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EXACT2: the semantics of biomedical protocols.

Soldatova LN, Nadis D, King RD, Basu PS, Haddi E, Baumlé V, Saunders NJ, Marwan W, Rudkin BB - BMC Bioinformatics (2014)

Bottom Line: There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results.We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2)protocols.It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2)protocols.

Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility.

Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed.

Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.

Show MeSH
The identification of experimental actions in the text. The Translator engine searches the input text for experimental actions defined in EXACT2. The experimental actions incubate and adjust have been identified in this example protocol.
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Figure 2: The identification of experimental actions in the text. The Translator engine searches the input text for experimental actions defined in EXACT2. The experimental actions incubate and adjust have been identified in this example protocol.

Mentions: We assume that the text has been processed using appropriate text mining tools, and all NEs and POSs have been recognised and disambiguated. For example, TCA will be found in the text and checked against both the list of abbreviations and biochemical entities. The abbreviation will be replaced by the term Trichloroacetic acid and assigned with the ID NCBI Pubchem: CID 6421. All verbs then will be checked against subclasses of the class EXACT2: experimental action. The verb 'incubate' will be matched with the class EXACT2 000049: incubate and the verb 'adjust' will be matched with the class EXACT2 000089: adjust (see Figure 2). EXACT2 defines the following descriptors for the experimental action incubate:


EXACT2: the semantics of biomedical protocols.

Soldatova LN, Nadis D, King RD, Basu PS, Haddi E, Baumlé V, Saunders NJ, Marwan W, Rudkin BB - BMC Bioinformatics (2014)

The identification of experimental actions in the text. The Translator engine searches the input text for experimental actions defined in EXACT2. The experimental actions incubate and adjust have been identified in this example protocol.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4255744&req=5

Figure 2: The identification of experimental actions in the text. The Translator engine searches the input text for experimental actions defined in EXACT2. The experimental actions incubate and adjust have been identified in this example protocol.
Mentions: We assume that the text has been processed using appropriate text mining tools, and all NEs and POSs have been recognised and disambiguated. For example, TCA will be found in the text and checked against both the list of abbreviations and biochemical entities. The abbreviation will be replaced by the term Trichloroacetic acid and assigned with the ID NCBI Pubchem: CID 6421. All verbs then will be checked against subclasses of the class EXACT2: experimental action. The verb 'incubate' will be matched with the class EXACT2 000049: incubate and the verb 'adjust' will be matched with the class EXACT2 000089: adjust (see Figure 2). EXACT2 defines the following descriptors for the experimental action incubate:

Bottom Line: There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results.We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2)protocols.It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2)protocols.

Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility.

Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed.

Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.

Show MeSH