ArticleBMC bioinformatics2010
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed, 13 citations in OpenAlex.
- OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows.Journal of biomedical semantics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported by a diverse series of tools, but the lack of a consistent terminology to label these data still presents significant hurdles. As a consequence, much of the available biological data remains disconnected or worse: becomes misconnected. The need to address this terminology problem has spawned the building of a large number of bio-ontologies. OBOF, RDF and OWL are among the most used ontology formats to capture terms and relationships in the Life Sciences, opening the potential to use the Semantic Web to support data integration and further exploitation of integrated resources via automated retrieval and reasoning procedures.
methodsWe extended the Perl suite ONTO-PERL and functionally integrated it into the Galaxy platform. The resulting ONTO-ToolKit supports the analysis and handling of OBO-formatted ontologies via the Galaxy interface, and we demonstrated its functionality in different use cases that illustrate the flexibility to obtain sets of ontology terms that match specific search criteria.
resultsONTO-ToolKit is available as a tool suite for Galaxy. Galaxy not only provides a user friendly interface allowing the interested biologist to manipulate OBO ontologies, it also opens up the possibility to perform further biological (and ontological) analyses by using other tools available within the Galaxy environment. Moreover, it provides tools to translate OBO-formatted ontologies into Semantic Web formats such as RDF and OWL.
conclusionsONTO-ToolKit reaches out to researchers in the biosciences, by providing a user-friendly way to analyse and manipulate ontologies. This type of functionality will become increasingly important given the wealth of information that is becoming available based on ontologies.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.