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Merging Biomedical Ontologies with BioSTransformers

Ontologies play a key role in representing and structuring domain knowledge. In the biomedical domain, the need for this type of representation is crucial for structuring, coding, and retrieving data. However, available ontologies do not encompass all the relevant concepts and relationships.
Menad, Safaa, Abdeddaïm, Saïd, Soualmia, Lina F.   +2 more
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The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration [PDF]

, 2007
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ...
Ashburner, Michael, Bard, Jonathan, Bug, William, Ceusters, Werner, Eilbeck, Karen, Goldberg, Louis J, Ireland, Amelia, Leontis, Neocles, Lewissi, Suzanna, Mungall, Christopher J, OBI Consortium, The, Rocca‐Serra, a b, Rosse, Cornelius, Ruttenberg, Alan, Sansone, Susanna-Assunta, Shah, Migam, Smith, Barry, Whetzel, Patricia L   +17 more
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TGF-beta signaling proteins and the Protein Ontology [PDF]

, 2009
The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the ...
Cathy, Wu, Cecilia, Arighi, Darren, Natale, Harold, Drabkin, Hongfang, Liu, Judith, Blake, Smith, Barry, Winona, Barker   +7 more
core  

Clonal Complexes in Biomedical Ontologies

Nature Precedings, 2009
AbstractAn accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Se-quence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a
Albert Goldfain, Lindsay G. Cowell, Barry Smith   +2 more
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OntONeo: The Obstetric and Neonatal Ontology [PDF]

, 2016
This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information ...
Almeida, Mauricio, Elkin, Peter, Farinelli, Fernanda, Smith, Barry   +3 more
core  

Protein Ontology: A controlled structured network of protein entities [PDF]

, 2013
The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level ...
Arighi Cecilia, N., Blake Judith, A., Bult Carol, J., Christie Karen, R., Diehl Alexander, D., Drabkin Harold, J., Julie, Cowart, Natale Darren, A., Olivia, Helfer, Others, Peter, D’Eustachio, Smith, Barry   +11 more
core  

Dealing with elements of medical encounters: An approach based on ontological realism [PDF]

, 2016
Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens.
Fernanda, Farinelli, Mauricio, Almeida, Peter, Elkin, Smith, Barry   +3 more
core  

Adopting Ontologies: Sustainable Research Reusing the Biomedical Resource Ontology

The FAIR principles have been adopted across scientific disciplines to promote sustainable use of data. Ontologies play a crucial role in facilitating data interoperability and reusability. However, existing ontologies may become outdated or redundant, hindering their continued use.
Michaelis, Lea, Lobentanzer, Sebastian, Waltemath, Dagmar, Wodke, Judith A.H.   +3 more
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Function, Role, and Disposition in Basic Formal Ontology [PDF]

, 2008
Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and
Barry Smith, Robert Arp
core   +1 more source

An evolutionary approach to the representation of adverse events [PDF]

, 2009
One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented.
Capolupo, Maria, Ceusters, Werner, De Moor, Georges, Smith, Barry   +3 more
core   +1 more source