SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology
SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology
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DOI：
10.1093/bioinformatics/btaa106
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发表时间：
2020-05-15
期刊：
影响因子：
5.8
通讯作者：
Cui，Licong
中科院分区：
文献类型：
--
作者：
Abeysinghe，Rashmie;Hinderer，Eugene W.;Cui，Licong
基因本体论（GO）是一个统一的生物学词汇，用于编纂、管理和共享生物学知识。GO中的质量问题如果不解决，可能会导致误导性结果或错过生物学发现。鉴于GO的规模不断扩大，手动识别GO中的潜在质量问题是一项具有挑战性和艰巨的任务。我们引入了一个自动化的审计方法，建议潜在的missingis-arelations，这可能会进一步揭示conceousis-arelations.ResultsWe开发了一个基于包容的子项推理框架（SSIF），利用一个新的术语代数上的一个基于序列的表示GO概念沿着与三个条件规则（单调性，交集和子概念规则）。将SSIF应用于2018年10月3日发布的GO，表明1938个独特的潜在缺失关系。领域专家评估了210个潜在缺失关系的随机样本。结果表明，SSIF对单调性、交集和子概念规则的准确率分别为60.61%、60.49%和46.03%。源代码可在https://github.com/rashmie/SSIF.Supplementary上获得信息补充数据可在Bioinformaticsonline上获得。
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 missingis-arelations, which may further reveal erroneousis-arelations.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 missingis-arelations. Domain experts evaluated a random sample of 210 potentially missingis-arelations. 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 implementationSSIF is implemented in Java. The source code is available at https://github.com/rashmie/SSIF.Supplementary informationSupplementary data are available atBioinformaticsonline.