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Using Semantics and NLP in Experimental Protocols

In this paper we present “SMART Protocols”, a semantic and NLP-based infrastructure for processing and enacting experimental protocols. Our contribution is twofold; on the one hand, SMART Protocols delivers a semantic layer that represents the knowledge encoded in experimental protocols. On the other hand, it builds the groundwork for making use of such semantics within an NLP framework. We emphasize on the semantic and NLP components, namely the SMART Protocols (SP) Ontology, the Sample Instrument Reagent Objective (SIRO) model and the text mining integrative architecture GATE. The SMART Protocols (SP) Ontology results from the analysis of over 300 experimental protocols in various domains –molecular biology, cell and developmental biology and others. The gathered terminology is then evaluated, rules are improved accordingly and then a new iteration starts. The SIRO model defines an extended layer of metadata for experimental protocols; SIRO is also a Minimal Information (MI) model conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes. The SIRO ontology development process includes NLP as well as domain expertise in the extraction of the vocabulary; domain experts extract an initial seed of terminology, then the process is automated by using gazetteers and extraction rules in JAPE. Both SIRO and the SP ontology are then used by our NLP engine, GATE. By combining comprehensive vocabularies with NLP rules and gazetteers we identify meaningful parts of speech in experimental protocols. Moreover, in cases for which SIRO is not available, our NLP automatically extracts it; also, searching for queries such as: ”What bacteria have been used in protocols for persister cells isolation”