Uberon, an integrative multi-species anatomy ontology

By C. Mungall, Carlo Torniai, Georgios Vasileios Gkoutos, Suzanna Lewis, Melissa A. Haendel. 2012

749 citations recorded by the source corpus.

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org

Subfields: Artificial Intelligence, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Artificial Intelligence

In Molecular Biology

Citations in the corpus

The Gene Ontology Resource: 20 years and still GOing strong (2018, background): “GO imports subsets of these external ontologies that include information about anatomical structures, cell types, chemicals and taxonomic groupings: Uberon (14), Protein Ontology (15), Plant Ontology (16) (23) and MetaCyc (24).”
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data (2022, background): “Moreover, the tissue type ID and cell type ID are from Uberon muti-species anatomy ontology(24) and Cell Ontology(25), respectively.”
Standardized description of scientific evidence using the Evidence Ontology (ECO) (2014, background): “These include ontologies for phenotype (3), cell type (4), anatomy (5) and many more (6).”
The Ontology for Biomedical Investigations (2016, methodology): “Several subclasses of material entity are imported from external ontologies: Classes under organism are imported from the NCBI Taxonomy[18], gross anatomical part and its subclasses from the Uber anatomy ontology (UBERON)[24] or the Common Anatomy Reference Ontology (CARO)[25], and the molecular ent”
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines (2015, methodology): “Tissues and cell-lines are annotated with controlled vocabularies; in the case of tissues we use the Uberon ontology [20], which natively allows cross-species comparisons of homologous tissues/organs.”
Comparative Toxicogenomics Database (CTD): update 2021 (2020, background): “To promote interoperability, CTD Anatomy pages are enhanced with external synonyms, accession identifiers, and links to Uberon and Cell Ontology. which itself is a synonym for vorinostat), or other reasons.”
Finding Our Way through Phenotypes (2015, background): “, descriptive terms) are linked to upper-level classes in the UBERON anatomy ontology [55,56].”
Enabling semantic queries across federated bioinformatics databases (2019, methodology): “require transforming the original attributes in the relational data for interoperability – for example, replacing “:” with “_” in the case of anatomical entity identifiers from Bgee to be compliant with the existing UBERON ontology IRI (Internationalized resource identifier) terms (54), as shown in ”
PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life (2012, methodology): “Because there is currently no single, unified provider for anatomical ontologies across organisms, we employ several ontology frameworks, most of which are cross-referenced by the “Uberon” project (59).”
The BioGRID interaction database: 2019 update (2018, methodology): “This approach allows BioGRID and the MODs to make use of deep species-specific phenotype ontologies across model organisms and humans, including the Ascomycete Phenotype Ontology (52), Uberon (53), the Human Phenotype Ontology (54), and the Monarch Initiative (55).”
The ChEMBL database in 2017 (2016, background): “It should be noted that the aim here is not to create new cell-line/tissue ontologies – entries in the ChEMBL dictionaries are imported from established vocabularies and ontologies wherever possible (e.g. Cell Line Ontology (23), Experimental Factor Ontology (EFO) (24), Cellosaurus (http://web.expas”
Gateways to the FANTOM5 promoter level mammalian expression atlas (2015, methodology): “To classify samples systematically, we assembled the FANTOM Five (FF) Sample Ontology [23] consisting of the existing basic ontologies: cell types (CL), anatomical systems (UBERON), and diseases (DOID) [30-32].”
A promoter-level mammalian expression atlas (2014, methodology): “To facilitate data mining all samples were annotated using structured ontologies (Cell Ontology 7 , Uberon 8 , Disease Ontology 9 ).”
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability (2016, background): “The set of ontologies imported into the CL to provide logical definitions remains constant, and consists of Uberon [22, 37], Protein Ontology (PRO) [38], GO [9], the Chemical Entities of Biological Interest (ChEBI) ontology [39], and the Phenotypic And Trait Ontology (PATO) [40].”
Gene Ontology Annotations and Resources (2012, methodology): “In addition to this fully validated set of logical deﬁnitions, we have partially validated logical deﬁnitions that make use of terms from other ontologies, such as the Cell Ontology (10) the Plant Anatomy Ontology (11) and the Uberon multi-species metazoan anatomy ontology (12).”