1,106 research outputs found
The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age
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 zebrafish 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.This work was supported by the National Science Foundation (NSF DBI 0641025), National Institutes of Health (HG002659), and the National Evolutionary Synthesis Center (NSF EF-0423641)
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
BACKGROUND: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.
RESULTS: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued.
CONCLUSIONS: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases
Integrating phenotype ontologies across multiple species
Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology
An ontology for Xenopus anatomy and development
YesFunding provided by the Open Access Authors Fund
The role of skeletal development in body size evolution of two North American frogs
In order to better understand the evolution of miniaturization in Acris blanchardi, a North American Hylid with a unique life history and of ecological interest in the United States. The development and ossification sequences of 48 larvae, 5 juveniles and 5 adult A. blanchardi were examined. The adult was described by Maglia et al. (2007) to be a miniature and to display morphological novelties. In addition, 44 larvae, 2 juvenile and 5 adults of Pseudacris crucifer a closely related frog that has been suggested to be a miniature, were examined. The cranial and postcranial adult elements of this species, as well as development and ossification of the larvae were described. The onset of ossification is described for both species and, to better understand timing relative to other hylids, they are compared to a non-miniature, Hyla lanciformis. Ossification of the cranial elements in A. blanchardi begins at similar Gosner Stages as Hyla lanciformis, but most elements never fully ossify. P. crucifer begins ossification of cranial elements much later in development but continues ossification longer and ossifies more completely. In addition to poor ossification, A. blanchardi also adds novel endochondral ossification and random mineralization to the cranium to support under-ossified elements such as the nasals and otic capsule. Based on these results, the patterns of ossification leading to miniaturization in A. blanchardi are revealed, and no evidence of miniaturization in page crucifer was discovered --Abstract, page iv
AXOLOTL PAEDOMORPHOSIS: A COMPARISON OF JUVENILE, METAMORPHIC, AND PAEDOMORPHIC AMBYSTOMA MEXICANUM BRAIN GENE TRANSCRIPTION
Unlike many amphibians, the paedomorphic axolotl (Ambystoma mexicanum) rarely undergoes external morphological changes indicative of metamorphosis. However, internally, some axolotl tissues undergo cryptic metamorphic changes. A previous study examined interspecific patterns of larval brain gene expression and found that these species exhibited unique temporal expression patterns that were hypothesized to be morph specific. This thesis tested this hypothesis by examining differences in brain gene expression between juvenile (JUV), paedomorphic (PAED), and metamorphic (MET) axolotls. I identified 828 genes that were expressed differently between JUV, PAED, and MET. Expression estimates from JUV were compared to estimates from PAED and MET brains to identify genes that changed significantly during development. Genes that showed statistically equivalent expression changes across MET and PAED brains provide a glimpse at aging and maturation in an amphibian. The genes that showed statistically different expression estimates between metamorphic and paedomorphic brains provide new functional insights into the maintenance and regulation of paedomorphosis. For genes that were not commonly regulated due to aging, paedomorphs exhibited greater transcriptional similarity to juvenile than metamorphs did to juvenile. Overall, gene expression differences between metamorphic and paedomorphic development exhibit a mosaic pattern of expression as a function of aging and metamorphosis in axolotls
Emerging semantics to link phenotype and environment
abstract: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.The final version of this article, as published in PeerJ, can be viewed online at: https://peerj.com/articles/1470
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