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Semantics-based composition of EMBOSS services.

Lamprecht AL, Naujokat S, Margaria T, Steffen B - J Biomed Semantics (2011)

Bottom Line: Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection.However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized.Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services.

View Article: PubMed Central - HTML - PubMed

Affiliation: Chair for Programming Systems, Technical University Dortmund, Dortmund, D-44227, Germany. anna-lena.lamprecht@cs.tu-dortmund.de.

ABSTRACT

Background: More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner. The Semantic Web, which is meant to address exactly this challenge, is currently one of the most ambitious projects in computer science. Collective efforts within the community have already led to a basis of standards for semantic service descriptions and meta-information. In combination with process synthesis and planning methods, such knowledge about types and services can facilitate the automatic composition of workflows for particular research questions.

Results: In this study we apply the synthesis methodology that is available in the Bio-jETI workflow management framework for the semantics-based composition of EMBOSS services. EMBOSS (European Molecular Biology Open Software Suite) is a collection of 350 tools (March 2010) for various sequence analysis tasks, and thus a rich source of services and types that imply comprehensive domain models for planning and synthesis approaches. We use and compare two different setups of our EMBOSS synthesis domain: 1) a manually defined domain setup where an intuitive, high-level, semantically meaningful nomenclature is applied to describe the input/output behavior of the single EMBOSS tools and their classifications, and 2) a domain setup where this information has been automatically derived from the EMBOSS Ajax Command Definition (ACD) files and the EMBRACE Data and Methods ontology (EDAM). Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection. However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized.

Conclusions: Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services. Finding or defining semantically appropriate service and type descriptions is a difficult task, but the bioinformatics community appears to be on the right track towards a Life Science Semantic Web, which will eventually allow automatic service composition methods to unfold their full potential.

No MeSH data available.


Related in: MedlinePlus

Model checking examples. Model checking of a formula expressing that each built HMM must be calibrated before it actually emits sequences.
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Figure 11: Model checking examples. Model checking of a formula expressing that each built HMM must be calibrated before it actually emits sequences.

Mentions: As already mentioned, the domain modeler can define high-level constraints using model checking [39] formulas to express properties that must hold for any model in this domain. For an example, consider the process in Figure 11(A), where a HMM is built from a multiple sequence alignment (obtained via emma) and used to produce sequences that are finally displayed using showseq. The workflow designer now might want to express that each built HMM has to be calibrated before it actually emits sequences. Formally, this can be expressed with the PLTL formula ehmmbuild (ehmmemit WUehmmcalibrate) denoting that the use of ehmmbuild implies that ehmmemit is not used before ehmmcalibrate has been executed. As Figure 11(A) shows, this requirement is not met by the previously created process, because at the ehmmbuild service’s node, the property is not fulfilled (indicated by the red ”x” overlay icon in the lower right corner). Inserting the ehmmcalibrate service into the workflow fixes this issue, as Figure 11(B) shows: all services are marked by a green icon. Naturally, and as 11(C) shows, this constraint is also fulfilled if the HMM is not built by the process, but fetched from an HMM database.


Semantics-based composition of EMBOSS services.

Lamprecht AL, Naujokat S, Margaria T, Steffen B - J Biomed Semantics (2011)

Model checking examples. Model checking of a formula expressing that each built HMM must be calibrated before it actually emits sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105497&req=5

Figure 11: Model checking examples. Model checking of a formula expressing that each built HMM must be calibrated before it actually emits sequences.
Mentions: As already mentioned, the domain modeler can define high-level constraints using model checking [39] formulas to express properties that must hold for any model in this domain. For an example, consider the process in Figure 11(A), where a HMM is built from a multiple sequence alignment (obtained via emma) and used to produce sequences that are finally displayed using showseq. The workflow designer now might want to express that each built HMM has to be calibrated before it actually emits sequences. Formally, this can be expressed with the PLTL formula ehmmbuild (ehmmemit WUehmmcalibrate) denoting that the use of ehmmbuild implies that ehmmemit is not used before ehmmcalibrate has been executed. As Figure 11(A) shows, this requirement is not met by the previously created process, because at the ehmmbuild service’s node, the property is not fulfilled (indicated by the red ”x” overlay icon in the lower right corner). Inserting the ehmmcalibrate service into the workflow fixes this issue, as Figure 11(B) shows: all services are marked by a green icon. Naturally, and as 11(C) shows, this constraint is also fulfilled if the HMM is not built by the process, but fetched from an HMM database.

Bottom Line: Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection.However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized.Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services.

View Article: PubMed Central - HTML - PubMed

Affiliation: Chair for Programming Systems, Technical University Dortmund, Dortmund, D-44227, Germany. anna-lena.lamprecht@cs.tu-dortmund.de.

ABSTRACT

Background: More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner. The Semantic Web, which is meant to address exactly this challenge, is currently one of the most ambitious projects in computer science. Collective efforts within the community have already led to a basis of standards for semantic service descriptions and meta-information. In combination with process synthesis and planning methods, such knowledge about types and services can facilitate the automatic composition of workflows for particular research questions.

Results: In this study we apply the synthesis methodology that is available in the Bio-jETI workflow management framework for the semantics-based composition of EMBOSS services. EMBOSS (European Molecular Biology Open Software Suite) is a collection of 350 tools (March 2010) for various sequence analysis tasks, and thus a rich source of services and types that imply comprehensive domain models for planning and synthesis approaches. We use and compare two different setups of our EMBOSS synthesis domain: 1) a manually defined domain setup where an intuitive, high-level, semantically meaningful nomenclature is applied to describe the input/output behavior of the single EMBOSS tools and their classifications, and 2) a domain setup where this information has been automatically derived from the EMBOSS Ajax Command Definition (ACD) files and the EMBRACE Data and Methods ontology (EDAM). Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection. However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized.

Conclusions: Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services. Finding or defining semantically appropriate service and type descriptions is a difficult task, but the bioinformatics community appears to be on the right track towards a Life Science Semantic Web, which will eventually allow automatic service composition methods to unfold their full potential.

No MeSH data available.


Related in: MedlinePlus