Establishing a distributed system for the simple representation and integration of diverse scientific assertions.

Journal of Biomedical Semantics
Matthias Samwald, Holger Stenzhorn

Abstract

Information technology has the potential to increase the pace of scientific progress by helping researchers in formulating, publishing and finding information. There are numerous projects that employ ontologies and Semantic Web technologies towards this goal. However, the number of applications that have found widespread use among biomedical researchers is still surprisingly small. In this paper we present the aTag ('associative tags') convention, which aims to drastically lower the entry barriers to the biomedical Semantic Web. aTags are short snippets of HTML+RDFa with embedded RDF/OWL based on the Semantically Interlinked Online Communities (SIOC) vocabulary and domain ontologies and taxonomies, such as the Open Biomedical Ontologies and DBpedia. The structure of aTags is very simple: a short piece of human-readable text that is 'tagged' with relevant ontological entities. This paper describes our efforts for seeding the creation of a viable ecosystem of datasets, tools and services around aTags. Numerous biomedical datasets in aTag format and systems for the creation of aTags have been set-up and are described in this paper. Prototypes of some of these systems are accessible at http://hcls.deri.org/atag The aTags convention...Continue Reading

References

May 17, 2005·Genome Biology·Barry SmithCornelius Rosse
Oct 6, 2005·Bioinformatics·Robert Hoffmann, Alfonso Valencia
Nov 17, 2007·Bioinformatics·Dietrich Rebholz-SchuhmannAntonio Jimeno
Mar 11, 2008·FEBS Letters·Giulio Superti-FurgaGiovanni Cesareni
Apr 11, 2008·Bioinformatics·Jung-Jae KimDietrich Rebholz-Schuhmann
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Dec 17, 2009·Artificial Intelligence in Medicine·Matthias SamwaldKei-Hoi Cheung

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Citations

Nov 15, 2012·Nature Reviews. Genetics·Dietrich Rebholz-SchuhmannRobert Hoehndorf

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Software Mentioned

BioPortal webservice
Open Biomedical Annotator
Whatizit
Open ( OBO ) Foundry
Solr
EBI Whatizit
Apache Lucene
aTag explorer
RDFa
Turtle

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