standards > terminology artifact > DOI:10.25504/FAIRsharing.4c0b6b


ready UBER anatomy ONtology

Abbreviation: UBERON


General Information
Uberon is an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies. It represents a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.


This record replaces or incorporates the following deprecated resources:

Homepage http://uberon.org/

Countries that developed this resource European Union , United States

Created in 2012

Taxonomic range




How to cite this record FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Sep 18 2019 5:11 p.m.

Publication for citation  Uberon, an integrative multi-species anatomy ontology. Mungall CJ,Torniai C,Gkoutos GV,Lewis SE,Haendel MA; Genome Biol ; 2012; 10.1186/gb-2012-13-1-r5;


This record is maintained by mhaendel  ORCID

Record updated: April 27, 2019, 10:14 p.m. by The FAIRsharing Team.

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Uberon, an integrative multi-species anatomy ontology.

Mungall CJ,Torniai C,Gkoutos GV,Lewis SE,Haendel MA
Genome Biol 2012

View Paper (PubMed) View Publication

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Haendel MA,Balhoff JP,Bastian FB,Blackburn DC,Blake JA,Bradford Y,Comte A,Dahdul WM,Dececchi TA,Druzinsky RE,Hayamizu TF,Ibrahim N,Lewis SE,Mabee PM,Niknejad A,Robinson-Rechavi M,Sereno PC,Mungall CJ
J Biomed Semantics 2014

View Paper (PubMed) View Publication

Uberon, an integrative multi-species anatomy ontology.

Mungall CJ,Torniai C,Gkoutos GV,Lewis SE,Haendel MA
Genome Biol 2012

View Paper (PubMed) View Publication

UBERON Ontology Display

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Implementing Databases (13)
ChEMBL
ChEMBL is an open large-scale bioactivity database containing information largely manually extracted from the medicinal chemistry literature. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions.

Bgee DataBase for Gene Expression Evolution
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.

Biological General Repository for Interaction Datasets
BioGRID is an interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.5.174 and searches 69,922 publications for 1,706,694 protein and genetic interactions, 28,093 chemical associations and 726,378 post translational modifications from major model organism species. All data are freely provided via our search index and available for download in standardized formats.

The Zebrafish Information Network
The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

SwissLipids
SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.

ENCODE Project
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.

NBDC RDF Portal
The NBDC RDF Portal provides a collection of life science datasets in RDF (Resource Description Framework). The portal aims to accelerate integrative utilization of the heterogeneous datasets deposited by various research institutions and groups. In this portal, each dataset comes with a summary, downloadable files and a SPARQL endpoint.

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.

Bovine Genome Database
The Bovine Genome Database project is developed to support the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.

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.

Functional ANnoTation Of the Mammalian genome Database
FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.

Genome-wide Integrated Analysis of gene Networks in Tissues 2.0
GIANT2 (Genome-wide Integrated Analysis of gene Networks in Tissues) is an interactive web server that enables biomedical researchers to analyze their proteins and pathways of interest and generate hypotheses in the context of genome-scale functional maps of human tissues. With GIANT2, researchers can explore predicted tissue-specific functional roles of genes and reveal changes in those roles across tissues, all through interactive multi-network visualizations and analyses.

SCPortalen
SCPortalen is a single-cell database created to facilitate and enable researchers to access and explore published single-cell datasets. It integrates human and mouse single-cell transcriptomics datasets, single-cell metadata, cell images and sequence information.

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Grant Number(s)

  • 1U24RR029825-01 (National Institutes of Health (NIH), Bethesda, MD, USA)

  • DE-AC02-05CH11231 (U.S. Department of Energy)

  • DEB-0956049 (National Science Foundation (NSF), USA)

  • P41HG002273 (National Institutes of Health (NIH), Bethesda, MD, USA)

  • P41HG002273-09S1 (National Institutes of Health (NIH), Bethesda, MD, USA)

  • R01HG004838 (National Institutes of Health (NIH), Bethesda, MD, USA)

  • R24OD011883 (National Institutes of Health (NIH), Bethesda, MD, USA)