Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature
Identifieur interne : 000182 ( Pmc/Corpus ); précédent : 000181; suivant : 000183Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature
Auteurs : Wasila M. Dahdul ; James P. Balhoff ; Jeffrey Engeman ; Terry Grande ; Eric J. Hilton ; Cartik Kothari ; Hilmar Lapp ; John G. Lundberg ; Peter E. Midford ; Todd J. Vision ; Monte Westerfield ; Paula M. MabeeSource :
- PLoS ONE [ 1932-6203 ] ; 2010.
Abstract
The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies.
We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish,
The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.
Url:
DOI: 10.1371/journal.pone.0010708
PubMed: 20505755
PubMed Central: 2873956
Links to Exploration step
PMC:2873956***** Acces problem to record *****\Le document en format XML
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/OcrV1/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000182 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000182 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= OcrV1 |flux= Pmc |étape= Corpus |type= RBID |clé= PMC:2873956 |texte= Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/RBID.i -Sk "pubmed:20505755" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd \ | NlmPubMed2Wicri -a OcrV1
This area was generated with Dilib version V0.6.32. |