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Literature DB >> 17094225

Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.

Helen L Johnson¹, K Bretonnel Cohen, William A Baumgartner, Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter.

Abstract

We used exact term matching, stemming, and inclusion of synonyms, implemented via the Lucene information retrieval library, to discover relationships between the Gene Ontology and three other OBO ontologies: ChEBI, Cell Type, and BRENDA Tissue. Proposed relationships were evaluated by domain experts. We discovered 91,385 relationships between the ontologies. Various methods had a wide range of correctness. Based on these results, we recommend careful evaluation of all matching strategies before use, including exact string matching. The full set of relationships is available at compbio.uchsc.edu/dependencies.

Entities: Chemical

Mesh：

Year: 2006 PMID： 17094225 PMCID： PMC1810343

Source DB: PubMed Journal: Pac Symp Biocomput ISSN： 2335-6928

15 in total

Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.

1. Linking biomedical language information and knowledge resources: GO and UMLS.

2. Evaluation of ontology merging tools in bioinformatics.

3. BRENDA, the enzyme database: updates and major new developments.

4. The compositional structure of Gene Ontology terms.

5. Non-lexical approaches to identifying associative relations in the gene ontology.

6. Implications of compositionality in the gene ontology for its curation and usage.

7. Finding GeneRIFs via gene ontology annotations.

8. Overview of BioCreAtIvE: critical assessment of information extraction for biology.

9. An ontology for cell types.

10. Obol: integrating language and meaning in bio-ontologies.

1. Creating mappings for ontologies in biomedicine: simple methods work.

2. Enrichment of OBO ontologies.

3. A fault model for ontology mapping, alignment, and linking systems.

4. Decompositional terminology translation using network analysis.

5. Automated comparative auditing of NCIT genomic roles using NCBI.

6. Development of the Gender, Sex, and Sexual Orientation ontology: Evaluation and workflow.

7. A network-theoretic approach for decompositional translation across Open Biological Ontologies.

8. Ontology translation: A case study on translating the Gene Ontology from English to German.

9. Improving precision in concept normalization.

10. Ontology quality assurance through analysis of term transformations.