| URL: | http://www.ontologyfingerprint.org |
| Full name: | Ontology Fingerprints |
| Description: | Ontology Fingerprint for a gene or a disease is a set of Gene Ontology terms overrepresented in the PubMed abstracts linked to a gene or disease along with those terms corresponding enrichment p-values. |
| Year founded: | 2015 |
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| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | United States |
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| University/Institution: | University of Texas Health Science Center at Houston |
| Address: | Center for Computational Biomedicine, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA |
| City: | Houston |
| Province/State: | Texas |
| Country/Region: | United States |
| Contact name (PI/Team): | W. Jim Zheng |
| Contact email (PI/Helpdesk): | wenjin.j.zheng@uth.tmc.edu |
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Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. [PMID: 25858285]
Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles. Database URL: http://www.ontologyfingerprint.org |