Relations in biomedical ontologies

By Barry Smith, Werner Ceusters, B. Klagges, J. Köhler, Anand Kumar, Jane Lomax, C. Mungall, F. Neuhaus, Alan L. Rector, Cornelius Rosse. 2005

1,162 citations recorded by the source corpus.

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Subfields: Artificial Intelligence, Language and Linguistics, 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 Language and Linguistics

Nigam H. Shah

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), ChEBI (17), Relations Ontology (18), NCBI Taxonomy (19), Sequence Ontology (20), Ontology of B”
Enabling semantic queries across federated bioinformatics databases (2019, methodology): “To the best of our knowledge, two semantic models currently exist as initial attempts to structure gene expression related data: the Relation Ontology (51) and the Expression Atlas model (52) We stress that GenEx is currently in draft state.”
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses (2012, methodology): “Formal, logical definitions of these relations can be found in the Relation Ontology (RO; Smith et al. 2005).”
The Gene Ontology (GO) project in 2006 (2005, background): “net/relationship/) is an ontology of core relationship types, such as is_a, part_of, located_in and derives_from, with explicit definitions, to be used by all ontologies in the OBO collection (33).”
Ontological realism: A methodology for coordinated evolution of scientific ontologies (2010, positive): “Many of the errors of the NCIT, then and now, grow out of confusions surrounding the term ‘concept’ and its cognates, as for example in the use-mention confusions present in NCIT deﬁnitions such as: Conceptual entity = def .”
Evolution of the Sequence Ontology terms and relationships (2010, background): “The SO has a large user community of established model organism databases and newer ‘emerging model organism’ systems who use on the Generic Model Organism Database (GMOD) [2] suite of tools to annotate and disseminate their genetic information.”
ChEBI: a database and ontology for chemical entities of biological interest (2007, background): “There is, in the OBO community, an effort to standardize the relationships used in biomedical ontologies (13).”
Bio-ontologies: current trends and future directions (2006, background): “The publication of the OBO relations [62] therefore represents an important contribution to bio-ontologies.”
The Cognitive Atlas: Toward a Knowledge Foundation for Cognitive Neuroscience (2011, background): “A standard set of ontological relations has been codified into the open biomedical ontologies (OBO) Relational Ontology (Smith et al., 2005), which provides guidelines regarding the consistent use of specific ontological relations across different ontologies.”
Chemical Entities of Biological Interest: an update (2009, background): “This has been resolved by the introduction of the relationship ‘has part’ which is the inverse of the ‘is part of’ relationship, replacing all former ambiguous usage of ‘is part of’ with a consistent usage according to the definition of ‘has part’ in the Relationship Ontology (4), namely that if Ent”
Integrating phenotype ontologies across multiple species (2010, neutral): “These anatomy ontologies are arranged as is_a hierarchies and often include additional relations such as part_of and develops_from [12].”
The Gene Ontology knowledgebase in 2023 (2023, background): “2014), Relation Ontology (Smith et al. 2005), Cell Ontology (Diehl et al.”
Standardized description of scientific evidence using the Evidence Ontology (ECO) (2014, methodology): “In the future, a more general-purpose relation may be selected from an ontology such as the Relationship Ontology (15), IAO or OBI.”
Controlled vocabularies and semantics in systems biology (2011, background): “The branches of SBO are linked to the root by standard is_a relationships (Smith et al , 2005).”