ArticleBMC evolutionary biology2009
Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment.
Article in BMC evolutionary biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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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.
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Who cites it
6 citing papers in PubMed.
- A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.).BMC genomics · 2017Article
- Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora).The Journal of eukaryotic microbiology · 2017Review
- Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group.BMC evolutionary biology · 2013Article
- A tale of two drug targets: the evolutionary history of BACE1 and BACE2.Frontiers in genetics · 2013Article
- Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish.BMC genomics · 2012Article
- Diversity of Streptomyces spp. in Eastern Himalayan region - computational RNomics approach to phylogeny.Bioinformation · 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
2 authors.
Funding
Abstract
backgroundTreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory.
resultsWe report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL http://spira.zoology.gla.ac.uk/app/tbasewrapper.phpThe methodology we developed is scalable and can be applied to new data, as those become available in the future.
conclusionSignificantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection.
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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.