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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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An example of a Petri net (a fragment). The semantics of the places and transitions of this Petri net is defined through the use of EXACT2. Two experimental actions streak and transfer, defined in EXACT2, are used as labels to represent the semantics of the transitions. The descriptors of those experimental actions and their values, e.g. equipment: 10 ml glass pipette are used to represent the semantics of the places. The tokens (dark dots) indicate the necessary conditions for the transitions to take place.
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Figure 4: An example of a Petri net (a fragment). The semantics of the places and transitions of this Petri net is defined through the use of EXACT2. Two experimental actions streak and transfer, defined in EXACT2, are used as labels to represent the semantics of the transitions. The descriptors of those experimental actions and their values, e.g. equipment: 10 ml glass pipette are used to represent the semantics of the places. The tokens (dark dots) indicate the necessary conditions for the transitions to take place.

Mentions: For example, we considered the experimental procedures for isolation of Physarum polycephalum plasmodial mutants altered in sporulation obtained by chemical mutagenesis of flagellates [33].Corresponding genetic screens are run in the Magdeburg Centre for Systems Biology [34]. Physarum polycephalum belongs to the amoebozoa group of organisms. The experimental procedure is complex, non deterministic and takes ten days to complete (see the 'Growth of amoeba and preparation of flagellate suspension' procedure in the materials and methods section, [33]). Figure 4 shows a fragment of this procedure represented with a Petri net. The semantics of the places and transitions is defined with the use of the EXACT2 classes. The experimental actions, e.g. streak, transfer, are represented as transitions, and the key descriptors of those experimental actions are represented as places, e.g. amoebae microcolony, DSPB agar plate . In order to support the representation of such workflows, we will have to add to EXACT2 such descriptor as time point. Also, transition firing rules have to be defined appropriately in order to ensure the correct dynamic behaviour of the Petri net.


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)

An example of a Petri net (a fragment). The semantics of the places and transitions of this Petri net is defined through the use of EXACT2. Two experimental actions streak and transfer, defined in EXACT2, are used as labels to represent the semantics of the transitions. The descriptors of those experimental actions and their values, e.g. equipment: 10 ml glass pipette are used to represent the semantics of the places. The tokens (dark dots) indicate the necessary conditions for the transitions to take place.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: An example of a Petri net (a fragment). The semantics of the places and transitions of this Petri net is defined through the use of EXACT2. Two experimental actions streak and transfer, defined in EXACT2, are used as labels to represent the semantics of the transitions. The descriptors of those experimental actions and their values, e.g. equipment: 10 ml glass pipette are used to represent the semantics of the places. The tokens (dark dots) indicate the necessary conditions for the transitions to take place.
Mentions: For example, we considered the experimental procedures for isolation of Physarum polycephalum plasmodial mutants altered in sporulation obtained by chemical mutagenesis of flagellates [33].Corresponding genetic screens are run in the Magdeburg Centre for Systems Biology [34]. Physarum polycephalum belongs to the amoebozoa group of organisms. The experimental procedure is complex, non deterministic and takes ten days to complete (see the 'Growth of amoeba and preparation of flagellate suspension' procedure in the materials and methods section, [33]). Figure 4 shows a fragment of this procedure represented with a Petri net. The semantics of the places and transitions is defined with the use of the EXACT2 classes. The experimental actions, e.g. streak, transfer, are represented as transitions, and the key descriptors of those experimental actions are represented as places, e.g. amoebae microcolony, DSPB agar plate . In order to support the representation of such workflows, we will have to add to EXACT2 such descriptor as time point. Also, transition firing rules have to be defined appropriately in order to ensure the correct dynamic behaviour of the Petri net.

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