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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.

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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 EXACT2 upper level classes (a fragment). EXACT2 has the following upper level classes: process (i.e. experimental actions, procedures and protocols), descriptor of experimental action (i.e. equipment, biochemical entities, temperature, speed, volume, etc.) and information content entity (i.e. author, licence, etc.).
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Figure 1: The EXACT2 upper level classes (a fragment). EXACT2 has the following upper level classes: process (i.e. experimental actions, procedures and protocols), descriptor of experimental action (i.e. equipment, biochemical entities, temperature, speed, volume, etc.) and information content entity (i.e. author, licence, etc.).

Mentions: The previous version of EXACT used SUMO (the Suggested Upper Merged Ontology) [13] and Time Ontology (see [14]) as upper-level ontologies [7]. Following OBO Foundry recommendations, the new version has been constructed with the use of the top-level classes from BFO (the Basic Formal Ontology) 1.1 [15], IAO (the Information Artifact Ontology) [16], PATO (Phenotype And Trait Ontology) [17] and OBI [2] (see Figure 1). The result is that the class SUMO: Object has been replaced with the class OBI: material entity, and the class EXACT: proposition has been replaced with the class IAO: information content entity. EXACT2 imports the PATO classes: volume, speed, temperature as descriptors of experimental actions. Such classes as IAO: document title, IAO: author identification were imported to EXACT2 to enable the representation of protocol's provenance. IAO classes textual entity and table were imported to capture information about such important textual elements of biomedical protocols as tables, notes, cautions, troubleshooting.


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 EXACT2 upper level classes (a fragment). EXACT2 has the following upper level classes: process (i.e. experimental actions, procedures and protocols), descriptor of experimental action (i.e. equipment, biochemical entities, temperature, speed, volume, etc.) and information content entity (i.e. author, licence, etc.).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: The EXACT2 upper level classes (a fragment). EXACT2 has the following upper level classes: process (i.e. experimental actions, procedures and protocols), descriptor of experimental action (i.e. equipment, biochemical entities, temperature, speed, volume, etc.) and information content entity (i.e. author, licence, etc.).
Mentions: The previous version of EXACT used SUMO (the Suggested Upper Merged Ontology) [13] and Time Ontology (see [14]) as upper-level ontologies [7]. Following OBO Foundry recommendations, the new version has been constructed with the use of the top-level classes from BFO (the Basic Formal Ontology) 1.1 [15], IAO (the Information Artifact Ontology) [16], PATO (Phenotype And Trait Ontology) [17] and OBI [2] (see Figure 1). The result is that the class SUMO: Object has been replaced with the class OBI: material entity, and the class EXACT: proposition has been replaced with the class IAO: information content entity. EXACT2 imports the PATO classes: volume, speed, temperature as descriptors of experimental actions. Such classes as IAO: document title, IAO: author identification were imported to EXACT2 to enable the representation of protocol's provenance. IAO classes textual entity and table were imported to capture information about such important textual elements of biomedical protocols as tables, notes, cautions, troubleshooting.

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