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Biological Ontologies and Vocabularies

SeCo is developing taxonomical ontologies and vocabularies of organisms and their names (checklists), and publishing them as services on the Semantic Web using the ONKI Ontology Service. Our goal is provide the public and researchers with easy to use services for finding out names of organisms in different languages, support semantic indexing of content using the URIs of taxa, facilitate biological data integration from different sources, places, and eras (publications, databases, observations, museum collections), and support development of semantic applications in the biology domain (query expansion, semantic linking etc.).

In 2009, we first transformed the checklists 'Mammals of the World' and 'Birds of the World', obtained from the Finnish Museum of Natural History and BirdLife, into SKOS vocabularies/ontologies. Based on this experiment, our goal is to publish all suitable checklists of organisms, used in the Finnish Museum of Natural History. The material includes many categories of insects, plants etc., altogether some 88,000 species.

On the research side, an ontological model for representing taxonomic data is being developed and integrated with the checklists.

The ontologies developed can be found on the ONKI Service.

Our work is part of the national FinnONTO programme aiming at developing a national semantic web ontology infrastructure in Finland.

Publications

2011

Nina Laurenne, Jouni Tuominen, Katharina Schleidt and Eero Hyvönen: Observing observations - an ontology-based approach for improving the reliability of biodiversity data. TDWG 2011 Annual Conference of the Taxonomic Databases Working Group, New Orleans, Lousiana, USA, October, 2011. Poster abstract. bib pdf
Nina Laurenne, Jouni Tuominen and Eero Hyvönen: Radiation of beetles into cyberspace - two case studies of modelling taxonomic information. TDWG 2011 Annual Conference of the Taxonomic Databases Working Group, New Orleans, Lousiana, USA, October, 2011. Poster abstract. bib pdf
Nina Laurenne, Jouni Tuominen, Arto Mertaniemi, Hannu Saarenmaa and Eero Hyvönen: LSID versus HTTP URI: Two approaches and e-infrastructures for managing information about taxon names. EIM 2011 Conference, Santa Barbara, California, USA, September, 2011. Poster abstract. bib pdf
Jouni Tuominen, Nina Laurenne and Eero Hyvönen: Biological Names and Taxonomies on the Semantic Web - Managing the Change in Scientific Conception. Proceedings of the 8th Extended Semantic Web Conference (ESWC 2011), Springer-Verlag, Heraklion, Greece, June, 2011. bib pdf
Biodiversity management requires the usage of heterogeneous biological information from multiple sources. Indexing, aggregating, and finding such information is based on names and taxonomic knowledge of organisms. However, taxonomies change in time due to new scientific findings, opinions of authorities, and changes in our conception about life forms. Furthermore, organism names and their meaning change in time, different authorities use different scientific names for the same taxon in different times, and various vernacular names are in use in different languages. This makes data integration and information retrieval difficult without detailed biological information. This paper introduces a meta-ontology for managing the names and taxonomies of organisms, and presents three applications for it: 1) publishing biological species lists as ontology services (ca. 20 taxonomies including more than 80,000 names), 2) collaborative management of the vernacular names of vascular plants (ca. 26,000 taxa), and 3) management of individual scientific name changes based on research results, covering a group of beetles. The applications are based on the databases of the Finnish Museum of Natural History and are used in a living lab environment on the web.

2010

Nina Laurenne, Jouni Tuominen, Mikko Koho and Eero Hyvönen: Taxon Meta-Ontology TaxMeOn - Towards an Ontology Model for Managing Changing Scientific Names in Time. TDWG 2010 Annual Conference of the Taxonomic Databases Working Group, Woods Hole, Massachusetts, USA, September, 2010. Contributed abstract. bib pdf
Jouni Tuominen, Matias Frosterus, Nina Laurenne and Eero Hyvönen: Publishing Biological Classifications as SKOS Vocabulary Services on the Semantic Web. TDWG 2010 Annual Conference of the Taxonomic Databases Working Group, Woods Hole, Massachusetts, USA, September, 2010. Demonstration abstract. bib pdf
Nina Laurenne, Jouni Tuominen, Mikko Koho and Eero Hyvönen: Modeling and Publishing Biological Names and Classifications on the Semantic Web. TDWG 2010 Annual Conference of the Taxonomic Databases Working Group, Woods Hole, Massachusetts, USA, September, 2010. Poster abstract. bib pdf

2009

Jouni Tuominen, Matias Frosterus, Kim Viljanen and Eero Hyvönen: ONKI SKOS Server for Publishing and Utilizing SKOS Vocabularies and Ontologies as Services. Proceedings of the 6th European Semantic Web Conference (ESWC 2009), Heraklion, Greece, May 31 - June 4, 2009. Springer-Verlag. bib pdf
Vocabularies are the building blocks of the Semantic Web providing shared terminological resources for content indexing, information retrieval, data exchange, and content integration. Most semantic web applications in practical use are based on lightweight ontologies and, more recently, on the Simple Knowledge Organization System (SKOS) data model being standardized by W3C. Easy and cost-efficient publication, integration, and utilization methods of vocabulary services are therefore highly important for the proliferation of the Semantic Web. This paper presents the ONKI SKOS Server for these tasks. Using ONKI SKOS, a SKOS vocabulary or a lightweight ontology can be published on the web as ready-to-use services in a matter of minutes. The services include not only a browser for human usage, but also Web Service and AJAX interfaces for concept finding, selecting and transporting resources from the ONKI SKOS Server to connected systems. Code generation services for AJAX and Web Service APIs are provided automatically, too. ONKI SKOS services are also used for semantic query expansion in information retrieval tasks. The idea of publishing ontologies as services is analogous to Google Maps. In our case, however, vocabulary services are provided and mashed-up in applications. ONKI SKOS was published in the beginning of 2008 and is to our knowledge the first generic SKOS server of its kind. The system has been used to publish and utilize some 60 vocabularies and ontologies in the National Finnish Ontology Service ONKI www.yso.fi.

Contact Information

PhD Nina Laurenne
University of Helsinki and Aalto University
nina.laurenne [at] helsinki.fi

MSc Jouni Tuominen
University of Helsinki and Aalto University
jouni.tuominen [at] tkk.fi

Professor Eero Hyvönen
Aalto University and University of Helsinki
eero.hyvonen [at] tkk.fi

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