ArticleBMC bioinformatics2008
Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Subjective data models in bioinformatics and how wet lab and computational biologists conceptualise data.Scientific data · 2023Article
- Comparative analysis of miRNA expression profiles in transgenic and non-transgenic rice using miRNA-Seq.Scientific reports · 2018Article
- Synergistic infection of two viruses MCMV and SCMV increases the accumulations of both MCMV and MCMV-derived siRNAs in maize.Scientific reports · 2016Article
- High-throughput sequencing of small RNAs and anatomical characteristics associated with leaf development in celery.Scientific reports · 2015Article
- De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development.Scientific reports · 2015Article
- Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.Journal of biomedical semantics · 2015Article
- Article
- GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution.Journal of biomedical semantics · 2011Article
- Benchmarking ontologies: bigger or better?PLoS computational biology · 2011Article
- Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology.PloS one · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMuch effort is currently made to develop the Gene Ontology (GO). Due to the dynamic nature of information it addresses, GO undergoes constant updates whose results are released at regular intervals as separate versions. Although there are a large number of computational tools to aid the development of GO, they are operating on a particular version of GO, making it difficult for GO curators to anticipate the full impact of particular changes along the time axis on a larger scale. We present a method for tapping into such an evolutionary aspect of GO, by making it possible to keep track of important temporal changes to any of the terms and relations of GO and by consequently making it possible to recognize associated trends.
resultsWe have developed visualization methods for viewing the changes between two different versions of GO by constructing a colour-coded layered graph. The graph shows both versions of GO with highlights to those GO terms that are added, removed and modified between the two versions. Focusing on a specific GO term or terms of interest over a period, we demonstrate the utility of our system that can be used to make useful hypotheses about the cause of the evolution and to provide new insights into more complex changes.
conclusionsGO undergoes fast evolutionary changes. A snapshot of GO, as presented by each version of GO alone, overlooks such evolutionary aspects, and consequently limits the utilities of GO. The method that highlights the differences of consecutive versions or two different versions of an evolving ontology with colour-coding enhances the utility of GO for users as well as for developers. To the best of our knowledge, this is the first proposal to visualize the evolutionary aspect of GO.
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.