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Science Forum Wikidata as a knowledge graph for the life sciences Köhler S, Stupp GS. 2020. SuLab/boqa: release v1.0 2020-01-21. Zenodo. http://doi.org/10.5281/zenodo. 3620979 Lam C, Ferreira C, Krasnewich D, Toro C, Latham L, Zein WM, Lehky T, Brewer C, Baker EH, Thurm A, Farmer CA, Rosenzweig SD, Lyons JJ, Schreiber JM, Gropman A, Lingala S, Ghany MG, Solomon B, Macnamara E, Davids M, et al. 2017. Prospective phenotyping of NGLY1-CDDG, the first congenital disorder of deglycosylation. Genetics in Medicine 19: 160–168. DOI: https://doi.org/10.1038/gim.2016.75, PMID: 27388694 Lewis J, Snyder M, Hyatt-Knorr H. 2017. Marking 15 years of the Genetic and Rare Diseases Information Center. Translational Science of Rare Diseases 2:77– 88. DOI: https://doi.org/10.3233/TRD-170011, PMID: 2 9152459 Lin XV, Socher R, Xiong C. 2018. Multi-hop knowledge graph reasoning with reward shaping. arXiv. https://arxiv.org/abs/1808.10568. Maiella S, Olry A, Hanauer M, Lanneau V, Lourghi H, Donadille B, Rodwell C, Köhler S, Seelow D, Jupp S, Parkinson H, Groza T, Brudno M, Robinson PN, Rath A. 2018. Harmonising phenomics information for a better interoperability in the rare disease field. European Journal of Medical Genetics 61:706–714. DOI: https://doi.org/10.1016/j.ejmg.2018.01.013, PMID: 29425702 Manske M. 2020. Mix’n’match. https://tools.wmflabs. org/mix-n-match/#/ Mayers MD, Su AI. 2020. SuLab/WD-rephetio-analysis: v1.1 release on 2020-01-21. Zenodo. http://doi.org/10. 5281/zenodo.3620811 Mayers MD, Stupp GS, Su AI. 2020. SuLab/ genewikiworld: v1.1 release on 2020-01-21. Zenodo. http://doi.org/10.5281/zenodo.3620812 McKusick VA. 2007. Mendelian Inheritance In Man and its online version, OMIM. The American Journal of Human Genetics 80:588–604. DOI: https://doi.org/10. 1086/514346, PMID: 17357067 Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, et al. 2019. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Research 47:D351–D360. DOI: https://doi.org/10.1093/nar/gky1100, PMID: 303 98656 Mora-Cantallops M, Sánchez-Alonso S, Garcı́aBarriocanal E. 2019. A systematic literature review on Wikidata. Data Technologies and Applications 53:250– 268. DOI: https://doi.org/10.1108/DTA-12-2018-0110 Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, et al. 2017. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research 45:D712–D722. DOI: https:// doi.org/10.1093/nar/gkw1128, PMID: 27899636 Nelson SJ, Zeng K, Kilbourne J, Powell T, Moore R. 2011. Normalized names for clinical drugs: RxNorm at 6 years. Journal of the American Medical Informatics Association 18:441–448. DOI: https://doi.org/10.1136/ amiajnl-2011-000116, PMID: 21515544

Waagmeester et al. eLife 2020;9:e52614. DOI: https://doi.org/10.7554/eLife.52614

Nielsen FA, Mietchen D, Willighagen E. 2017. Scholia, Scientometrics and Wikidata. In: Blomqvist E, Hose K, Paulheim H, Ławrynowicz A, Ciravegna F, Hartig O (Eds). The Semantic Web: ESWC 2017 Satellite Events, Lecture Notes in Computer Science. Springer International Publishing. p. 237–259. DOI: https://doi. org/10.1007/978-3-319-70407-4_36 Pawson AJ, Sharman JL, Benson HE, Faccenda E, Alexander SP, Buneman OP, Davenport AP, McGrath JC, Peters JA, Southan C, Spedding M, Yu W, Harmar AJ, NC-IUPHAR. 2014. The IUPHAR/BPS guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. Nucleic Acids Research 42:D1098–D1106. DOI: https://doi.org/10. 1093/nar/gkt1143, PMID: 24234439 Putman TE, Lelong S, Burgstaller-Muehlbacher S, Waagmeester A, Diesh C, Dunn N, Munoz-Torres M, Stupp GS, Wu C, Su AI, Good BM. 2017. WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. Database 2017:bax025. DOI: https://doi. org/10.1093/database/bax025 Putman T, Hybiske K, Jow D, Afrasiabi C, Lelong S, Cano MA, Wu C, Su AI. 2019. ChlamBase: a curated model organism database for the Chlamydia research community. Database 2019:baz041. DOI: https://doi. org/10.1093/database/baz041, PMID: 30985891 Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E. 2016. Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscriptionbased funding model. Database 2016:baw018. DOI: https://doi.org/10.1093/database/baw018, PMID: 26989150 Sansone SA, McQuilton P, Rocca-Serra P, GonzalezBeltran A, Izzo M, Lister AL, Thurston M, FAIRsharing Community. 2019. FAIRsharing as a community approach to standards, repositories and policies. Nature Biotechnology 37:358–367. DOI: https://doi. org/10.1038/s41587-019-0080-8, PMID: 30940948 Scholia. 2019. Scholia, ACE Inhibitor Pathway. https:// tools.wmflabs.org/scholia/pathway/Q29892242 Schriml LM, Mitraka E, Munro J, Tauber B, Schor M, Nickle L, Felix V, Jeng L, Bearer C, Lichenstein R, Bisordi K, Campion N, Hyman B, Kurland D, Oates CP, Kibbey S, Sreekumar P, Le C, Giglio M, Greene C. 2019. Human Disease Ontology 2018 update: classification, content and workflow expansion. Nucleic Acids Research 47:D955–D962. DOI: https://doi.org/ 10.1093/nar/gky1032, PMID: 30407550 Shin J-M. 2004. PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. Nucleic Acids Research 33:D238–D241. DOI: https://doi.org/ 10.1093/nar/gki059 Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E, Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida K, Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, et al. 2018. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Research 46:D661– D667. DOI: https://doi.org/10.1093/nar/gkx1064, PMID: 29136241 Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ,

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