!
81	'@type': 'Dataset',
82	'@id':
83	config.root.website.protocol +
84	config.root.website.href +
85	descriptionToPath({
86	main: { key: main },
87	[main]: { db },
88	}),
89	version,
90	name: db,
91	description,
92	license: 'https://creativecommons.org/licenses/by/4.0/',
93	});
94	export const schemaProcessIntegrated = ({ name, version }) => ({	16✔
95	'@type': ['Dataset'],
96	// '@type': ['Entry', 'BioChemEntity', 'CreativeWork'],
97	'@id': '@isBasisFor',
98	isPartOf: isPartOf('entry', 'InterPro', version, INTERPRO_DESCRIPTION),
99	name,
100	url:
101	config.root.website.protocol +
102	config.root.website.href +
103	descriptionToPath({
104	main: { key: 'entry' },
105	entry: { db: 'InterPro', accession: name },
106	}),
107	});
108
109	export const isContainedInOrganism = ({ taxId, fullName = null }) => ({	16!
110	'@id': '@additionalProperty',
111	'@type': 'PropertyValue',
112	name: 'isContainedIn',
113	value: {
114	'@type': 'StructuredValue',
115	additionalType: [
116	'bio:Taxon',
117	'bio:BioChemEntity',
118	'http://semanticscience.org/resource/SIO_010000',
119	],
120	identifier: taxId,
121	name: fullName,
122	url: `http://purl.bioontology.org/ontology/NCBITAXON/${taxId}`,
123	sameAs: `http://purl.uniprot.org/taxonomy/${taxId}`,
124	},
125	});
126
127	export const isTranscribedFrom = ({ gene }) => ({	16✔
128	'@id': '@additionalProperty',
129	'@type': 'PropertyValue',
130	additionalType: 'http://semanticscience.org/resource/SIO_010081',
131	name: 'gene',
132	value: {
133	'@type': 'StructuredValue',
134	additionalType: [
135	'bio:Gene',
136	'bio:BioChemEntity',
137	'http://semanticscience.org/resource/SIO_010035',
138	],
139	identifier: gene,
140	name: gene,
141	},
142	});
143	// const mapTypeToOntology = new Map([
144	// ['Domain', 'DomainAnnotation'],
145	// ['Family', 'FamilyAnnotation'],
146	// ['Repeat', 'RepeatAnnotation'],
147	// ['Unknown', 'UnknownAnnotation'],
148	// ['Conserved_site', 'ConservedSiteAnnotation'],
149	// ['Binding_site', 'BindingSiteAnnotation'],
150	// ['Active_site', 'ActiveSiteAnnotation'],
151	// ['PTM', 'PTMAnnotation'],
152	// ]);
153
154	// export const schemaProcessDataRecord = ({ data, endpoint, version }) => ({
155	// '@type': 'Dataset',
156	// '@id': '@mainEntityOfPage',
157	// identifier: data.metadata.source_database,
158	// name: data.metadata.source_database,
159	// description: data.metadata.description,
160	// url: `https://www.ebi.ac.uk/interpro/${endpoint}/${data.metadata.source_database}/${data.metadata.accession}`,
161	// mainEntity: '@mainEntity',
162	// seeAlso: '@seeAlso',
163	// isBasedOn: '@isBasedOn',
164	// isBasisFor: '@isBasisFor',
165	// citation: '@citation',
166	// license: 'https://creativecommons.org/licenses/by/4.0/',
167	// });
168
169	export const endpoint2type = {	16✔
170	entry: 'bio:ProteinAnnotation',
171	protein: 'bio:Protein',
172	taxonomy: 'bio:Taxon',
173	proteome: 'bio:DataRecord',
174	structure: 'bio:ProteinStructure',
175	set: 'bio:DataRecord',
176	};
177
178	const cleanUpDescription = (description /: string /) =>	16✔
NEW 179	getDescriptionText(	×
180	(Array.isArray(description) ? description[0] : description) \|\| '',	×
181	)
182	.replace(/\r/g, '')
183	.replace(/\n/g, '')
184	.replace(/<\/?[a-zA-Z]+>/g, '')
185	.replace(/\[(\[cite:[a-zA-Z0-9]+\](, )?)+\]/g, '')
186	.replace(/\[(PMID: [0-9]+(, )?)+\]/g, '');
187
188	export const schemaProcessMainEntity = ({ data, type }) => {	16✔
189	const schema = {	×
190	// '@type': [type, 'StructuredValue', 'BioChemEntity', 'CreativeWork'],
191	'@type': ['Dataset'],
192	'@id': '@mainEntity',
193	additionalType: endpoint2type[type],
194	identifier: data.accession,
195	url: `https://www.ebi.ac.uk/interpro/${type}/${data.source_database}/${data.accession}`,
196	name: data.name.name \|\| data.accession,	×
197	alternateName: data.name.long \|\| null,	×
198	additionalProperty: '@additionalProperty',
199	hasPart: '@hasPart',
200	isContainedIn: '@isContainedIn',
201	isPartOf: `https://www.ebi.ac.uk/interpro/${type}/${data.source_database}/`,
202	license: 'https://creativecommons.org/licenses/by/4.0/',
203	};
204	if (data.description) {	×
205	schema.description = cleanUpDescription(data.description);	×
206	} else
207	schema.description = `The main entity of this document is a ${type} with accession number ${data.accession}`;	×
208	// if (type === 'Entry') {
209	// schema['@type'].push(
210	// mapTypeToOntology.get(data.type) \|\| mapTypeToOntology.get('Unknown'),
211	// );
212	// }
213	return schema;	×
214	};
215
216	export const schemaProcessCitations = ({ identifier, author, name }) => ({	16✔
217	'@type': 'CreativeWork',
218	'@id': '@citation',
219	identifier,
220	name,
221	author,
222	});
223
224	export const schemaProcessDataWebPage = ({ name, description, location }) => ({	16✔
225	'@type': 'WebPage',
226	'@id': '@mainEntityOfPage',
227	name,
228	description,
229	url: location.href,
230	keywords: ['InterPro', 'Domain', 'Family', 'Annotation', 'Protein'],
231	provider: {
232	'@type': 'Organization',
233	name: 'European Bioinformatics Institute',
234	url: 'https://www.ebi.ac.uk/',
235	},
236	hasPart: '@hasPart',
237	});
238
239	export const schemaProcessDataPageSection = ({ name, description }) => ({	16✔
240	'@type': 'WebPageElement',
241	'@id': '@mainEntity',
242	name,
243	description,
244	});
245
246	export const schemaProcessInterProCitation = () => ({	16✔
247	'@type': 'CreativeWork',
248	'@id': '@mainCitation',
249	mainEntityOfPage: 'https://www.ebi.ac.uk/interpro/',
250	name: 'The InterPro protein families and domains database: 20 years on',
251	headline: 'The InterPro protein families and domains database: 20 years on',
252	url: 'https://doi.org/10.1093/nar/gkaa977',
253	datePublished: '2020-11',
254	dateModified: '2020-11',
255	publisher: {
256	'@type': 'Organization',
257	'@id': 'https://academic.oup.com/nar',
258	name: 'Nucleic Acids Research',
259	url: 'https://academic.oup.com/nar',
260	logo: {
261	'@type': 'imageObject',
262	url: 'https://example.com/logo.png',
263	},
264	},
265	image:
266	'https://proteinswebteam.github.io/interpro-blog/assets/media/images/logo_medium.png',
267	author: [
268	'Blum M',
269	'Chang H',
270	'Chuguransky S',
271	'Grego T',
272	'Kandasaamy S',
273	'Mitchell A',
274	'Nuka G',
275	'Paysan-Lafosse T',
276	'Qureshi M',
277	'Raj S',
278	'RichardsonL',
279	'Salazar GA',
280	'Williams L',
281	'Bork P',
282	'Bridge A',
283	'Gough J',
284	'Haft DH',
285	'Letunic I',
286	'Marchler-Bauer A',
287	'Mi H',
288	'Natale DA',
289	'Necci M',
290	'Orengo CA',
291	'Pandurangan AP',
292	'Rivoire C',
293	'Sigrist CJA',
294	'Sillitoe I',
295	'Thanki N',
296	'Thomas PD',
297	'Tosatto SCE',
298	'Wu CH',
299	'Bateman A',
300	'Finn RD',
301	],
302	sameAs: [
303	'https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa977/5958491',
304	'https://pubmed.ncbi.nlm.nih.gov/33156333/',
305	],
306	});

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