Aligning the parasite experiment ontology and the ontology for biomedical investigations using agreementmaker
Year: 2011
Type: article
Abstract: . Tremendous amounts of data exist in life sciences along with many bio-ontologies. Though these databases contain important infor-mation about gene, proteins, functions, etc., this information is not well utilized due to the heterogeneous formats of these databases. Therefore, ontology alignment (OA) is now very critical for life science domain. Our work utilizes AgreementMaker for OA and describes results, difficulties faced in the process, and lessons learned. We aligned two real-world on-tologies, the Parasite Experiment Ontology (PEO) and the Ontology for Biomedical Investigations (OBI). The former is more application-oriented and the latter is a reference ontology for any biomedical or clinical investigations. Our study led to several enhancements to Agree-mentMaker: annotation profiling, mapping provenance information, and tailored lexicon building. These enhancements, which are applicable to any OA system, greatly improved the alignment of these real world on-tologies, producing 90 % precision with 60 % recall from the BSMlex+, the Base Similarity Matcher, and 57 % precision with 67 % recall from the PSMlex+, the Parametric String Matcher, both using lexicon lookup for synonyms. The mappings obtained through this study are posted on BioPortal site for public use.
Language: English
Subfield: Health Informatics
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W1604017289