HCLSIG BioRDF Subgroup/RDFa text annotation service

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This page should give an overview of RDFa-based, biomedical text annotation services on the web.

Science Commons text annotation service


This service recognizes entities and relations from biomedical texts and and returns documents in Semantic Web formats (OWL, RDFa). You can use Semantic Web software to easily query, integrate and visualize the relevant information. Currently, the service can recognize entities from Gene Ontology, ChEBI, some smaller OBO ontologies, Uniprot and NCBI Taxonomy. Bibliographical information about articles is provided in the Dublin Core metadata standard.

Using the Science Commons text annotation service to create aTags

aTags are a simple convention for representening assertions (facts, hypotheses, ideas etc.). They are encoded in RDF and are often found embedded in HTML pages (in the RDFa syntax). The Science Commons text annotation service can generate aTags out of sentences found in PubMed abstracts.

The text is analyzed by the Whatizit webservice of EBI. See http://www.ebi.ac.uk/webservices/whatizit/info.jsf for further information, such as the processing pipelines offered by the service.


Query for 10 Pubmed abstracts with the search term "nmda receptor", using the "whatizitEBIMedDiseaseChemicals" analysis pipeline:


Note that you could yield the same results with a shorter URI by using the default settings:


Look at the results. The "<a>" signs carry embedded RDF statements. You could potential copy & paste them to other HTML-based applications, carrying the embedded data along. So what kind of data is embedded in the page? Let's have a look.

RDF/XML extracted from these results:


Instead of querying for several PubMed abstracts with a PubMed query string, we can also analyze a specific PubMed abstract based on its PubMed ID. For example:


Result converted to RDF/XML format:


Contact for further information: Matthias Samwald ([6])

Other services

Add other services here