ArticleBMC bioinformatics2011
OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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
11 citing papers in PubMed.
- Where to search top-K biomedical ontologies?Briefings in bioinformatics · 2019Review
- ontologyX: a suite of R packages for working with ontological data.Bioinformatics (Oxford, England) · 2017Article
- KneeTex: an ontology-driven system for information extraction from MRI reports.Journal of biomedical semantics · 2015Article
- BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing.Journal of the American Medical Informatics Association : JAMIA · 2015Article
- The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.Database : the journal of biological databases and curation · 2013Article
- LibKiSAO: a Java library for Querying KiSAO.BMC research notes · 2012Article
- MageComet--web application for harmonizing existing large-scale experiment descriptions.Bioinformatics (Oxford, England) · 2012Article
- An ICT infrastructure to integrate clinical and molecular data in oncology research.BMC bioinformatics · 2012Article
- The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications.Frontiers in genetics · 2012Article
- The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes.Database : the journal of biological databases and curation · 2012Article
- Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.Nucleic acids research · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOntologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.
resultsOntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.
conclusionsOntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. AVAILABILITY: http://www.ontocat.org.
Indexed as
Identifiers
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.