article (9)

Hoehndorf, Robert, Oellrich, Anika, and Rebholz-Schuhmann, Dietrich (2010).

Interoperability between phenotype and anatomy ontologies.

Bioinformatics.

[link]

Motivation: Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning.Results: We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge.Availability: http://bioonto.de/pmwiki.php/Main/PheneOntology Contact: rh497@cam.ac.uk
Hoehndorf, Robert, Oellrich, Anika, Dumontier, Michel, Kelso, Janet, Rebholz-Schuhmann, Dietrich, and Herre, Heinrich (2010).

Relations as patterns: bridging the gap between OBO and OWL..

BMC Bioinformatics, 11(1), 441+.

[link]

BACKGROUND: most biomedical ontologies are represented in the OBO Flatfile Format, which is an easy-to-use graph-based ontology language. The semantics of the OBO Flatfile Format 1.2 enforces a strict predetermined interpretation of relationship statements between classes. It does not allow flexible specifications that provide better approximations of the intuitive understanding of the considered relations. If relations cannot be accurately expressed then ontologies built upon them may contain false assertions and hence lead to false inferences. Ontologies in the OBO Foundry must formalize the semantics of relations according to the OBO Relationship Ontology (RO). Therefore, being able to accurately express the intended meaning of relations is of crucial importance. Since the Web Ontology Language (OWL) is an expressive language with a formal semantics, it is suitable to de ne the meaning of relations accurately. RESULTS: we developed a method to provide definition patterns for relations between classes using OWL and describe a novel implementation of the RO based on this method. We implemented our extension in software that converts ontologies in the OBO Flatfile Format to OWL, and also provide a prototype to extract relational patterns from OWL ontologies using automated reasoning. The conversion software is freely available at http://bioonto.de/obo2owl, and can be accessed via a web interface. CONCLUSIONS: explicitly defining relations permits their use in reasoning software and leads to a more flexible and powerful way of representing biomedical ontologies. Using the extended langua0067e and semantics avoids several mistakes commonly made in formalizing biomedical ontologies, and can be used to automatically detect inconsistencies. The use of our method enables the use of graph-based ontologies in OWL, and makes complex OWL ontologies accessible in a graph-based form. Thereby, our method provides the means to gradually move the representation of biomedical ontologies into formal knowledge representation languages that incorporates an explicit semantics. Our method facilitates the use of OWL-based software in the back-end while ontology curators may continue to develop ontologies with an OBO-style front-end.
Hoehndorf, Robert, Ngonga Ngomo, Axel-Cyrille, Dannemann, Michael, and Kelso, Janet (2010).

Statistical tests for associations between two directed acyclic graphs..

PloS ONE, 5(6), e10996+.

Public Library of Science

[link]

Biological data, and particularly annotation data, are increasingly being represented in directed acyclic graphs (DAGs). However, while relevant biological information is implicit in the links between multiple domains, annotations from these different domains are usually represented in distinct, unconnected DAGs, making links between the domains represented difficult to determine. We develop a novel family of general statistical tests for the discovery of strong associations between two directed acyclic graphs. Our method takes the topology of the input graphs and the specificity and relevance of associations between nodes into consideration. We apply our method to the extraction of associations between biomedical ontologies in an extensive use-case. Through a manual and an automatic evaluation, we show that our tests discover biologically relevant relations. The suite of statistical tests we develop for this purpose is implemented and freely available for download.
Hoehndorf, Robert, Ngonga Ngomo, Axel-Cyrille, and Kelso, Janet (2010).

Applying the functional abnormality ontology pattern to anatomical functions..

Journal of biomedical semantics, 1(1), 4+.

[link]

ABSTRACT: BACKGROUND: Several biomedical ontologies cover the domain of biological functions, including molecular and cellular functions. However, there is currently no publicly available ontology of anatomical functions.Consequently, no explicit relation between anatomical structures and their functions is expressed in the anatomy ontologies that are available for various species. Such an explicit relation between anatomical structures and their functions would be useful both for defining the classes of the anatomy and the phenotype ontologies accurately. RESULTS: We provide an ontological analysis of functions and functional abnormalities. From this analysis, we derive an approach to the automatic extraction of anatomical functions from existing ontologies which uses a combination of natural language processing, graph-based analysis of the ontologies and formal inferences. Additionally, we introduce a new relation to link material objects to processes that realize the function of these objects. This relation is introduced to avoid a needless duplication of processes already covered by the Gene Ontology in a new ontology of anatomical functions. CONCLUSIONS: Ontological considerations on the nature of functional abnormalities and their representation in current phenotype ontologies show that we can extract a skeleton for an ontology of anatomical functions by using a combination of process, phenotype and anatomy ontologies automatically. We identify several limitations of the current ontologies that still need to be addressed to ensure a consistent and complete representation of anatomical functions and their abnormalities. AVAILABILITY: The source code and results of our analysis are available at http://bioonto.de.
Hoehndorf, Robert, Kelso, Janet, and Herre, Heinrich (2009).

The ontology of biological sequences..

BMC Bioinformatics, 10(1), 377+.

[link]

BACKGROUND: Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. RESULTS: We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. CONCLUSION: Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.
Hoehndorf, Robert, Bacher, Joshua, Backhaus, Michael, Gregorio, Sergio E., Loebe, Frank, Prüfer, Kay, Uciteli, Alexandr, Visagie, Johann, Herre, Heinrich, and Kelso, Janet (2009).

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology..

BMC Bioinformatics, 10 Suppl 5(Suppl 5), S5+.

[link]

MOTIVATION: Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. RESULTS: We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. AVAILABILITY: The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.
Hoehndorf, Robert, Loebe, Frank, Poli, Roberto, Kelso, Janet, and Herre, Heinrich (2008).

GFO-Bio: A biomedical core ontology.

Applied Ontology, 3(4), 219-227.

[link]

The rapid increase in the number and use of biological ontologies necessitates developing systems for their integration. In this paper we present a core ontology for biology, and outline its application for integrating biological domain ontologies. Our ontology rests on a foundational ontology, which offers higher-order categories and a theory of levels of reality. The core ontology is implemented in two separate components, each of which adheres to OWL-DL. These can be used independently with efficient DL reasoners, but they will be most effective when used together, which necessitates working with an OWL-Full ontology. The ontology is freely available from our website at: http://bioonto.de/pmwiki.php/Main/GFO-Bio.
Hoehndorf, Robert, Loebe, Frank, Kelso, Janet, and Herre, Heinrich (2007).

Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies.

BMC Bioinformatics, 8(1).

[link]

BACKGROUND:Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will contribute to the creation of a rich knowledge base that can be used for querying, as well as generating and testing novel hypotheses. The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability. However, semantic extensions are required to meet the OBO Foundry interoperability goals. Inconsistencies may arise when ontologies of properties - mostly phenotype ontologies - are combined with ontologies taking a canonical view of a domain - such as many anatomical ontologies. Currently, there is no support for a correct and consistent integration of such ontologies.RESULTS:We have developed a methodology for accurately representing canonical domain ontologies within the OBO Foundry. This is achieved by adding an extension to the semantics for relationships in the biomedical ontologies that allows for treating canonical information as default. Conclusions drawn from default knowledge may be revoked when additional information becomes available. We show how this extension can be used to achieve interoperability between ontologies, and further allows for the inclusion of more knowledge within them. We apply the formalism to ontologies of mouse anatomy and mammalian phenotypes in order to demonstrate the approach.CONCLUSION:Biomedical ontologies require a new class of relations that can be used in conjunction with default knowledge, thereby extending those currently in use. The inclusion of default knowledge is necessary in order to ensure interoperability between ontologies.
Burek, Patryk, Hoehndorf, Robert, Loebe, Frank, Visagie, Johann, Herre, Heinrich, and Kelso, Janet (2006).

A top-level ontology of functions and its application in the Open Biomedical Ontologies..

Bioinformatics, 22(14), e66-e73.

[link]

MOTIVATION: A clear understanding of functions in biology is a key component in accurate modelling of molecular, cellular and organismal biology. Using the existing biomedical ontologies it has been impossible to capture the complexity of the community's knowledge about biological functions. RESULTS: We present here a top-level ontological framework for representing knowledge about biological functions. This framework lends greater accuracy, power and expressiveness to biomedical ontologies by providing a means to capture existing functional knowledge in a more formal manner. An initial major application of the ontology of functions is the provision of a principled way in which to curate functional knowledge and annotations in biomedical ontologies. Further potential applications include the facilitation of ontology interoperability and automated reasoning. A major advantage of the proposed implementation is that it is an extension to existing biomedical ontologies, and can be applied without substantial changes to these domain ontologies. AVAILABILITY: The Ontology of Functions (OF) can be downloaded in OWL format from http://onto.eva.mpg.de/. Additionally, a UML profile and supplementary information and guides for using the OF can be accessed from the same website. CONTACT: bioonto@lists.informatik.uni-leipzig.de.

incollection (1)

Kelso, Janet, Hoehndorf, Robert, and Prüfer, Kay (2010).

Ontologies in Biology.

Theory and Applications of Ontology: Computer Applications, 347-371.

Springer Netherlands

[link]

In recent years ontologies have come to play an increasingly important role in the biomedical domain. Primary applications have been the formalisation of community knowledge in molecular biology, and the provision of a shared vocabulary for the annotation of the growing amount of biological data being generated. Ontologies now play a key role in the analysis and reporting of biological data and act as the basis for new biological services being hosted by various GRID projects. More formal methods from ontology theory are gradually being adopted, and have made the existing ontologies more robust. These approaches will continue to extend the number of potential applications for ontologies in the biomedical domain.

inproceedings (15)

2010-10 (1)

Hoehndorf, Robert, Ngonga Ngomo, Axel-Cyrille, Pyysalo, Sampo, Ohta, Tomoko, Oellrich, Anika, and Rebholz-Schuhmann, Dietrich (2010).

Applying ontology design patterns to the implementation of relations in GENIA.

Proceedings of the Fourth Symposium on Semantic Mining in Biomedicine (SMBM 2010).

[link]

Motivation: Annotated reference corpora such as the GENIA corpus play an important role in biomedical infor-mation extraction. A semantic annotation of the natural language texts in these reference corpora using formalontologies and logic is challenging due to the ambiguous use of natural language and natural language semantics.Providing formal definitions and axioms for these relations would offer the means for developing consistent andverifiable annotation guidelines and allow for the automatic verification of annotations as well as enabling thediscovery of new information through deductive inferences.Results: We developed a formal ontology of relations based on the relations used in the recent GENIA corpusannotations. For this purpose, we selected existing axiom systems based on the desired properties of the relationswithin the domain and provided new axioms for several relations. To apply this ontology of relations to thesemantic annotation of natural language texts, we developed and implemented two ontology design patterns. Weprovide an implementation of the ontology of relations in the Web Ontology Language (OWL). By combining theimplementation of the design patterns and that of the relation ontology, we also provide a software applicationto convert annotated GENIA abstracts into OWL ontologies. In this way, we make these ontologies amenable forautomated verification, deductive inferences and other knowledge-based applications.Availability: Documentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/.Contact: rh497@cam.ac.uk

2010-09 (1)

Adams, Nico, Hennig, Christian, Hoehndorf, Robert, Oellrich, Anika, Rebholz-Schuhmann, Dietrich, and Hansen, Gesine (2010).

The Ontology of Primary Immunodeficiency Diseases (PIDs): Using PIDs to Rethink the Ontology of Phenotypes.

Proceedings of the 2nd Workshop for Ontologies in Biomedicine and Life sciences (OBML).

[link]

Primary immunodeficiency diseases (PIDs) are the consequence of genetic disorders and usually manifest themselves in very young patients. Because of their rarity, they are notoriously difficult to diagnose both for general practitioners and clinicians. In this paper, we present the foundations of an ontology of PIDs, which will be at the heart of an expert system designed to assist the clinician in the diagnosis of these diseases. To achieve this, the PIDOntology characterises Primary Immunodefieciencies in terms of Phenotypes. While there are a number of different ontologies already available that allow the description of phenotypes and phenotypic qualities, these have a number of associated ontological problems, which we will also address as part of this paper. We use the subtype of Hyper-IgE Syndrome caused by a STAT3 defects as an example of a primary immunodeficiency and show how the clinical phenotype of the disease can be modeled in terms of other phenotypes by introducing the notion of the -Y¡ phene¡. Furthermore, we develop patterns for different types of phenes and show, that these patterns can be mapped onto more traditional entity-quality statements, which are the current state of the art in phenotypic modeling.

2010-07 (1)

Hoehndorf, Robert, Oellrich, Anika, Dumontier, Michel, Kelso, Janet, Herre, Heinrich, and Rebholz-Schuhmann, Dietrich (2010).

OWLDEF: Integrating OBO and OWL.

Proceedings of the 13th Annual Bio-Ontologies Meeting.

An integration of the OBO Flatfile Format and the Web Ontology Language OBOF with OWL while maintaining the semantics for relations provided by the RO. (OWL) would enable automated reasoning, inferences and consistency checking of biomedical ontologies and support the development and maintenance of ontologies developed in the OBO Flatfile Format. So far, the translation of relations in the OBO language to OWL is performed according to a single rigid pattern and in violation of the relation definitions of the OBO Relationship Ontology. We extend both the OBO Flatfile Format and the Manchester OWL Syntax to accommodate relation definitions. Based on these extensions, we implemented and evaluated two software applications. The first converts the OBO Flatfile Format to an OWL representation. The second uses automated inferences to convert OWL ontologies back to a representation in the OBO Flatfile Format. The OWLDEF method is generally applicaple whenever ontologies are developed primarily using patterns and not a detailled knowledge representation language. The tools and libraries we developed for the OWLDEF method are available from http://bioonto. de/obo2owl.

2010-06 (1)

Hoehndorf, Robert, Oellrich, Anika, Dumontier, Michel, Kelso, Janet, Herre, Heinrich, and Rebholz-Schuhmann, Dietrich (2010).

Relational patterns in OWL and their application to OBO.

OWL: Experiences and Directions (OWLED).

[link]

Directed acyclic graphs are commonly used to represent on-tologies in the biomedical domain. They provide an intuitive means toformalize relations that hold between ontological categories. However,their semantics is usually not explicit. We provide a semantics for a partof the OBO Flatfile Format by extending OWL with a method to expressrelational patterns. These patterns are OWL axioms with variables forclasses. The variables can only be filled with named classes. Addition-ally, we provide a semantics for open patterns in OWL. Our method isapplicable to the OBO Flatfile Format, and provides a means to designOWL ontologies using complex ontology design patterns. Therefore, itleads not only to an integration of the OBO Flatfile Format and OWL,but extends OWL with an intuitive interface for designing ontologies us-ing complex definition patterns. A prototypic implementation and testresults are available at http://bioonto.de/obo2owl.

2010-05 (1)

Dumontier, Michel and Hoehndorf, Robert (2010).

Realism for scientific ontologies.

Formal Ontology in Information Systems, Proceedings of the Sixth International Conference, FOIS 2010, 209(), 387-399.

Toronto, Canada: IOS Press

[link]

Science aims to develop an accurate understanding of reality through a variety of rigorously empirical and formal methods. Ontologies are used to formalize the meaning of terms within a domain of discourse. The Basic Formal Ontology (BFO) is an ontology of particular importance in the biomedical domains, where it provides the top-level for numerous ontologies, including those admitted as part of the OBO Foundry collection. The BFO requires that all classes in an ontology are actually instantiated in reality. Despite the fact that it is hard to show whether entities of some kind exist or do not exist in reality (especially for unobservable entities like elementary particles), this criterion fails to satisfy the need of scientists to communicate their findings and theories unambiguously. We discuss the problems that arise due to the BFO's realism criterion and suggest viable alternatives.

2009-10 (1)

Hoehndorf, Robert, Ngonga Ngomo, Axel-Cyrille, and Kelso, Janet (2009).

The application of an ontology design pattern for functional abnormalities to phenotype ontologies and the extraction of an ontology of anatomical functions.

Proceedings of the The 3rd International Symposium on Languages in Biology and Medicine.

[link]

Functions play an important role throughoutbiology. Although molecular functions are cov-ered in the Gene Ontology, there is currently nopublicly available ontology of anatomical func-tions. Ontological considerations on the natureof functional abnormalities and their represen-tation in current phenotype ontologies showthat we can automatically extract a skeletonfor such an ontology of anatomical functionsby using a combination of process, phenotypeand anatomy ontologies. We provide an onto-logical analysis of the nature of functions andfunctional abnormalities. From this analysis,we derive an approach to the automatic ex-traction of anatomical functions from existingontologies using a combination of natural lan-guage processing, graph-based analysis of theontologies and formal inferences. Alternatively,we introduce a new relation to relate materialobjects to processes that realize the functionof the object to avoid a needless duplication ofprocesses already present in the Gene Ontol-ogy in a new ontology of anatomical functions.We discuss several limitations of the currentontologies that still need to be addressed to en-sure a consistent and complete representationof anatomical functions and functional abnor-malities.

2009-09 (1)

Hoehndorf, Robert, Ngonga Ngomo, Axel-Cyrille, and Herre, Heinrich (2009).

Developing Consistent and Modular Software Models with Ontologies.

SoMeT, 399-412.

[link]

The development and verification of software models that are applica- ble across multiple domains remains a difficult problem. We propose a novel ap- proach to model-driven software development based on ontologies and Semantic Web technology. Our approach uses three ontologies to define software models: a task ontology, a domain ontology and a top-level ontology. The task ontology serves as the conceptual model for the software, the domain ontology provides domain- specific knowledge and the top-level ontology integrates the task and domain on- tologies. Our method allows the verification of these models both for consistency and ontological adequacy. This verification can be performed both at development and runtime. Domain ontologies are replaceable modules, which enables the com- parison and application of the models built using our method across multiple do- mains. We demonstrate the viability of our approach through the design and im- plementation of a semantic wiki and a social tagging system, and compare it with model-driven software development to illustrate its benefits.

2009-07 (1)

Hoehndorf, Robert, Kelso, Janet, and Herre, Heinrich (2009).

A Formal Ontology of Sequences.

Proceedings of the First International Conference on Biomedical Ontologies (ICBO).

Nature Precedings.

Buffalo, NY: Nature Publishing Group

[link]

The Sequence Ontology is an OBO Foundry ontology that provides categories of sequences and sequence features that are applied to the annotation of genomes. To facilitate interoperability with other domain ontologies and to provide a foundation for automated inference, we provide here an axiom system for the Sequence and Junction categories in first- and second-order predicate logics.

2009-06-28 (1)

Hoehndorf, Robert, Kelso, Janet, and Herre, Heinrich (2009).

Contributions to the formal ontology of functions and dispositions: an application of non-monotonic reasoning.

Proceedings of the 12th Annual Bio-Ontologies Meeting.

[link]

We introduce a basic ontology of functions and dispositions. The theory we suggest is compatible both with major philosophical theories of biological functions and with most top-level ontologies. The particular focus of the suggested formalism is on the inference of causal relationships from functionality and the explicit formalization of the normative character of functions using non-monotonic forms of knowledge representation.

2008-09 (2)

Hoehndorf, Robert, Ngonga Ngomo, Axel-Cyrille, Dannemann, Michael, and Kelso, Janet (2008).

From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories.

Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, 53-60.

Turku Centre for Computer Science (TUCS)

[link]

The co-occurrence of terms in a text corpus may indicate the presence of a relation between the referents of these terms. We expect co-occurrence-based methods to identify association relations that cannot be found using static patterns. We developed a new method to identify associations between ontological categories in text using the co-occurrence of terms that designate these categories. We use the taxonomic structure of the ontologies to cumulate the number of co-occurrences of terms designating categories. Based on these cumulated values, we designed a novel family of statistical tests to identify associated categories. These tests take both co-occurrence specificity and relevance into consideration. We applied our method to a 2.2 GB text corpus containing fulltext articles and used Gene Ontology's biological process ontology and the Celltype Ontology. The software and results can be found at http: //bioonto.de/pmwiki.php/Main/ ExtractingBiologicalRelations.
Hoehndorf, Robert, Ngonga Ngomo, Axel-Cyrille, and Dannemann, Michael (2008).

Towards Ontological Interpretations for Improved Text Mining.

Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, 165-166.

Turku Centre for Computer Science (TUCS)

[link]

2008-06 (1)

Hoehndorf, Robert, Bacher, Joshua, Backhaus, Michael, Gregorio, Sergio E., Loebe, Frank, Prüfer, Kay, Uciteli, Alexandr, Visagie, Johann, Herre, Heinrich, and Kelso, Janet (2008).

BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology.

Proceedings of the 11th Annual Bio-Ontologies Meeting.

Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently requires input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities such as wikis for the description, discussion and annotation of the functions of genes and gene products [Wang, 2006, Hoehndorf et al., 2006, Giles, 2007]. However, an open approach like wikis frequently raises concerns regarding the quality of the information captured. The information represented in the wiki should adhere to particular quality criteria such as internal consistency (the wiki content does not contain contradictory information) and consistency with biological background knowledge (the wiki content should be semantically correct). To address some of these concerns, logic-based tools can be employed. We have developed the BOWiki, a wiki system that uses a core ontology together with an automated reasoner to maintain a consistent knowledge base. It is specifically targeted at small- to medium-sized communities. to collaboratively integrate information and annotate data. The BOWiki and supplementary material is available at http://www. bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki. Contact: bowiki-users@lists.informatik.uni-leipzig.de

2007-05 (1)

Backhaus, Michael, Kelso, Janet, Bacher, Joshua, Herre, Heinrich, Hoehndorf, Robert, Loebe, Frank, and Visagie, Johann (2007).

BOWiki - a collaborative annotation and ontology curation framework.

Proceedings of Workshop on Social and Collaborative Construction of Structured Knowledge.

As the amount of data being generated in biology has in- creased, a major challenge has been how to store and rep- resent this data in a way that makes it easily accessible to researchers from diverse domains. Understanding the rela- tionship between genotype and phenotype is a major focus of biological research. Various approaches to providing the link between genes and their functions have been undertaken – most require significant and dedicated manual curation. Advances in web technologies make possible an alternative route for the construction of such knowledge bases - large- scale community collaboration. We describe here a system, the BOWiki, for the collaborative annotation of gene infor- mation. We argue that a semantic wiki provides the func- tionality required for this project since this can capitalize on the existing representations in biological ontologies. We describe our implementation and show how formal ontolo- gies could be used to increase the usability of the software through type-checking and automatic reasoning.

2006-11 (1)

Hoehndorf, Robert, Prüfer, Kay, Backhaus, Michael, Herre, Heinrich, Kelso, Janet, Loebe, Frank, and Visagie, Johann (2006).

A proposal for a gene functions wiki.

OTM Workshops 2006, 669-678.

Springer-Verlag

[link]

Large knowledge bases integrating dierent domains canprovide a foundation for new applications in biology such as data miningor automated reasoning. The traditional approach to the constructionof such knowledge bases is manual and therefore extremely time consuming.The ubiquity of the internet now makes large-scale communitycollaboration for the construction of knowledge bases, such as the successfulonline encyclopedia -Y¡ Wikipedia¡, possible.We propose an extension of this model to the collaborative annotationof molecular data. We argue that a semantic wiki provides the functionalityrequired for this project since this can capitalize on the existingrepresentations in biological ontologies. We discuss the use of a differentrelationship model than the one provided by RDF and OWL torepresent the semantic data. We argue that this leads to a more intuitiveand correct way to enter semantic content in the wiki. Furthermore, weshow how formal ontologies could be used to increase the usability ofthe software through type-checking and automatic reasoning.

2006-07 (1)

Hoehndorf, Robert, Prüfer, Kay, Backhaus, Michael, Visagie, Johann, and Kelso, Janet (2006).

The design of a wiki-based curation system for the Ontology of Functions.

Proceedings of the Joint BioLINK and 9th Bio-Ontologies Meeting.

[link]

Recently, studies argued that statistical and linguistic methods can be applied to extract information from biomedical ontologies, and represent the identified relations in the top-level ontology Ontology of Functions (OF). However, human intervention is required in order to clear noise from the generated data. A simple platform for collaborative work is needed. We propose here the use of a semantic wiki to represent relations between terms. We provide a relationship model for this semantic wiki, and add a core ontology as top-level type system to this wiki. We then discuss a design for the implementation of a platform for the curation of the OF, thereby enabling the community to curate the results of automatic extraction methods, and to add and correct ontology and annotation information. The aim of this collaborative effort is to provide a means to extend and correct the numerous ontologies which are used to describe biological functions in the OF.

mastersthesis (1)

Hoehndorf, Robert (2005).

Situoid Theory - An ontological approach to Situation Theory.

Institute for Informatics, University of Leipzig

[link]

Situations are entities that have been discussed in philosophy, ontology and computer science for applications in the field of knowledge representation, conceptual modelling and natural language semantic. On the basis of an extensive literature review, situations and entities we call situoids, which are more basic than situations, will be discussed and their ontological features investigated. As far as possible, the results of this investigation are formulated as axioms. This is done with respect to a background top-level ontology, the ontology of GOL. The belief that situoids are ``parts of reality that can be comprehended as a whole'' is central to this research, and will be investigated thoroughly. Situations as derived entities are not given as much attention, but some of their features will be discussed as well. While attempting to describe situoids, other categories have to be mentioned, such as states of affairs and infons. The theory is built up systematically from states of affairs over infons, situoids to situations. Some applications known from situation theory are revisited in the framework of situoids. Finally, it is shown how the theory if situoids can be used to introduce modality in GOL.

misc (1)

Hoehndorf, Robert (2010).

What is an upper-level ontology?.

Ontogenesis blog.

[link]

Upper level ontologies are used to facilitate the semantic integration of domain ontologies and guide the development of new ontologies. For this purpose, they contain general categories that are applicable across multiple domains. Upper level ontologies usually provide rich definitions and axioms for their categories. Different upper level ontologies provide different distinctions based on the kinds of entities they include, their theories of space and time as well as the relation of individuals to space and time.

phdthesis (1)

Hoehndorf, Robert (2009).

Basic considerations for improving interoperability between ontology-based biological information systems.

University of Leipzig

[link]

techreport (1)

Herre, Heinrich, Heller, Barbara, Burek, Patryk, Hoehndorf, Robert, Loebe, Frank, and Michalek, Hannes (2006).

General Formal Ontology (GFO) - A Foundational Ontology Integrating Objects and Processes [Version 1.0].

Research Group Ontologies in Medicine, Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig

[link]

This report is a living document of the Research Group Ontologies in Medicine (Onto-Med) which represents work in progress towards a proposal for an integrated system of foundational ontologies. It will be applied to several fields of medicine, biomedicine, and biology, and a number of applications are carried out in collaboration with the Max-Planck-Institute for Evolutionary Anthropology and the Coordination Center for Clinical Trials at the University of Leipzig. The General Formal Ontology (GFO) is a component of the Integrated System of Foundational Ontologies (ISFO), and ISFO is a part of the Integrated Framework for the Development and Application of Ontologies (IFDAO). The predecessor of IFDAO was the GOL project which was launched in 1999 as a collaborative research effort of the Institute of Medical Informatics, Statistics and Epidemiology (IMISE) and the Institute of Informatics (IfI) at the University of Leipzig.

Robert Hoehndorf

Publication list