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OLS dialog: an open-source front end to the ontology lookup service.

Barsnes H, Côté RG, Eidhammer I, Martens L - BMC Bioinformatics (2010)

Bottom Line: However, using the Ontology Lookup Service as a web service is not always feasible, especially for researchers without bioinformatics support.We have therefore created a Java front end to the Ontology Lookup Service, called the OLS Dialog, which can be plugged into any application requiring the annotation of data using controlled vocabulary terms, making it possible to find and use controlled vocabulary terms without requiring any additional knowledge about web services or ontology formats.As a user-friendly open source front end to the Ontology Lookup Service, the OLS Dialog makes it straightforward to include controlled vocabulary support in third-party tools, which ultimately makes the data even more valuable to the biomedical community.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Informatics, University of Bergen, Bergen, Norway. harald.barsnes@ii.uib.no

ABSTRACT

Background: With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled vocabulary terms and ontologies makes it much easier to compare and analyze data from different sources. However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data.

Results: In order to facilitate the location of the correct term in the correct controlled vocabulary or ontology, the Ontology Lookup Service was created. However, using the Ontology Lookup Service as a web service is not always feasible, especially for researchers without bioinformatics support. We have therefore created a Java front end to the Ontology Lookup Service, called the OLS Dialog, which can be plugged into any application requiring the annotation of data using controlled vocabulary terms, making it possible to find and use controlled vocabulary terms without requiring any additional knowledge about web services or ontology formats.

Conclusions: As a user-friendly open source front end to the Ontology Lookup Service, the OLS Dialog makes it straightforward to include controlled vocabulary support in third-party tools, which ultimately makes the data even more valuable to the biomedical community.

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Related in: MedlinePlus

Browse Ontology. Here the OLS Dialog is used to locate the term GO:0012501 ('cell death resulting from activation of endogenous cellular processes') in the Gene Ontology using the Browse Ontology feature.
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Figure 3: Browse Ontology. Here the OLS Dialog is used to locate the term GO:0012501 ('cell death resulting from activation of endogenous cellular processes') in the Gene Ontology using the Browse Ontology feature.

Mentions: For examples of how the OLS Dialog can be used, see Figure 1, 2 and 3. In Figure 1 Term Name Search is used to find the possible CV terms for the search term 'Oxidation', while in Figure 2 the same term is found using PSI-MOD Mass Search. Figure 3 shows how the Browse Ontology feature can be used to locate the term 'GO:001250'.


OLS dialog: an open-source front end to the ontology lookup service.

Barsnes H, Côté RG, Eidhammer I, Martens L - BMC Bioinformatics (2010)

Browse Ontology. Here the OLS Dialog is used to locate the term GO:0012501 ('cell death resulting from activation of endogenous cellular processes') in the Gene Ontology using the Browse Ontology feature.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823706&req=5

Figure 3: Browse Ontology. Here the OLS Dialog is used to locate the term GO:0012501 ('cell death resulting from activation of endogenous cellular processes') in the Gene Ontology using the Browse Ontology feature.
Mentions: For examples of how the OLS Dialog can be used, see Figure 1, 2 and 3. In Figure 1 Term Name Search is used to find the possible CV terms for the search term 'Oxidation', while in Figure 2 the same term is found using PSI-MOD Mass Search. Figure 3 shows how the Browse Ontology feature can be used to locate the term 'GO:001250'.

Bottom Line: However, using the Ontology Lookup Service as a web service is not always feasible, especially for researchers without bioinformatics support.We have therefore created a Java front end to the Ontology Lookup Service, called the OLS Dialog, which can be plugged into any application requiring the annotation of data using controlled vocabulary terms, making it possible to find and use controlled vocabulary terms without requiring any additional knowledge about web services or ontology formats.As a user-friendly open source front end to the Ontology Lookup Service, the OLS Dialog makes it straightforward to include controlled vocabulary support in third-party tools, which ultimately makes the data even more valuable to the biomedical community.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Informatics, University of Bergen, Bergen, Norway. harald.barsnes@ii.uib.no

ABSTRACT

Background: With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled vocabulary terms and ontologies makes it much easier to compare and analyze data from different sources. However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data.

Results: In order to facilitate the location of the correct term in the correct controlled vocabulary or ontology, the Ontology Lookup Service was created. However, using the Ontology Lookup Service as a web service is not always feasible, especially for researchers without bioinformatics support. We have therefore created a Java front end to the Ontology Lookup Service, called the OLS Dialog, which can be plugged into any application requiring the annotation of data using controlled vocabulary terms, making it possible to find and use controlled vocabulary terms without requiring any additional knowledge about web services or ontology formats.

Conclusions: As a user-friendly open source front end to the Ontology Lookup Service, the OLS Dialog makes it straightforward to include controlled vocabulary support in third-party tools, which ultimately makes the data even more valuable to the biomedical community.

Show MeSH
Related in: MedlinePlus