Taxonomic names, metadata, and the Semantic Web

Page, Roderic

doi:10.17161/bi.v3i0.25

Cited by 49 publications

(44 citation statements)

References 16 publications

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“…An obvious extension to current publishing practice is to extend linking to these additional objects, thus building a web of data biodiversity data [6,7]. Some publishers have made efforts in this direction.…”

Section: Datamentioning

confidence: 99%

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Page

2008

Nature Precedings

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This paper describes my entry in the Elsevier Grand Challenge "Knowledge Enhancement in the Life Sciences" contest. The entry takes a collection of fulltext issues of Molecular Phylogenetics and Evolution as the starting point, then extracts citation links to both papers and data, such as Genbank sequences and specimens, together with geotagged localities, and builds a "web" of objects linked by typed relationships. Each object (such as a publication, a sequence, a specimen, a taxon name, etc.) is treated equally, so that you can take a publication and see what taxa it refers to, or take the taxon and find all the publications that refer to the taxon. Although the database has been seeded with some articles from Molecular Phylogenetics and Evolution, much of the data comes from GenBank, PubMed, and specimen databases. These are accessed through http://bioguid.info, a tool I constructed to resolve globally unique identifiers and return associated metadata.

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Section: Datamentioning

confidence: 99%

“…• GUID, Globally Unique Identifier 6 There seems to be some confusion among publishers as to what "Open Access" means. See [33] for an explicit statement that licenses such as the Creative Commons Attribution License and the Creative Commons Attribution Non-Commercial License are consistent with Open Access.…”

Section: Abbreviationsmentioning

confidence: 99%

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2008

Nature Precedings

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“…For this purpose, management of information about plants and animals is needed, a task requiring an efficient usage of heterogeneous, dynamic biological data from distributed sources, such as observational records, literature, and natural history collections. Central resources in biodiversity management are names and ontological taxonomies of organisms [1,19,20,3,4]. Animal ontologies are stereotypical examples in the semantic web text books, but in reality semantic web technologies have hardly been applied to managing the real life taxonomies of biological organisms and biodiversity on the web.…”

Section: Introductionmentioning

confidence: 99%

Biological Names and Taxonomies on the Semantic Web – Managing the Change in Scientific Conception

Tuominen

Laurenne

Hyvönen

2011

The Semanic Web: Research and Applications

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Abstract. 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.

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“…Modeling and managing scientific and common names is not trivial [2,3] because names change over time. For example, a species may be shifted into another genus, which is reflected in the scientific name.…”

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The Birds of the World Ontology AVIO

Tuominen

Laurenne

Koho

et al. 2013

Advanced Information Systems Engineering

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Abstract. We present an ontology for managing the scientific and common names of birds. The ontology is based on the TaxMeOn metaontology model for biological names. The ontology is in use as an ontology service and it has been applied in a bird watching system.Biologists refer to organisms by using scientific names although most people use common (vernacular) names. Modeling and managing scientific and common names is not trivial [2,3] because names change over time. For example, a species may be shifted into another genus, which is reflected in the scientific name.We present "The Birds of the World Ontology AVIO" 1 encompassing all bird taxa of the world, including their scientific names and common names in English, Finnish, and Swedish. The ontology is an application of our earlier work, the meta-ontology model TaxMeOn for biological names and classifications [3]. The aim of the AVIO ontology is to provide a reference to the species names of the birds, e.g., for indexing bird related information.The AVIO ontology is available as open data and as an operational ontology service in the Finnish Ontology Library Service ONKI [4]. The ontology has been used in an online mobile birding system BirdWatch 2 [1]. AVIO OntologyThe AVIO Ontology is based on the Finnish names of the birds of the world published by BirdLife Finland 3 , containing the common names for all the species of the world including their higher taxa-9,740 species, 1,227 genera, and 194 families. The English names and the scientific names are included, too. A CSV formatted species list was provided by BirdLife, and was converted into an RDF-based ontology conforming to the TaxMeOn schema. The classification of taxa was completed with additional higher level taxa.The CSV formatted species list contained a scientific name and its common name equivalents per line. The hierarchy between the scientific names was expressed using hierarchically numbered identifiers for the names (e.g., 061.0449. Sterna and 061.0449.1664 Sterna paradisaea). In the RDF conversion, every scientific and common name was given a URI and the relations between them 1 This work is part of the FinnONTO project (http://www.seco.tkk.fi/projects/ finnonto/) funded mainly by Tekes. 2

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Taxonomic names, metadata, and the Semantic Web

Cited by 49 publications

References 16 publications

Visualising a scientiﬁc article

Visualising a scientiﬁc article

Biological Names and Taxonomies on the Semantic Web – Managing the Change in Scientific Conception

The Birds of the World Ontology AVIO

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