Motivation Applications for Modeling Life Science data in Wikidata. Tim E. Putman1, Sebastian Burgstaller-Muehlbacher1, Andra Waagmeester2, Chunlei Wu1, Andrew I. Su1, and Benjamin M. Good1 1 Department of Integrative, Structural and Computational Biology, the Scripps Research Institute, La Jolla, USA 2 Micelio, Antwerp, Belgium Wikidata provides an extensible open framework ideal for aggregating distributed data in a centralized database that supports: •complex querying based a semantic data model •providing data for domain speciﬁc web applications that allow the user to both read and write data A A) Semantic microbial data model consisting of a hierarchical taxonomic schema and separate entities for gene and protein. The nodes are Wikidata ‘items’ and ‘properties’ deﬁne the relationships. B) Python based ‘Bot’ software for gathering data from different resources and reading and writing directly to Wikidata (https:// github.com/SuLab/WikidataIntegrator). Bacteria (Q10876) domain C. trachomatis 434/BU (Q20800254) strain trpA (Q21153861) gene TRPA (Q21153984) protein found in taxon (P703) parent taxon (P171) encodes (P688) encoded by (P702) subclass of (P279) Entrez ID (P351) gen. start (P644) gen. stop (P645) subclass of (P279) UniProt ID (P352) RefSeq ID (P637) molecular function (P680) locus tag (P2393) C. trachomatis (Q131065) species biological process (P681) cell component (P682) Data model and implementation B Figure2. NCBI Genome Assemblies. A) Various data sources for microbial genetic data. B) Cumulative sum of bacterial and eukaryotic genome assemblies submitted to NCBI GenBank by year. A B Scope and diversity of microbial data 0 10000 20000 30000 40000 50000 60000 70000 80000 90000 100000 Bacteria Eukaryotes Sequenced Genomes Modeling microbial interactions trpA C. trachomatis genome www.ncbi.nlm.nih.gov/ genome/ indole www.drugbank.ca/ Chlamydia trachomatis: genes www.ncbi.nlm.nih.gov/gene/ Human: indoleamine 2, 3-dioxygenase www.uniprot.org/ tryptophanase www.uniprot.org/ C.trachomatis: trp. synth. alpha and beta www.uniprot.org/ C.trachomatis: tryptophan synthase www.rhea-db.org C.trachomatis: trpRBA operon www.operondb.jp/ Akers et al. 2006 trpB trpR organismLabel Escherichia coli IAI39 Treponema denticola ATCC 35405 Yersinia enterocolitica subsp. enterocolitica 8081 Aeromonas hydrophila subsp. hydrophila ATCC 7966 Vibrio cholerae O1 biovar El Tor str. N16961 Vibrio parahaemolyticus RIMD 2210633 Fusobacterium nucleatum subsp. nucleatum ATCC 25586 Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough Salinibacter ruber DSM 13855 Escherichia coli UMN026 Escherichia coli O104:H4 str. 2011C-3493 Escherichia coli O83:H1 str. NRG 857C A) The interactions between host, pathogen, microbiome, and small molecules that lead to pathogen persistence during a chlamydial infection in humans (originally hypothesized by Caldwell et al. 2003). Blue URLs indicate source of data and edges are deﬁned by properties in Wikidata. B) SPARQL query results for organisms that are capable of producing indole . A B. Organisms that produce indole Acknowledgements We would like to thank Lynn Schriml and Elvira Mitraka of the University of Maryland, the members of The Apollo Project and the many members of the Wikidata community for valuable contributions to this project. References/Funding Caldwell et al. 2003 (PMID:12782678) Putman et al. 2016 (PMID:27022157) Burgstaller-Muehlbacher et al. 2015 (PMID: 26989148) This work is supported by the National Institutes of Health under grant GM089820, GM083924, GM114833 and DA036134. Domain Speciﬁc Portals into Wikidata A) WikiGenomes: a centralized model organism database for bacterial reference genomes that supports community annotation. B) Wikidata as the universal, community owned, backend database for any domain speciﬁc application. A B L-tryptophan www.drugbank.ca/ N-Formylkynurenine www.drugbank.ca/