Semantically linking and browsing PubMed abstracts with gene ontology

Semantically Linking and Browsing Provenance Logs for E-science

e-Science experiments are those performed using computerbased resources such as database searches, simulations or other applications. Like their laboratory based counterparts, the data associated with an e-Science experiment are of reduced value if other scientists are not able to identify the origin, or provenance, of those data. Provenance is the term given to metadata about experiment proces...

GoPubMed: exploring PubMed with the Gene Ontology

The biomedical literature grows at a tremendous rate and PubMed comprises already over 15 000 000 abstracts. Finding relevant literature is an important and difficult problem. We introduce GoPubMed, a web server which allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology. GoPubMed provides the following benefits: ...

PSE: A Tool for Browsing a Large Amount of PubMed Abstracts with Gene Names and Common Words as the Keywords

Knowledge Retrieval from PubMed Abstracts and Electronic Medical Records with the Multiple Sclerosis Ontology

BACKGROUND In order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS). METHODS The MS Ontology was created using scientific literature and expert review under the Protégé OWL environment. We developed a dictionary with semantic synonyms and translations to different languages for mining ...

GO2PUB: Querying PubMed with semantic expansion of gene ontology terms

BACKGROUND With the development of high throughput methods of gene analyses, there is a growing need for mining tools to retrieve relevant articles in PubMed. As PubMed grows, literature searches become more complex and time-consuming. Automated search tools with good precision and recall are necessary. We developed GO2PUB to automatically enrich PubMed queries with gene names, symbols and syno...