| License | CCZero |
Wikidata is not a life sciences database, but a general database related to Wikipedia [1]. That said, various research groups have started using Wikidata for the life sciences [2,3]. For example, CAS registry numbers in Wikidata and Wikipedia have been validated against the Common Chemistry database [4], and Wikidata has been used to make chemicals in taxon available in the LOTUS project [5].
The RDF contains all pathways, their datanodes (genes, proteins, metabolites, etc.), author information, molecular descriptors, and more. The main classes are:
…
We can list proteins with the following query:
SPARQL sparql/wikidataProteins.rq (run, edit)
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
SELECT * WHERE {
?o wdt:P31 wd:Q8054.
?o rdfs:label ?l.
FILTER(LANG(?l)='en')
} LIMIT 10
which gives:
| o | l |
| http://www.wikidata.org/entity/Q409065 | Uroporphyrinogen decarboxylase |
| http://www.wikidata.org/entity/Q409106 | marker of proliferation Ki-67 |
| http://www.wikidata.org/entity/Q409114 | Sex determining region Y |
| http://www.wikidata.org/entity/Q409166 | Coagulation factor II, thrombin |
| http://www.wikidata.org/entity/Q24190 | Neurotrophin 3 |
| http://www.wikidata.org/entity/Q30530 | Histidine ammonia-lyase |
| http://www.wikidata.org/entity/Q58321 | protein kinase |
| http://www.wikidata.org/entity/Q63398 | Chromogranin B |
| http://www.wikidata.org/entity/Q74314 | Titin |
| http://www.wikidata.org/entity/Q74581 | Growth differentiation factor 15 |
We can also list chemicals, with this query:
SPARQL sparql/wikidataChemicals.rq (run, edit)
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
SELECT * WHERE {
?o wdt:P31 wd:Q113145171 .
?o rdfs:label ?l.
FILTER(LANG(?l)='en')
} LIMIT 50
which gives:
| o | l |
| http://www.wikidata.org/entity/Q153 | ethanol |
| http://www.wikidata.org/entity/Q50703 | cesium iodide |
| http://www.wikidata.org/entity/Q50980 | xanthine |
| http://www.wikidata.org/entity/Q52353 | benzyl alcohol |
| http://www.wikidata.org/entity/Q150681 | octane |
| http://www.wikidata.org/entity/Q150694 | nonane |
| http://www.wikidata.org/entity/Q150717 | decane |
| http://www.wikidata.org/entity/Q150731 | undecane |
| This table is truncated. See the full table at sparql/wikidataChemicals.rq | |