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Employing the Inference Rules of Predicate Logic for Predicting Protein Functions

机译：利用谓词逻辑推理规则预测蛋白质功能

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The functions of a protein can be inferred from the molecules that associate with it. A protein-molecules association can be identified from their co-occurrences in biomedical literature. Based on this, recent computational methods predict protein functions, especially with the exponential explosion of biomedical literatures post-genomic era. These methods extract information from the literatures that explicitly describe the functions of proteins. We observe that some molecule terms pertaining protein functions may co-occur implicitly with proteins in biomedical texts. Thus, these recent methods may miss vital information about protein functions that is implicitly mentioned in the literature. To overcome this, we propose an Information Extraction system called PLPF that adopts techniques for predicting the functions of proteins from their both explicit and implicit co-occurrences in biomedical texts with molecule terms pertaining protein functions. It uses a combination of explicit term extraction methods and logic-based implicit term extraction methods. Let t be a functional term that co-occurrence with an unannotated protein pu. PLPF will assign pu the functional category t, if: (1) the co-occurrences of the pair t-pu are explicit and the pair is semantically related bases on the syntactic structures of sentences, or (2) the co-occurrences of the pair t-pu are implicit based on the inference rules of predicate logic. We evaluated PLPF by comparing it experimentally with four existing methods. Results showed marked improvement.
机译：蛋白质的功能可以从与蛋白质结合的分子中推断出来。可以从生物医学文献中它们的共现中识别出蛋白质-分子的关联。基于此，最近的计算方法可以预测蛋白质的功能，尤其是在基因组时代后生物医学文献呈指数级增长的情况下。这些方法从明确描述蛋白质功能的文献中提取信息。我们观察到一些与蛋白质功能有关的分子术语可能与生物医学文献中的蛋白质隐含地同时出现。因此，这些最近的方法可能会错过文献中隐含提及的有关蛋白质功能的重要信息。为了克服这个问题，我们提出了一种称为PLPF的信息提取系统，该系统采用了从生物医学文本中具有蛋白质功能相关分子术语的显式和隐式共现来预测蛋白质功能的技术。它结合了显式术语提取方法和基于逻辑的隐式术语提取方法。令t为与未注释蛋白pu共存的功能性术语。如果满足以下条件，则PLPF将为pu分配功能类别t：（1）t-pu对的共现是显性的，并且该对基于句子的句法结构在语义上相关，或者（2）对t-pu对基于谓词逻辑的推理规则是隐式的。我们通过与四种现有方法进行实验比较来评估PLPF。结果显示明显改善。

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