- Large-scale extraction of gene regulation for model organisms in an ontological contextJasmin Saric
European Media Laboratory GmbH, D 69118 Heidelberg, Germany
In Silico Biol 5:21-32. 2005..The main reason for the comparable precision rates is the ontological model that was built beforehand and served as a guiding force for the manual coding of the syntactosemantic rules...
- Extraction of regulatory gene/protein networks from MedlineJasmin Saric
EML Research gGmbH D 69118 Heidelberg, Germany
Bioinformatics 22:645-50. 2006..The biomedical literature, however, contains information on several other equally important regulatory mechanisms, in particular phosphorylation, which we now expanded for our rule-based system also to extract...
- Notes on the use of ontologies in the biochemical domainIsabel Rojas
Scientific Databases and Visualisation Group, EML Research, Heidelberg, Germany
In Silico Biol 4:89-96. 2004..The paper does not intend to be a thorough review of the existing work in the area. It highlights the uses that are given to ontologies in the Scientific Databases and Visualisation Group at EML Research, in Heidelberg...
- A database system for the analysis of biochemical pathwaysIsabel Rojas
European Media Laboratory, Heidelberg, Germany
In Silico Biol 2:75-86. 2002..In this paper we describe the general structure of our system, concentrating on the ontology-based database as the key component of the system...
- Literature mining for the biologist: from information retrieval to biological discoveryLars Juhl Jensen
European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
Nat Rev Genet 7:119-29. 2006..However, the latter will require the integration of literature and high-throughput data, which should encourage close collaborations between biologists and computational linguists...