Files and links (1)
Published, Version of Record (VoR)Open Access (License Unspecified), Open
Journal article
The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age
Systematic biology, v 59(4), pp 369-383
01 Jul 2010
PMID: 20547776
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebra fish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.
Metrics
Details
- Title
- The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age
- Creators
- Wasila M. Dahdul - University of South DakotaJohn G. Lundberg - Drexel UniversityPeter E. Midford - National Evolutionary Synthesis CenterJames P. Balhoff - University of North Carolina at Chapel HillHilmar Lapp - National Evolutionary Synthesis CenterTodd J. Vision - Natl Evolutionary Synth Ctr, Durham, NC 27705 USAMelissa A. Haendel - Oregon Health & Science UniversityMonte Westerfield - University of OregonPaula M. Mabee - University of South Dakota
- Publication Details
- Systematic biology, v 59(4), pp 369-383
- Publisher
- Oxford Univ Press
- Number of pages
- 15
- Grant note
- NSF EF-0423641 / National Evolutionary Synthesis Center P41HG002659 / NATIONAL HUMAN GENOME RESEARCH INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) 1062542 / Direct For Biological Sciences; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) HG002659 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA NSF DBI 0641025 / National Science Foundation; National Science Foundation (NSF)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biodiversity, Earth, and Environmental Science (BEES); Academy of Natural Sciences of Drexel University
- Web of Science ID
- WOS:000279316400001
- Scopus ID
- 2-s2.0-77953795230
- Other Identifier
- 991019335239904721
UN Sustainable Development Goals (SDGs)
This publication has contributed to the advancement of the following goals:
InCites Highlights
Data related to this publication, from InCites Benchmarking & Analytics tool:
- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Evolutionary Biology