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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.

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The identification of descriptors of experimental actions in the text. The Translator engine searches the text for the descriptors defined in EXACT2. Where possible values for the specified descriptors are extracted, and such ambiguous expressions as overnight are resolved. In this example the value of the descriptor temperature is 30°C and assigned with the ID: "UO:0000027" from the Units Ontology (see [39]).
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Figure 3: The identification of descriptors of experimental actions in the text. The Translator engine searches the text for the descriptors defined in EXACT2. Where possible values for the specified descriptors are extracted, and such ambiguous expressions as overnight are resolved. In this example the value of the descriptor temperature is 30°C and assigned with the ID: "UO:0000027" from the Units Ontology (see [39]).

Mentions: A translating engine recognises the defined in EXACT2 descriptors in the given sentence. It is easy to recognize the value of the descriptor temperature by the clue '°C' and the value of the descriptor period as 16 hours (see Figure 3). However, the information about the participating biochemical entity and a condition is missing. This information is defined in EXACT2 as essential and therefore has to be specified. Therefore a translating engine will ask the user to input information about what is to be incubated, and under what condition. Thus all the essential information for the reproducibility of the protocol information will be captured and represented in a semantically defined form.


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 descriptors of experimental actions in the text. The Translator engine searches the text for the descriptors defined in EXACT2. Where possible values for the specified descriptors are extracted, and such ambiguous expressions as overnight are resolved. In this example the value of the descriptor temperature is 30°C and assigned with the ID: "UO:0000027" from the Units Ontology (see [39]).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The identification of descriptors of experimental actions in the text. The Translator engine searches the text for the descriptors defined in EXACT2. Where possible values for the specified descriptors are extracted, and such ambiguous expressions as overnight are resolved. In this example the value of the descriptor temperature is 30°C and assigned with the ID: "UO:0000027" from the Units Ontology (see [39]).
Mentions: A translating engine recognises the defined in EXACT2 descriptors in the given sentence. It is easy to recognize the value of the descriptor temperature by the clue '°C' and the value of the descriptor period as 16 hours (see Figure 3). However, the information about the participating biochemical entity and a condition is missing. This information is defined in EXACT2 as essential and therefore has to be specified. Therefore a translating engine will ask the user to input information about what is to be incubated, and under what condition. Thus all the essential information for the reproducibility of the protocol information will be captured and represented in a semantically defined form.

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