ArticleBioinformatics (Oxford, England)2020
SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations.Briefings in bioinformatics · 2022Article
- A Comparison of Exhaustive and Non-lattice-based Methods for Auditing Hierarchical Relations in Gene Ontology.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2021Article
- A lexical-based approach for exhaustive detection of missing hierarchical IS-A relations in SNOMED CT.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2020Article
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Authors and funding
4 authors.
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Abstract
motivationThe Gene Ontology (GO) is the unifying biological vocabulary for codifying, managing and sharing biological knowledge. Quality issues in GO, if not addressed, can cause misleading results or missed biological discoveries. Manual identification of potential quality issues in GO is a challenging and arduous task, given its growing size. We introduce an automated auditing approach for suggesting potentially missing is-a relations, which may further reveal erroneous is-a relations.
resultsWe developed a Subsumption-based Sub-term Inference Framework (SSIF) by leveraging a novel term-algebra on top of a sequence-based representation of GO concepts along with three conditional rules (monotonicity, intersection and sub-concept rules). Applying SSIF to the October 3, 2018 release of GO suggested 1938 unique potentially missing is-a relations. Domain experts evaluated a random sample of 210 potentially missing is-a relations. The results showed SSIF achieved a precision of 60.61, 60.49 and 46.03% for the monotonicity, intersection and sub-concept rules, respectively. AVAILABILITY AND IMPLEMENTATION: SSIF is implemented in Java. The source code is available at https://github.com/rashmie/SSIF. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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