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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

Synthesis Execution Shows a loosely specified process (background, cf. Figure 8 - Synthesis example 3) and the wizard windows (foreground) that query the user for additional input. Step 1 shows the constraint editor that is based on natural language templates, and in Step 2, the user can choose one out of all the solutions that the synthesis algorithm found.
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Figure 9: Synthesis Execution Shows a loosely specified process (background, cf. Figure 8 - Synthesis example 3) and the wizard windows (foreground) that query the user for additional input. Step 1 shows the constraint editor that is based on natural language templates, and in Step 2, the user can choose one out of all the solutions that the synthesis algorithm found.

Mentions: After a domain has been set up by the domain expert, it can be used by the workflow designer to model processes. As part of the seamless integration into the jABC, PROPHETS concentrates on the usability for non-technical users. It mainly differs from our previous synthesis approaches [18] in the idea of loose specification: branches in the model can be marked as loosely specified, which then automatically are replaced by reasonable services by our framework. Therefore, the process designer neither needs to model fully executable processes (the standard Bio-jETI way) nor formally specify a synthesis or planning problem with some first-order or temporal logic. Behind the scenes the algorithm still requires formal specifications of the synthesis problem, but our goal with the here presented approach is to hide this formal complexity from the user and replace it by intuitive (graphical) modeling concepts. Furthermore, the actual execution of the synthesis is presented to the user as a set of wizard windows where he finally can choose the favored solution from the list of all possible solutions (”Wizard Step 2” in Figure 9).


Semantics-based composition of EMBOSS services.

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

Synthesis Execution Shows a loosely specified process (background, cf. Figure 8 - Synthesis example 3) and the wizard windows (foreground) that query the user for additional input. Step 1 shows the constraint editor that is based on natural language templates, and in Step 2, the user can choose one out of all the solutions that the synthesis algorithm found.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 9: Synthesis Execution Shows a loosely specified process (background, cf. Figure 8 - Synthesis example 3) and the wizard windows (foreground) that query the user for additional input. Step 1 shows the constraint editor that is based on natural language templates, and in Step 2, the user can choose one out of all the solutions that the synthesis algorithm found.
Mentions: After a domain has been set up by the domain expert, it can be used by the workflow designer to model processes. As part of the seamless integration into the jABC, PROPHETS concentrates on the usability for non-technical users. It mainly differs from our previous synthesis approaches [18] in the idea of loose specification: branches in the model can be marked as loosely specified, which then automatically are replaced by reasonable services by our framework. Therefore, the process designer neither needs to model fully executable processes (the standard Bio-jETI way) nor formally specify a synthesis or planning problem with some first-order or temporal logic. Behind the scenes the algorithm still requires formal specifications of the synthesis problem, but our goal with the here presented approach is to hide this formal complexity from the user and replace it by intuitive (graphical) modeling concepts. Furthermore, the actual execution of the synthesis is presented to the user as a set of wizard windows where he finally can choose the favored solution from the list of all possible solutions (”Wizard Step 2” in Figure 9).

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