ArticleBioinformatics (Oxford, England)2012
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- The anatomy of phenotype ontologies: principles, properties and applications.Briefings in bioinformatics · 2018Article
- Sharing and reusing cell image data.Molecular biology of the cell · 2018Article
- Improving the interoperability of biomedical ontologies with compound alignments.Journal of biomedical semantics · 2018Article
- Integrating phenotype ontologies with PhenomeNET.Journal of biomedical semantics · 2017Article
- How can functional annotations be derived from profiles of phenotypic annotations?BMC bioinformatics · 2017Article
- The cellular microscopy phenotype ontology.Journal of biomedical semantics · 2016Article
- A generic methodological framework for studying single cell motility in high-throughput time-lapse data.Bioinformatics (Oxford, England) · 2015Article
- Label-free drug discovery.Frontiers in pharmacology · 2014Review
- TermGenie - a web-application for pattern-based ontology class generation.Journal of biomedical semantics · 2014Article
- POEAS: Automated Plant Phenomic Analysis Using Plant Ontology.Bioinformatics and biology insights · 2014Article
- CellFinder: a cell data repository.Nucleic acids research · 2014Article
- Using ontologies to study cell transitions.Journal of biomedical semantics · 2013Article
- FYPO: the fission yeast phenotype ontology.Bioinformatics (Oxford, England) · 2013Article
- Learning to recognize phenotype candidates in the auto-immune literature using SVM re-ranking.PloS one · 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.
Funding
Abstract
motivationThe systematic observation of phenotypes has become a crucial tool of functional genomics, and several large international projects are currently underway to identify and characterize the phenotypes that are associated with genotypes in several species. To integrate phenotype descriptions within and across species, phenotype ontologies have been developed. Applying ontologies to unify phenotype descriptions in the domain of physiology has been a particular challenge due to the high complexity of the underlying domain.
resultsIn this study, we present the outline of a theory and its implementation for an ontology of physiology-related phenotypes. We provide a formal description of process attributes and relate them to the attributes of their temporal parts and participants. We apply our theory to create the Cellular Phenotype Ontology (CPO). The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes. The CPO can be used for the annotation of observed abnormalities in domains, such as systems microscopy, in which cellular abnormalities are observed and for which no phenotype ontology has been created. AVAILABILITY AND IMPLEMENTATION: The CPO and the source code we generated to create the CPO are freely available on http://cell-phenotype.googlecode.com.
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.