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Linking the Resource Description Framework to cheminformatics and proteochemometrics.

Willighagen EL, Alvarsson J, Andersson A, Eklund M, Lampa S, Lapins M, Spjuth O, Wikberg JE - J Biomed Semantics (2011)

Bottom Line: Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet.Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility.The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.

View Article: PubMed Central - HTML - PubMed

Affiliation: Uppsala University, Department of Pharmaceutical Biosciences, Box 591, SE-751 24 Uppsala, Sweden. egon.willighagen@farmbio.uu.se.

ABSTRACT

Background: Semantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet. The semantic web technology Resource Description Framework (RDF) and related methods show to be sufficiently versatile to change that situation.

Results: The work presented here focuses on linking RDF approaches to existing molecular chemometrics fields, including cheminformatics, QSAR modeling and proteochemometrics. Applications are presented that link RDF technologies to methods from statistics and cheminformatics, including data aggregation, visualization, chemical identification, and property prediction. They demonstrate how this can be done using various existing RDF standards and cheminformatics libraries. For example, we show how IC50 and Ki values are modeled for a number of biological targets using data from the ChEMBL database.

Conclusions: We have shown that existing RDF standards can suitably be integrated into existing molecular chemometrics methods. Platforms that unite these technologies, like Bioclipse, makes this even simpler and more transparent. Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility. The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.

No MeSH data available.


Related in: MedlinePlus

Notation3 file with a small RDF network for methoxymethane. Available from additional file 1.
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Figure 3: Notation3 file with a small RDF network for methoxymethane. Available from additional file 1.

Mentions: Bioclipse is used in this paper to integrate various RDF functions, and the Zest graph visualization library is used to create a graphical browser for RDF networks. Figure 2 used this functionality and shows a small graph depicting an RDF resource sdb:mol1, which is of type sdb:Molecule and has a name (Methanol) and a SMILES (CO). It also has a statement on the molecular identity and a few alternative identifiers from the NMRShiftDB and ChEBI, retrieved via the website http://rdf.openmolecules.net/. This graph visualization functionality in Bioclipse recognizes objects of a supported ontological type, sdb:Molecule in the example. The icon in front of the sdb:mol1 resource indicates that the resource is recognized as a molecule. The icon also implies that Bioclipse knows what to do with such resources. If the user clicks a resource with an icon, it will visualize and compute additional information. Figure 2 shows this in action for the RDF graph shown in Figure 3, where an InChIKey and molecular mass are computed and shown in the Properties view, as well as the matching 2D diagram shown in the 2D-Structure view. Double clicking such a resource will open it in an appropriate Bioclipse editor. For example, this allows a molecule resource in the RDF graph to be opened in a JChemPaint editor.


Linking the Resource Description Framework to cheminformatics and proteochemometrics.

Willighagen EL, Alvarsson J, Andersson A, Eklund M, Lampa S, Lapins M, Spjuth O, Wikberg JE - J Biomed Semantics (2011)

Notation3 file with a small RDF network for methoxymethane. Available from additional file 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105498&req=5

Figure 3: Notation3 file with a small RDF network for methoxymethane. Available from additional file 1.
Mentions: Bioclipse is used in this paper to integrate various RDF functions, and the Zest graph visualization library is used to create a graphical browser for RDF networks. Figure 2 used this functionality and shows a small graph depicting an RDF resource sdb:mol1, which is of type sdb:Molecule and has a name (Methanol) and a SMILES (CO). It also has a statement on the molecular identity and a few alternative identifiers from the NMRShiftDB and ChEBI, retrieved via the website http://rdf.openmolecules.net/. This graph visualization functionality in Bioclipse recognizes objects of a supported ontological type, sdb:Molecule in the example. The icon in front of the sdb:mol1 resource indicates that the resource is recognized as a molecule. The icon also implies that Bioclipse knows what to do with such resources. If the user clicks a resource with an icon, it will visualize and compute additional information. Figure 2 shows this in action for the RDF graph shown in Figure 3, where an InChIKey and molecular mass are computed and shown in the Properties view, as well as the matching 2D diagram shown in the 2D-Structure view. Double clicking such a resource will open it in an appropriate Bioclipse editor. For example, this allows a molecule resource in the RDF graph to be opened in a JChemPaint editor.

Bottom Line: Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet.Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility.The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.

View Article: PubMed Central - HTML - PubMed

Affiliation: Uppsala University, Department of Pharmaceutical Biosciences, Box 591, SE-751 24 Uppsala, Sweden. egon.willighagen@farmbio.uu.se.

ABSTRACT

Background: Semantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet. The semantic web technology Resource Description Framework (RDF) and related methods show to be sufficiently versatile to change that situation.

Results: The work presented here focuses on linking RDF approaches to existing molecular chemometrics fields, including cheminformatics, QSAR modeling and proteochemometrics. Applications are presented that link RDF technologies to methods from statistics and cheminformatics, including data aggregation, visualization, chemical identification, and property prediction. They demonstrate how this can be done using various existing RDF standards and cheminformatics libraries. For example, we show how IC50 and Ki values are modeled for a number of biological targets using data from the ChEMBL database.

Conclusions: We have shown that existing RDF standards can suitably be integrated into existing molecular chemometrics methods. Platforms that unite these technologies, like Bioclipse, makes this even simpler and more transparent. Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility. The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.

No MeSH data available.


Related in: MedlinePlus