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[iaoa-general] Applied Ontology, Volume 6, Number 1/2011 now available

To: ontolog forum <ontolog-forum@xxxxxxxxxxxxxxxx>, IAOA general <iaoa-general@xxxxxxxxxxxxxxxx>
From: Nicola Guarino <guarino@xxxxxxxxxx>
Date: Fri, 29 Apr 2011 15:47:17 +0200
Message-id: <6C6A0A51-9271-4479-BFDB-CFDC3FAD1F3E@xxxxxxxxxx>

Applied Ontology Volume 6, Number 1 / 2011 is now available on http://iospress.metapress.com/content/p34254783vq4/

Members of IAOA can access the issue by logging in on www.iaoa.org.


This is a special issue on Biomedical Ontologies

Guest editors: Alan Ruttenberg and Albert Goldfain


Regular Articles


Consolidating SNOMED CT's ontological commitment

Stefan Schulz, Ronald Cornet and Kent Spackman

Abstract. SNOMED CT is a clinical terminology that uses logical axioms to provide terms with meaning. This enforces precise agreements about the ontological nature of the entities denoted by the terms, commonly described as ontological commitment. We demonstrate that SNOMED CT implicitly supports at least three different kinds of ontological commitments: (i) commitments to independently existing entities, (ii) commitments to representational artifacts and (iii) commitments to clinical situations. Our analysis shows how the truth-value of a sentence changes according to one of these perspectives. We argue that a clear understanding of to what kind of entities SNOMED CT terms denote is crucial for the proper use and maintenance of SNOMED CT. We argue that the three kinds of commitment can co-exist but need to be clearly distinguished.


Overcoming the ontology enrichment bottleneck with Quick Term Templates

Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan R. Brinkman, Susanna Assunta Sansone, Richard Scheuermann, The OBI Consortium and Bjoern Peters

Abstract. When developing the Ontology of Biomedical Investigations (OBI), the process of adding classes with similar patterns of logical definition is time consuming, error prone, and requires an editor to have some expertise in OWL. Moreover, the process is poorly suited for a large number of domain experts who have limited experience with ontology development, and this can hinder contributions. We have developed a procedure to ease this task and allow such domain experts to add terms to the ontology in a way that both effectively includes complex logical definitions, yet requires minimal manual intervention by the OBI developers. The procedure is based on editing a Quick Term Template in a spreadsheet format that is subsequently converted into an OWL file. This procedure promises to be a robust and scalable approach for ontology enrichment as evidenced by encouraging results obtained when evaluated with an early version of the MappingMaster Protégé plugin.


MIREOT: The minimum information to reference an external ontology term

Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman and Alan Ruttenberg

Abstract. While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. Current editing tools present challenges for working with large ontologies and direct OWL imports can prove impractical for day-to-day development. Furthermore, external ontologies often undergo continuous change which can introduce conflicts when integrated with multiple efforts. Finally, importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the methodology, its implementation, present some examples of this application, and outline future work and extensions.


Open Biomedical Ontologies applied to prostate cancer

James A. Overton, Cesare Romagnoli and Rethy Chhem

Abstract. This paper surveys preliminary results from the Interdisciplinary Prostate Ontology Project (IPOP), in which ontologies from the OBO Foundry have been used to annotate clinical reports about prostate cancer. Our analysis shows that only half of the terms required to annotate these reports are currently included in OBO. However, we discuss methods for filling these gaps, and our reasons for preferring the OBO Foundry approach to annotation using controlled vocabularies such as SNOMED CT, the NCI Thesaurus, RadLex and the UMLS Metathesaurus. We end with a discussion of our ongoing work on image annotation and structured reporting with ontologies.


The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Robert Hoehndorf, Colin Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris J. Mungall, Jane S. Richardson, Jesse Stombaugh, Eric Westhof, Craig L. Zirbel and Neocles B. Leontis

Abstract. Biomedical Ontologies integrate diverse biomedical data and enable intelligent data-mining and help translate basic research into useful clinical knowledge. We present the RNA Ontology (RNAO), an ontology for integrating diverse RNA data, including RNA sequences and sequence alignments, three-dimensional structures, and biochemical and functional data. For example, individual atomic resolution RNA structures have broader significance as representatives of classes of homologous molecules, which can differ significantly in sequence while sharing core structural features and common roles or functions. Thus, structural data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise, the value of genomic data is enhanced by annotation of shared structural features, especially when these can be linked to specific functions. Moreover, the significance of biochemical, functional and mutational analyses of RNA molecules are most fully understood when linked to molecular structures and phylogenies. To achieve these goals, RNAO provides logically rigorous definitions of the components of RNA primary, secondary and tertiary structure and the relations between these entities. RNAO is being developed to comply with the developing standards of the Open Biomedical Ontologies (OBO) Consortium. The RNAO can be accessed at http://code.google.com/p/rnao/.




Creating the ontologists of the future

Fabian Neuhaus, Elizabeth Florescu, Antony Galton, Michael Gruninger, Nicola Guarino, Leo Obrst, Arturo Sanchez, Amanda Vizedom, Peter Yim and Barry Smith

Abstract. The goal of the Ontology Summit 2010 was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue.

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