Vertebrate Trait Ontology
Abbreviation: VT
Homepage https://github.com/AnimalGenome/vertebrate-trait-ontology
Countries that developed this resource United States
Created in 2011
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: VT; Vertebrate Trait Ontology; DOI: https://doi.org/10.25504/FAIRsharing.10gr18; Last edited: Feb. 4, 2020, 10:05 a.m.; Last accessed: Jun 20 2021 2:38 p.m.
Record updated: Feb. 4, 2020, 10:05 a.m. by The FAIRsharing Team.
| support email | Carissa Park |
| forum | GitHub Issue Tracker |
Additional Information
| Contact | Jim Reecy |
External Links
| Bioportal | http://bioportal.bioontology.org/ontologies/VT |
| OBO | http://obofoundry.org/ontology/vt.html |
No XSD schemas defined
Conditions of Use
Applies to: Data useData Access
| AgroPortal: Browse / Download | http://agroportal.lirmm.fr/ontologies/VT |
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species.
Park CA,Bello SM,Smith CL,Hu ZL,Munzenmaier DH,Nigam R,Smith JR,Shimoyama M,Eppig JT,Reecy JM
J Biomed Semantics 2013
View in BioPortal.
View in OBO Foundry.
Reporting Guidelines
Terminology Artifacts
No semantic standards defined
Models and Formats
No syntax standards defined
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys.
Rat Genome Database
The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually and via an automated pipeline, giving RGD users integrated access to a wide variety of data to support their research.
Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.
Animal Quantitative Trait Loci (QTL) Database
The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped to livestock animal genomes, in order to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features such as annotated genes.
Animal Trait Correlation Database
A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies
OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
BovineMine
BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-curated data sets to be applied to ruminants using orthology.
Chickspress
Chickspress is a gene expression database for chicken tissues. Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL information. By linking gene models from both NCBI and Ensembl gene prediction pipelines, researchers can compare gene models from each of these prediction workflows to available experimental data. We use Chickspress data to show the differences between these gene annotation pipelines. Chickspress also provides rapid search, visualization and download capacity for chicken gene sets based upon tissue type, developmental stage and experiment type. Chickspress includes a core set of Red Jungle Fowl RNA and peptide data collected across multiple tissues from both male and female birds and public expression data sets.
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This record is not implemented by any policy.
Record Maintainer
This record is maintained by AnimalGenome
Funds
National Institute of Food and Agriculture (NIFA), US Department of Agriculture (USDA), Washington DC, USA (Government body)
U.S. National Library of Medicine (Government body)
Maintains
University of Iowa (University)
Grant Number(s)
2008-35205-18765 (National Institute of Food and Agriculture (NIFA), US Department of Agriculture (USDA), Washington DC, USA)
