OpenBiodiv Computer Demo: an Implementation of a Semantic System Running on top of the Biodiversity Knowledge Graph
We presentOpenBiodiv- an implementation of the Open Biodiversity Knowledge Management System. We believe OpenBiodiv is possibly the first pilot-stage implenatation of a semantic system running on top of the biodiversity knowledge graph. The need for an integrated information system serving the needs...
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| Published in: | Biodiversity Information Science and Standards 2017-08, Vol.1, p.e20193 |
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| Main Authors: | , , , , , , , , , |
| Format: | Article |
| Language: | eng |
| Subjects: | |
| Online Access: | Get full text |
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| Summary: | We presentOpenBiodiv- an implementation of the Open Biodiversity Knowledge Management System. We believe OpenBiodiv is possibly the first pilot-stage implenatation of a semantic system running on top of the biodiversity knowledge graph. 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 TDWG2016 (Fig.1) we presented the prototype of the sytem - then called Open Biodiversity Knolwedge Management System (OBKMS). The specification and design of OpenBiodiv was outlined bySenderov and Penev (2016)and in this computer demo we would like to showcase its pilot. We will show how to use the SPARQL*2endpoint directly, we will illustrate the semantic search capabilities of the system, and we will showcase some high-level applications that run on top of it. We will also look at the core dataset (the Biodiversity Knowledge Graph) and the R tools used to create it. OpenBiodiv has several components: OpenBiodiv ontology: general data model allowing 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 allowing to interlink these disparate ontologies and to create a LOD of biodiversity knowledge. New is the Taxonomic Name Usage class, accompanied by a Vocabulary of Taxonomic Statuses (created via an analysis of 4, 000 Pensoft articles) allowing for the automated inference of the taxonomic status of Latinized scientific names. The ontology allows for 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. In practice, it has realized part of what has been proposed duringpro-iBiosphereand 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 occur |
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| ISSN: | 2535-0897 2535-0897 |