| Website | https://www.wikidata.org/ |
| 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/Q24190 | Neurotrophin 3 |
| http://www.wikidata.org/entity/Q25902 | chymosin |
| 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/Q418781 | Catechol-O-methyltransferase |
| http://www.wikidata.org/entity/Q418896 | proopiomelanocortin |
| http://www.wikidata.org/entity/Q418934 | TNF superfamily member 11 |
| http://www.wikidata.org/entity/Q419004 | Cannabinoid receptor 1 |
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/Q150808 | tetradecane |
| http://www.wikidata.org/entity/Q150831 | pentadecane |
| http://www.wikidata.org/entity/Q150843 | hexadecane |
| http://www.wikidata.org/entity/Q116587 | diisononyl adipate |
| http://www.wikidata.org/entity/Q116907 | glutathione |
| http://www.wikidata.org/entity/Q117422 | glycol salicylate |
| http://www.wikidata.org/entity/Q118033 | cycloundecane |
| http://www.wikidata.org/entity/Q118040 | cyclododecane |
| This table is truncated. See the full table at sparql/wikidataChemicals.rq | |