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Wikidata

| Website | https://www.wikidata.org/ | | License | CCZero |

Wikidata is not a life sciences database, but a general database related to Wikipedia [Q118130164]. That said, various research groups have started using Wikidata for the life sciences [Q87830400,Q105037759]. For example, CAS registry numbers in Wikidata and Wikipedia have been validated against the Common Chemistry database [Q111987319], and Wikidata has been used to make chemicals in taxon available in the LOTUS project [Q112143478].

Entities

The RDF contains all pathways, their datanodes (genes, proteins, metabolites, etc.), author information, molecular descriptors, and more. The main classes are:

  • Pathway: a biological pathway
  • GeneProduct: can be a gene, strand of RNA, and a protein.
  • Rna: RNA, e.g. miRNA.
  • Protein: a protein. Post-translational modifications can be indicated with states
  • Metabolite: metabolites, ions, and other small molecules. It includes peptides.

Data model

...

Example queries

Proteins

We can list proteins with the following query:

wikidataProteins

which gives:

wikidataProteins

Chemicals

We can also list chemicals, with this query:

wikidataChemicals

which gives:

wikidataChemicals

References