Feature Article
Science Forum Wikidata as a knowledge graph for the life sciences
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protein 961,210 RefSeq Protein ID: 750,780 UniProt protein ID: 646,506 Ensembl Protein ID: 251,125 PDB structure ID: 44,732 cell component (907)
mechanism of action 182 MeSH Code: 288 MeSH ID: 168
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gene 1,176,028 Entrez Gene ID: 737,302 RefSeq RNA ID: 561,824 NCBI Locus tag: 502,347 Ensembl Transcript ID: 401,691 Ensembl Gene ID: 122,639 MGI Gene Symbol: 71,959 Mouse Genome Informatics ID: 65,989 ...
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MeSH ID: 608 ChEBI ID: 478 MeSH Code: 443 Freebase ID: 422 KEGG ID: 395 ATC code: 390 ChemSpider ID: 316 ...
pharmaceutical product 2,731
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taxon 2,600,217 Global Biodiversity Information Facility ID: 2,058,609 Encyclopedia of Life ID: 1,354,013 IRMNG ID: 1,214,539 iNaturalist taxon ID: 569,998 ITIS TSN: 533,003 IPNI plant ID: 488,933 NCBI Taxonomy ID: 471,220 ...
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part of / has part (726)
physically interacts with (675)
stereoisomer of (642) physically interacts with (3,924) significant drug interaction (1,725)
Figure 1. A simplified class-level diagram of the Wikidata knowledge graph for biomedical entities. Each box represents one type of biomedical entity. The header displays the name of that entity type (e.g., pharmaceutical product) and the number of Wikidata items for that entity type. The lower portion of each box displays a partial listing of attributes about each entity type and the number of Wikidata items for each attribute. Edges between boxes represent the number of Wikidata statements corresponding to each combination of subject type, predicate, and object type. For example, there are 1505 statements with ’pharmaceutical product’ as the subject type, ’therapeutic area’ as the predicate, and ’disease’ as the object type. For clarity, edges for reciprocal relationships (e.g., ’has part’ and ’part of’) are combined into a single edge, and scientific articles (which are widely cited in statement references) have been omitted. All counts of Wikidata items are current as of September 2019. The most common data sources cited as references are available in Figure 1—source data 1. Data are generated using the code in https://github.com/SuLab/genewikiworld (archived at Mayers et al., 2020). A more complete version of this graph diagram can be found at https://commons.wikimedia.org/wiki/File:Biomedical_ Knowledge_Graph_in_Wikidata.svg. The online version of this article includes the following source data and figure supplement(s) for figure 1: Source data 1. Most frequent data sources cited as references for the biomedical subset of the Wikidata knowledge graph shown in Figure 1. Figure supplement 1. Trends in Wikidata edits.
focused on those with a clear clinical or therapeutic relevance. Chemical compounds including drugs: Wikidata has items for over 150 thousand chemical compounds, including over 3500 items which are specifically designated as medications. Compound attributes are drawn from a diverse set of databases, including PubChem
Waagmeester et al. eLife 2020;9:e52614. DOI: https://doi.org/10.7554/eLife.52614
(Wang et al., 2009), RxNorm (Nelson et al., 2011), the IUPHAR Guide to Pharmacology (Harding et al., 2018; Pawson et al., 2014; Southan et al., 2016), NDF-RT (National Drug File – Reference Terminology), and LIPID MAPS (Sud et al., 2007). These items typically contain statements describing chemical structure and key physicochemical properties, and links to
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