OpenBiodiv Poster: an Implementation of a Semantic System Running on top of the Biodiversity Knowledge Graph

• Published in: Biodiversity Information Science and Standards 2017-08, Vol.1, p.e20246
• Main Authors: Senderov, Viktor, Georgiev, Teodor, Agosti, Donat, Catapano, Terry, Sautter, Guido, Ó Tuama, Éamonn, Franz, Nico, Simov, Kiril, Stoev, Pavel, Penev, Lyubomir
• Format: Article
• Language: English
• Subjects: Biodiversity; Information systems; Knowledge management; Linked Data; Names; Ontology; Running; Semantics; Taxonomy
• ISSN: 2535-0897; 2535-0897
• DOI: 10.3897/tdwgproceedings.1.20246

We presentOpenBiodiv- an implementation of the Open Biodiversity Knowledge Management System. The need for an integrated information system serving the needs of the biodiversity community can be dated at least as far back as the sanctioning of theBouchout declarationin 2007. The Bouchout declaration proposes to make biodiversity knowledge freely available as Linked Open Data (LOD)*1. At TDWG 2016 (Fig.1) we presented the prototype of the system - then called Open Biodiversity Knolwedge Management System (OBKMS) (Senderov et al. 2016). The specification and design of OpenBiodiv was then outlined in more detail bySenderov and Penev (2016). In this poster, we describe the pilot implementation. We believe OpenBiodiv is possibly the first pilot-stage implementation of a semantic system running on top of a biodiversity knowledge graph. OpenBiodiv has several components: OpenBiodiv ontology: A general data model supporting the extraction of biodiversity knowledge from taxonomic articles or from databases such as GBIF. The ontology (in preparation, Journal of Biomedical Semantics, available on GitHub) incorporates several pre-existing models: Darwin-SW (Baskauf and Webb 2016), SPAR (Peroni 2014), Treatment Ontology, and several others. It defines classes, properties, and rules supporting the interlinking of these disparate ontologies to create a LOD biodiversity knowledge graph. A new addition is the Taxonomic Name Usage class, accompanied by a Vocabulary of Taxonomic Statuses (created via an analysis of 4, 000 Pensoft articles) enabling for the automated inference of the taxonomic status of Latinized scientific names. The ontology supports multiple backbone taxonomies via the introduction of a Taxon Concept class (equivalent to DarwinCore Taxon) and Taxon Concept Labels as a subclass of biological name. The Biodiversity Knowledge Graph: A LOD dataset of information extracted from taxonomic literature and databases. To date, this resource has realized part of what was proposed during thepro-iBiosphereproject and later discussed byPage (2016). Its main resources are articles, sub-article componets (tables, figures, treatents, references), author names, institution names, geographical locations, biological names, taxon concepts, and occurrences. Authors have been disambiguated via their affiliation with the use of fuzzy-logic based on theGraphDB Lucene connector. The graph interlinks: (1) Prospectively published literature viaPensoft Publishers.(2) Legacy literature