Page:Wikidata as a knowledge graph for the life sciences.pdf/13

From Wikisource
Jump to navigation Jump to search
This page needs to be proofread.

Feature Article

Science Forum Wikidata as a knowledge graph for the life sciences Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Costanzo LD, Christie C, Duarte JM, Dutta S, Feng Z, Ghosh S, Goodsell DS, Green RK, Guranovic V, Guzenko D, Hudson BP, Liang Y, Lowe R, Peisach E, Periskova I, et al. 2019. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Research 47:D520–D528. DOI: https:// doi.org/10.1093/nar/gky949, PMID: 30357364 Caglayan AO, Comu S, Baranoski JF, Parman Y, Kaymakçalan H, Akgumus GT, Caglar C, Dolen D, Erson-Omay EZ, Harmanci AS, Mishra-Gorur K, Freeze HH, Yasuno K, Bilguvar K, Gunel M. 2015. NGLY1 mutation causes neuromotor impairment, intellectual disability, and neuropathy. European Journal of Medical Genetics 58:39–43. DOI: https://doi.org/10. 1016/j.ejmg.2014.08.008, PMID: 25220016 Chandras C, Weaver T, Zouberakis M, Smedley D, Schughart K, Rosenthal N, Hancock JM, Kollias G, Schofield PN, Aidinis V. 2009. Models for financial sustainability of biological databases and resources. Database 2009:bap017. DOI: https://doi.org/10.1093/ database/bap017, PMID: 20157490 Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M. 2014. Standardized description of scientific evidence using the Evidence Ontology (ECO). Database 2014: bau075. DOI: https://doi.org/10.1093/database/ bau075, PMID: 25052702 Cohen D. 2013. CC0 (+BY). https://dancohen.org/ 2013/11/26/cc0-by/ Das R, Dhuliawala S, Zaheer M, Vilnis L, Durugkar I, Krishnamurthy A, Smola A, McCallum A. 2017. Go for a walk and arrive at the answer: reasoning over paths in knowledge bases using reinforcement learning. arXiv. https://arxiv.org/abs/1711.05851. de Coronado S, Wright LW, Fragoso G, Haber MW, Hahn-Dantona EA, Hartel FW, Quan SL, Safran T, Thomas N, Whiteman L. 2009. The NCI Thesaurus quality assurance life cycle. Journal of Biomedical Informatics 42:530–539. DOI: https://doi.org/10.1016/ j.jbi.2009.01.003, PMID: 19475726 El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD. 2019. The Pfam protein families database in 2019. Nucleic Acids Research 47:D427–D432. DOI: https://doi.org/10. 1093/nar/gky995, PMID: 30357350 Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, Crimian R, Schoch K, Platt J, Cox R, Bernstein JA, Scavina M, Walter RS, Bibb A, Jones M, Hegde M, Graham BH, Need AC, Oviedo A, Schaaf CP, et al. 2014. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genetics in Medicine 16:751– 758. DOI: https://doi.org/10.1038/gim.2014.22, PMID: 24651605 Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, et al. 2018. The Reactome Pathway Knowledgebase. Nucleic Acids Research 46:D649– D655. DOI: https://doi.org/10.1093/nar/gkx1132, PMID: 29145629 Gabella C, Durinx C, Appel R. 2018. Funding knowledgebases: towards a sustainable funding model

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

for the UniProt use case. F1000Research 6:2051. DOI: https://doi.org/10.12688/f1000research.12989.2 Gil Y, Garijo D, Ratnakar V, Khider D, Emile-Geay J, McKay N. 2017. A Controlled Crowdsourcing Approach for Practical Ontology Extensions and Metadata Annotations. In: d’Amato C, Fernandez M, Tamma V, Lecue F, Cudré-Mauroux P, Sequeda J, Lange C, Heflin J (Eds). The Semantic Web – ISWC 2017, Lecture Notes in Computer Science. Springer International Publishing. p. 231–246. DOI: https://doi. org/10.1007/978-3-319-68204-4 Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, et al. 2017. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics 49:170–174. DOI: https://doi.org/10.1038/ng.3774, PMID: 28138153 Harding SD, Sharman JL, Faccenda E, Southan C, Pawson AJ, Ireland S, Gray AJG, Bruce L, Alexander SPH, Anderton S, Bryant C, Davenport AP, Doerig C, Fabbro D, Levi-Schaffer F, Spedding M, Davies JA, NC-IUPHAR. 2018. The IUPHAR/BPS guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. Nucleic Acids Research 46:D1091–D1106. DOI: https://doi.org/10.1093/nar/ gkx1121, PMID: 29149325 Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, Green A, Khankhanian P, Baranzini SE. 2017. Systematic integration of biomedical knowledge prioritizes drugs for repurposing. eLife 6: e26726. DOI: https://doi.org/10.7554/eLife.26726, PMID: 28936969 Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, et al. 2010. MassBank: a public repository for sharing mass spectral data for life sciences. Journal of Mass Spectrometry 45:703–714. DOI: https://doi.org/10. 1002/jms.1777, PMID: 20623627 Jacobsen A, Kaliyaperumal R, Stupp GS, Schriml LM, Thompson M, Su AI, Roos M. 2018. Wikidata as an intuitive resource towards semantic data modeling in data FAIRification. In: Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, {SWAT4LS} 2018, Antwerp, Belgium, December 3-6, 2018. 2275 CEURWS.org. Köhler S, Schulz MH, Krawitz P, Bauer S, Dölken S, Ott CE, Mundlos C, Horn D, Mundlos S, Robinson PN. 2009. Clinical diagnostics in human genetics with semantic similarity searches in ontologies. The American Journal of Human Genetics 85:457–464. DOI: https://doi.org/10.1016/j.ajhg.2009.09.003, PMID: 19800049 Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, et al. 2017. The Human Phenotype Ontology in 2017. Nucleic Acids Research 45:D865–D876. DOI: https://doi.org/10. 1093/nar/gkw1039, PMID: 27899602

13 of 15