Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data

Dumontier, Michel

Sansone, Susanna-Assunta

Shah, Nigam H

Soldatova, Larisa N

Journal of Biomedical Semantics

English

PubMed

Soldatova, LN

Sansone, SA

Dumontier, M

Shah, NH

Brunel University Research Archive

INTRODUCTION Open AccessSelected papers from the 14th Annual Bio-Ontologies Special Interest Group MeetingLarisa N Soldatova1*, Susanna-Assunta Sansone2, Michel Dumontier3, Nigam H Shah4From Bio-Ontologies 2011Vienna, Austria. 15-16 July 2011* Correspondence: lss@aber.ac.uk1Aberystwyth University, Wales, UKAbstractOver the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum fordiscussion of the latest and most innovative research in the bio-ontologiesdevelopment, its applications to biomedicine and more generally the organisation,presentation and dissemination of knowledge in biomedicine and the life sciences.The seven papers selected for this supplement span a wide range of topicsincluding: web-based querying over multiple ontologies, integration of data fromwikis, innovative methods of annotating and mining electronic health records,advances in annotating web documents and biomedical literature, quality control ofontology alignments, and the ontology support for predictive models about toxicityand open access to the toxicity data.Summary of selected papersIn 2011, the SIG received 29 paper submissions, 5 flash updates and 4 poster abstracts.18 papers and 11 flash updates (some papers were converted to flush updates) wereselected for presentation at the meeting, out of which 7 appear in this supplement.The seven papers selected for this supplement are extended versions of the originalpapers presented at the 2011 SIG. The papers include research on web-based queryingover multiple ontologies [3], integration of data from wikis into a meta semantic wiki[6], advances in the annotation of electronic health records [5], web documents [1] andbiomedical literature [2], quality control of ontology alignments [4], and the ontologybased support for the toxicity predictive models and access to the toxicity data [7].Paolo Ciccarese et al in the paper titled “DOMEO: a web-based tool for semanticannotation of online documents” describe work to date on an advancement in scienti-fic document automated annotation and collaborative curation using integrated ontolo-gies and frameworks in bioscience. The authors report on a user-friendly web basedinterface Domeo for the implementation of annotations of existing web resources.Domeo is an extensible web application enabling users to visually and efficiently createand share ontology-based stand-off annotation on HTML or XML document targets.The Domeo annotation tool supports manual, fully automated, and semi-automatedannotation with complete provenance records, as well as personal or community anno-tation with access authorization and control.Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1 JOURNAL OFBIOMEDICAL SEMANTICS© 2012 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.Domeo has been deployed in beta release as part of the NIH Neuroscience Informa-tion Framework (http://www.neuinfo.org). The Domeo annotation tool is available athttp://annotationframework.org/.The paper titled “A maximum entropy approach for accurate document annotation”by George Tsatsaronis et al addresses the critical task of document tagging for annota-tion of biomedical literature against ontologies of medical concern such as anatomy,disease and phycology. The authors present an automated and robust method, basedon maximum-entropy approach, for annotating biomedical literature documents withterms from Medical Subject Headings (MeSH). The suggested approach has increasedF-measure results when tested against title, journal and abstract text even using asmall number of documents. The work demonstrates the potential benefit of usingontologies to address the problem of information retrieval/extraction given the expo-nential growth of biomedical literature.Simon Jupp et al in the paper titled “Exploring Gene Ontology annotations withOWL” demonstrate that the controlled vocabulary annotations of gene products usingGO terms can be engineered to represent logical property restrictions on classes andindividuals in the OWL language such that it becomes possible to execute rich, logicalqueries over genes utilizing both the semantics of the gene annotations, as well as thesemantics of the GO itself. To do multi-perspective rich querying, the authors createdthe GOAL (Logical Gene Ontology) that combines the Gene ontology, Human DiseaseOntology, and the Mammalian Phenotype Ontology, together with classes for mousegene products. Defined classes were used to query these protein classes through auto-mated reasoning. This was presented through a Web interface that allows rich queriesand displays results. The GOAL ontology is available at http://owl.cs.manchester.ac.uk/goal.The paper “Towards valid and reusable reference alignments – ten basic qualitychecks for reference alignments and their application to three different reference datasets” by Elena Beisswanger and Udo Hahn outlines work in the area of ontology align-ment and highlights different checks that should be completed to assess whether align-ment is valid.The basic quality checks maybe of help to editors and curators evaluating the align-ment of ontologies, focusing on the reliability and reusability aspects.The checks are applied to the anatomy reference alignment datasets (the anatomybranch of the NCI Thesaurus and the Mouse adult gross anatomy ontology), also usedin the yearly Ontology Alignment Evaluation Initiative (OAEI); to the alignments ofLinked Open Data schemes; and for assessing upper ontology-based alignmentapproaches. The results reveal incorrect and missing correspondences, classes, andmissing or invalid relations between classes in the input ontologies. The basic checkscontribute to the quality of alignments. This is an area of growing importance.In “Annotation analysis for testing drug safety signals” by Paea LePendu et aldescribe a novel approach for leveraging resources for biomedical computing, such asthe NCBO Annotator tool and public biomedical ontologies for mining electronichealth records and to test drug safety signals. The authors analyzed over 9 millionunstructured clinical notes to compute the risk of having a myocardial infarction aftertaking Vioxx prescribed for rheumatoid arthritis. Their analysis reveals significant ele-vated risk for myocardial infarction in rheumatoid arthritis patients taking Vioxx asSoldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 2 of 4early as 2003 (2 years before the actual recall of the drug). The results demonstrate theutility of applying ontology based annotation analysis for detecting the relationshipsbetween drugs and health conditions in general. The results also demonstrate the feasi-bility of text-mining based approach for early detection of drug associated adverseevents by exploring a corpus of electronic health records.In the paper titled “Linking genes to diseases with a SNPedia-Gene Wiki mashup”,Benjamin Good et al present a semantic meta-wiki called the Gene Wiki+ that auto-matically integrates data from Gene Wiki and SNPedia. The Gene Wiki provides con-tinuously updated review articles for human genes, including descriptions of the rolethe gene may play in disease, and SNPedia provides textual information about linksbetween variations in human genes and human phenotypes. The Gene Wiki+ exposessubstantially more evidence of links between genes and diseases than either resourcecontains independently. Currently, it captures >8,000 distinct gene-disease relation-ships. The authors created an open source program SyncBot that continuously moni-tors the source wikis for changes and ensures that the Gene Wiki+ stays up-to-date.The content of the Gene Wiki+ is exported as RDF. The Gene Wiki+ is available athttp://genewikiplus.org.Olga Tcheremenskaia et al in the paper titled “OpenTox predictive toxicology frame-work: toxicological ontology and semantic media wiki-based OpenToxipedia” report ona suite of ontologies developed for the OpenTox project (http://www.opentox.org). TheOpenTox framework aims at providing access to toxicity data, predictive models, andvalidation procedures. Interoperability of resources is based on the OpenTox ontolo-gies describing predictive algorithms, models, and toxicity data. These ontologies havebeen developed following the OBO Foundry principles. The authors also report onwiki for the OpenTox predictive toxicology framework. The described project is ofmajor importance and likely to lead to many results in toxicology. The OpenToxontologies are available at http://www.opentox.org/dev/ontology.AcknowledgementsAs editors of this supplement, we thank all the authors who submitted papers, the Program Committee members andthe reviewers for their excellent work. We are grateful for help from Isobel Peters from BioMed Central as well as Dr.Goran Nenadic and Dr. Dietrich Rebholz-Schuhmann in putting this supplement together.This article has been published as part of Journal of Biomedical Semantics Volume 3 Supplement 1, 2012: Proceedingsof the Bio-Ontologies Special Interest Group Meeting 2012. The full contents of the supplement are available online athttp://www.jbiomedsem.com/supplements/3/S1Author details1Aberystwyth University, Wales, UK. 2University of Oxford, Oxford e-Research Centre, UK. 3Carleton University, Ottawa,Canada. 4Stanford University, CA, USA.Published: 24 April 2012References1. Ciccarese Paolo, Ocana Marco, Clark Tim: DOMEO: a web-based tool for semantic annotation of online documents.[http://www.jbiomedsem.com/supplements/3/S1/S1].2. Tsatsaronis George, Macari Natalia, Torge Sunna, Dietze Heiko, Schroeder Michael: A maximum entropy approach foraccurate document annotation. [http://www.jbiomedsem.com/supplements/3/S1/S2].3. Jupp Simon, Stevens Robert, Hoehndorf Robert: Exploring Gene Ontology annotations with OWL. [http://www.jbiomedsem.com/supplements/3/S1/S3].4. Beisswanger Elena, Hahn Udo: Towards valid and reusable reference alignments – ten basic quality checks forreference alignments and their application to three different reference data sets. [http://www.jbiomedsem.com/supplements/3/S1/S4].5. Le Pendu Paea, Racunas Stephen, Iyer Srinivasan, Liu Yi, Fairon Cédrick, Shah Nigam: Annotation analysis for testingdrug safety signals. [http://www.jbiomedsem.com/supplements/3/S1/S5].Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 3 of 46. Good Benjamin, Loguercio Salvatore, Su Andrew: Linking genes to diseases with a SNPedia-Gene Wiki mashup.[http://www.jbiomedsem.com/supplements/3/S1/S6].7. Tcheremenskaia Olga, Benigni Romualdo, Nikolova Ivelina, Jeliazkova Nina, Escher Sylvia E, Grimm Helvi, Baier Thomas,Poroikov Vladimir, Lagunin Alexey, Rautenberg Micha, Hardy Barry: OpenTox predictive toxicology framework:toxicological ontology and semantic media wiki-based OpenToxipedia. [http://www.jbiomedsem.com/supplements/3/S1/S7].doi:10.1186/2041-1480-3-S1-I1Cite this article as: Soldatova et al.: Selected papers from the 14th Annual Bio-Ontologies Special Interest GroupMeeting. Journal of Biomedical Semantics 2012 3(Suppl 1):I1.Submit your next manuscript to BioMed Centraland take full advantage of: • Convenient online submission• Thorough peer review• No space constraints or color figure charges• Immediate publication on acceptance• Inclusion in PubMed, CAS, Scopus and Google Scholar• Research which is freely available for redistributionSubmit your manuscript at www.biomedcentral.com/submitSoldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 4 of 4

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.

Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data.</p

Soldatova, Larisa N.

Shah, Nigam Haresh

Maastricht University Research Portal

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Aberystwyth Research Portal

Aberystwyth UniversitySelected papers from the 14th Annual Bio-Ontologies Special Interest GroupMeetingSoldatova, Larisa N; Sansone, Susanna-Assunta; Dumontier, Michel; Shah, Nigam HPublished in:Journal of Biomedical SemanticsDOI:10.1186/2041-1480-3-S1-I1Publication date:2012Citation for published version (APA):Soldatova, L. N., Sansone, S-A., Dumontier, M., & Shah, N. H. (2012). Selected papers from the 14th AnnualBio-Ontologies Special Interest Group Meeting. Journal of Biomedical Semantics, 3(Suppl 1), [I1].https://doi.org/10.1186/2041-1480-3-S1-I1General rightsCopyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) areretained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by thelegal requirements associated with these rights.            • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study orresearch.            • You may not further distribute the material or use it for any profit-making activity or commercial gain            • You may freely distribute the URL identifying the publication in the Aberystwyth Research PortalTake down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.tel: +44 1970 62 2400email: is@aber.ac.ukDownload date: 09. Jul. 2020INTRODUCTION Open AccessSelected papers from the 14th Annual Bio-Ontologies Special Interest Group MeetingLarisa N Soldatova1*, Susanna-Assunta Sansone2, Michel Dumontier3, Nigam H Shah4From Bio-Ontologies 2011Vienna, Austria. 15-16 July 2011* Correspondence: lss@aber.ac.uk1Aberystwyth University, Wales, UKAbstractOver the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum fordiscussion of the latest and most innovative research in the bio-ontologiesdevelopment, its applications to biomedicine and more generally the organisation,presentation and dissemination of knowledge in biomedicine and the life sciences.The seven papers selected for this supplement span a wide range of topicsincluding: web-based querying over multiple ontologies, integration of data fromwikis, innovative methods of annotating and mining electronic health records,advances in annotating web documents and biomedical literature, quality control ofontology alignments, and the ontology support for predictive models about toxicityand open access to the toxicity data.Summary of selected papersIn 2011, the SIG received 29 paper submissions, 5 flash updates and 4 poster abstracts.18 papers and 11 flash updates (some papers were converted to flush updates) wereselected for presentation at the meeting, out of which 7 appear in this supplement.The seven papers selected for this supplement are extended versions of the originalpapers presented at the 2011 SIG. The papers include research on web-based queryingover multiple ontologies [3], integration of data from wikis into a meta semantic wiki[6], advances in the annotation of electronic health records [5], web documents [1] andbiomedical literature [2], quality control of ontology alignments [4], and the ontologybased support for the toxicity predictive models and access to the toxicity data [7].Paolo Ciccarese et al in the paper titled “DOMEO: a web-based tool for semanticannotation of online documents” describe work to date on an advancement in scienti-fic document automated annotation and collaborative curation using integrated ontolo-gies and frameworks in bioscience. The authors report on a user-friendly web basedinterface Domeo for the implementation of annotations of existing web resources.Domeo is an extensible web application enabling users to visually and efficiently createand share ontology-based stand-off annotation on HTML or XML document targets.The Domeo annotation tool supports manual, fully automated, and semi-automatedannotation with complete provenance records, as well as personal or community anno-tation with access authorization and control.Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1 JOURNAL OFBIOMEDICAL SEMANTICS© 2012 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.Domeo has been deployed in beta release as part of the NIH Neuroscience Informa-tion Framework (http://www.neuinfo.org). The Domeo annotation tool is available athttp://annotationframework.org/.The paper titled “A maximum entropy approach for accurate document annotation”by George Tsatsaronis et al addresses the critical task of document tagging for annota-tion of biomedical literature against ontologies of medical concern such as anatomy,disease and phycology. The authors present an automated and robust method, basedon maximum-entropy approach, for annotating biomedical literature documents withterms from Medical Subject Headings (MeSH). The suggested approach has increasedF-measure results when tested against title, journal and abstract text even using asmall number of documents. The work demonstrates the potential benefit of usingontologies to address the problem of information retrieval/extraction given the expo-nential growth of biomedical literature.Simon Jupp et al in the paper titled “Exploring Gene Ontology annotations withOWL” demonstrate that the controlled vocabulary annotations of gene products usingGO terms can be engineered to represent logical property restrictions on classes andindividuals in the OWL language such that it becomes possible to execute rich, logicalqueries over genes utilizing both the semantics of the gene annotations, as well as thesemantics of the GO itself. To do multi-perspective rich querying, the authors createdthe GOAL (Logical Gene Ontology) that combines the Gene ontology, Human DiseaseOntology, and the Mammalian Phenotype Ontology, together with classes for mousegene products. Defined classes were used to query these protein classes through auto-mated reasoning. This was presented through a Web interface that allows rich queriesand displays results. The GOAL ontology is available at http://owl.cs.manchester.ac.uk/goal.The paper “Towards valid and reusable reference alignments – ten basic qualitychecks for reference alignments and their application to three different reference datasets” by Elena Beisswanger and Udo Hahn outlines work in the area of ontology align-ment and highlights different checks that should be completed to assess whether align-ment is valid.The basic quality checks maybe of help to editors and curators evaluating the align-ment of ontologies, focusing on the reliability and reusability aspects.The checks are applied to the anatomy reference alignment datasets (the anatomybranch of the NCI Thesaurus and the Mouse adult gross anatomy ontology), also usedin the yearly Ontology Alignment Evaluation Initiative (OAEI); to the alignments ofLinked Open Data schemes; and for assessing upper ontology-based alignmentapproaches. The results reveal incorrect and missing correspondences, classes, andmissing or invalid relations between classes in the input ontologies. The basic checkscontribute to the quality of alignments. This is an area of growing importance.In “Annotation analysis for testing drug safety signals” by Paea LePendu et aldescribe a novel approach for leveraging resources for biomedical computing, such asthe NCBO Annotator tool and public biomedical ontologies for mining electronichealth records and to test drug safety signals. The authors analyzed over 9 millionunstructured clinical notes to compute the risk of having a myocardial infarction aftertaking Vioxx prescribed for rheumatoid arthritis. Their analysis reveals significant ele-vated risk for myocardial infarction in rheumatoid arthritis patients taking Vioxx asSoldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 2 of 4early as 2003 (2 years before the actual recall of the drug). The results demonstrate theutility of applying ontology based annotation analysis for detecting the relationshipsbetween drugs and health conditions in general. The results also demonstrate the feasi-bility of text-mining based approach for early detection of drug associated adverseevents by exploring a corpus of electronic health records.In the paper titled “Linking genes to diseases with a SNPedia-Gene Wiki mashup”,Benjamin Good et al present a semantic meta-wiki called the Gene Wiki+ that auto-matically integrates data from Gene Wiki and SNPedia. The Gene Wiki provides con-tinuously updated review articles for human genes, including descriptions of the rolethe gene may play in disease, and SNPedia provides textual information about linksbetween variations in human genes and human phenotypes. The Gene Wiki+ exposessubstantially more evidence of links between genes and diseases than either resourcecontains independently. Currently, it captures >8,000 distinct gene-disease relation-ships. The authors created an open source program SyncBot that continuously moni-tors the source wikis for changes and ensures that the Gene Wiki+ stays up-to-date.The content of the Gene Wiki+ is exported as RDF. The Gene Wiki+ is available athttp://genewikiplus.org.Olga Tcheremenskaia et al in the paper titled “OpenTox predictive toxicology frame-work: toxicological ontology and semantic media wiki-based OpenToxipedia” report ona suite of ontologies developed for the OpenTox project (http://www.opentox.org). TheOpenTox framework aims at providing access to toxicity data, predictive models, andvalidation procedures. Interoperability of resources is based on the OpenTox ontolo-gies describing predictive algorithms, models, and toxicity data. These ontologies havebeen developed following the OBO Foundry principles. The authors also report onwiki for the OpenTox predictive toxicology framework. The described project is ofmajor importance and likely to lead to many results in toxicology. The OpenToxontologies are available at http://www.opentox.org/dev/ontology.AcknowledgementsAs editors of this supplement, we thank all the authors who submitted papers, the Program Committee members andthe reviewers for their excellent work. We are grateful for help from Isobel Peters from BioMed Central as well as Dr.Goran Nenadic and Dr. Dietrich Rebholz-Schuhmann in putting this supplement together.This article has been published as part of Journal of Biomedical Semantics Volume 3 Supplement 1, 2012: Proceedingsof the Bio-Ontologies Special Interest Group Meeting 2012. The full contents of the supplement are available online athttp://www.jbiomedsem.com/supplements/3/S1Author details1Aberystwyth University, Wales, UK. 2University of Oxford, Oxford e-Research Centre, UK. 3Carleton University, Ottawa,Canada. 4Stanford University, CA, USA.Published: 24 April 2012References1. Ciccarese Paolo, Ocana Marco, Clark Tim: DOMEO: a web-based tool for semantic annotation of online documents.[http://www.jbiomedsem.com/supplements/3/S1/S1].2. Tsatsaronis George, Macari Natalia, Torge Sunna, Dietze Heiko, Schroeder Michael: A maximum entropy approach foraccurate document annotation. [http://www.jbiomedsem.com/supplements/3/S1/S2].3. Jupp Simon, Stevens Robert, Hoehndorf Robert: Exploring Gene Ontology annotations with OWL. [http://www.jbiomedsem.com/supplements/3/S1/S3].4. Beisswanger Elena, Hahn Udo: Towards valid and reusable reference alignments – ten basic quality checks forreference alignments and their application to three different reference data sets. [http://www.jbiomedsem.com/supplements/3/S1/S4].5. Le Pendu Paea, Racunas Stephen, Iyer Srinivasan, Liu Yi, Fairon Cédrick, Shah Nigam: Annotation analysis for testingdrug safety signals. [http://www.jbiomedsem.com/supplements/3/S1/S5].Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 3 of 46. Good Benjamin, Loguercio Salvatore, Su Andrew: Linking genes to diseases with a SNPedia-Gene Wiki mashup.[http://www.jbiomedsem.com/supplements/3/S1/S6].7. Tcheremenskaia Olga, Benigni Romualdo, Nikolova Ivelina, Jeliazkova Nina, Escher Sylvia E, Grimm Helvi, Baier Thomas,Poroikov Vladimir, Lagunin Alexey, Rautenberg Micha, Hardy Barry: OpenTox predictive toxicology framework:toxicological ontology and semantic media wiki-based OpenToxipedia. [http://www.jbiomedsem.com/supplements/3/S1/S7].doi:10.1186/2041-1480-3-S1-I1Cite this article as: Soldatova et al.: Selected papers from the 14th Annual Bio-Ontologies Special Interest GroupMeeting. Journal of Biomedical Semantics 2012 3(Suppl 1):I1.Submit your next manuscript to BioMed Centraland take full advantage of: • Convenient online submission• Thorough peer review• No space constraints or color figure charges• Immediate publication on acceptance• Inclusion in PubMed, CAS, Scopus and Google Scholar• Research which is freely available for redistributionSubmit your manuscript at www.biomedcentral.com/submitSoldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 4 of 4

Larisa N Soldatova

Susanna-Assunta Sansone

Michel Dumontier

Nigam H Shah

Springer - Publisher Connector

INTRODUCTION Open Access
Selected papers from the 14th Annual Bio-
Ontologies Special Interest Group Meeting
Larisa N Soldatova1*, Susanna-Assunta Sansone2, Michel Dumontier3, Nigam H Shah4
From Bio-Ontologies 2011
Vienna, Austria. 15-16 July 2011
* Correspondence: lss@aber.ac.uk
1Aberystwyth University, Wales, UK
Abstract
Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for
discussion of the latest and most innovative research in the bio-ontologies
development, its applications to biomedicine and more generally the organisation,
presentation and dissemination of knowledge in biomedicine and the life sciences.
The seven papers selected for this supplement span a wide range of topics
including: web-based querying over multiple ontologies, integration of data from
wikis, innovative methods of annotating and mining electronic health records,
advances in annotating web documents and biomedical literature, quality control of
ontology alignments, and the ontology support for predictive models about toxicity
and open access to the toxicity data.
Summary of selected papers
In 2011, the SIG received 29 paper submissions, 5 flash updates and 4 poster abstracts.
18 papers and 11 flash updates (some papers were converted to flush updates) were
selected for presentation at the meeting, out of which 7 appear in this supplement.
The seven papers selected for this supplement are extended versions of the original
papers presented at the 2011 SIG. The papers include research on web-based querying
over multiple ontologies [3], integration of data from wikis into a meta semantic wiki
[6], advances in the annotation of electronic health records [5], web documents [1] and
biomedical literature [2], quality control of ontology alignments [4], and the ontology
based support for the toxicity predictive models and access to the toxicity data [7].
Paolo Ciccarese et al in the paper titled “DOMEO: a web-based tool for semantic
annotation of online documents” describe work to date on an advancement in scienti-
fic document automated annotation and collaborative curation using integrated ontolo-
gies and frameworks in bioscience. The authors report on a user-friendly web based
interface Domeo for the implementation of annotations of existing web resources.
Domeo is an extensible web application enabling users to visually and efficiently create
and share ontology-based stand-off annotation on HTML or XML document targets.
The Domeo annotation tool supports manual, fully automated, and semi-automated
annotation with complete provenance records, as well as personal or community anno-
tation with access authorization and control.
Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1
http://www.jbiomedsem.com/supplements/3/S1/I1 JOURNAL OF
BIOMEDICAL SEMANTICS
© 2012 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
Domeo has been deployed in beta release as part of the NIH Neuroscience Informa-
tion Framework (http://www.neuinfo.org). The Domeo annotation tool is available at
http://annotationframework.org/.
The paper titled “A maximum entropy approach for accurate document annotation”
by George Tsatsaronis et al addresses the critical task of document tagging for annota-
tion of biomedical literature against ontologies of medical concern such as anatomy,
disease and phycology. The authors present an automated and robust method, based
on maximum-entropy approach, for annotating biomedical literature documents with
terms from Medical Subject Headings (MeSH). The suggested approach has increased
F-measure results when tested against title, journal and abstract text even using a
small number of documents. The work demonstrates the potential benefit of using
ontologies to address the problem of information retrieval/extraction given the expo-
nential growth of biomedical literature.
Simon Jupp et al in the paper titled “Exploring Gene Ontology annotations with
OWL” demonstrate that the controlled vocabulary annotations of gene products using
GO terms can be engineered to represent logical property restrictions on classes and
individuals in the OWL language such that it becomes possible to execute rich, logical
queries over genes utilizing both the semantics of the gene annotations, as well as the
semantics of the GO itself. To do multi-perspective rich querying, the authors created
the GOAL (Logical Gene Ontology) that combines the Gene ontology, Human Disease
Ontology, and the Mammalian Phenotype Ontology, together with classes for mouse
gene products. Defined classes were used to query these protein classes through auto-
mated reasoning. This was presented through a Web interface that allows rich queries
and displays results. The GOAL ontology is available at http://owl.cs.manchester.ac.uk/
goal.
The paper “Towards valid and reusable reference alignments – ten basic quality
checks for reference alignments and their application to three different reference data
sets” by Elena Beisswanger and Udo Hahn outlines work in the area of ontology align-
ment and highlights different checks that should be completed to assess whether align-
ment is valid.
The basic quality checks maybe of help to editors and curators evaluating the align-
ment of ontologies, focusing on the reliability and reusability aspects.
The checks are applied to the anatomy reference alignment datasets (the anatomy
branch of the NCI Thesaurus and the Mouse adult gross anatomy ontology), also used
in the yearly Ontology Alignment Evaluation Initiative (OAEI); to the alignments of
Linked Open Data schemes; and for assessing upper ontology-based alignment
approaches. The results reveal incorrect and missing correspondences, classes, and
missing or invalid relations between classes in the input ontologies. The basic checks
contribute to the quality of alignments. This is an area of growing importance.
In “Annotation analysis for testing drug safety signals” by Paea LePendu et al
describe a novel approach for leveraging resources for biomedical computing, such as
the NCBO Annotator tool and public biomedical ontologies for mining electronic
health records and to test drug safety signals. The authors analyzed over 9 million
unstructured clinical notes to compute the risk of having a myocardial infarction after
taking Vioxx prescribed for rheumatoid arthritis. Their analysis reveals significant ele-
vated risk for myocardial infarction in rheumatoid arthritis patients taking Vioxx as
Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1
http://www.jbiomedsem.com/supplements/3/S1/I1
Page 2 of 4
early as 2003 (2 years before the actual recall of the drug). The results demonstrate the
utility of applying ontology based annotation analysis for detecting the relationships
between drugs and health conditions in general. The results also demonstrate the feasi-
bility of text-mining based approach for early detection of drug associated adverse
events by exploring a corpus of electronic health records.
In the paper titled “Linking genes to diseases with a SNPedia-Gene Wiki mashup”,
Benjamin Good et al present a semantic meta-wiki called the Gene Wiki+ that auto-
matically integrates data from Gene Wiki and SNPedia. The Gene Wiki provides con-
tinuously updated review articles for human genes, including descriptions of the role
the gene may play in disease, and SNPedia provides textual information about links
between variations in human genes and human phenotypes. The Gene Wiki+ exposes
substantially more evidence of links between genes and diseases than either resource
contains independently. Currently, it captures >8,000 distinct gene-disease relation-
ships. The authors created an open source program SyncBot that continuously moni-
tors the source wikis for changes and ensures that the Gene Wiki+ stays up-to-date.
The content of the Gene Wiki+ is exported as RDF. The Gene Wiki+ is available at
http://genewikiplus.org.
Olga Tcheremenskaia et al in the paper titled “OpenTox predictive toxicology frame-
work: toxicological ontology and semantic media wiki-based OpenToxipedia” report on
a suite of ontologies developed for the OpenTox project (http://www.opentox.org). The
OpenTox framework aims at providing access to toxicity data, predictive models, and
validation procedures. Interoperability of resources is based on the OpenTox ontolo-
gies describing predictive algorithms, models, and toxicity data. These ontologies have
been developed following the OBO Foundry principles. The authors also report on
wiki for the OpenTox predictive toxicology framework. The described project is of
major importance and likely to lead to many results in toxicology. The OpenTox
ontologies are available at http://www.opentox.org/dev/ontology.
Acknowledgements
As editors of this supplement, we thank all the authors who submitted papers, the Program Committee members and
the reviewers for their excellent work. We are grateful for help from Isobel Peters from BioMed Central as well as Dr.
Goran Nenadic and Dr. Dietrich Rebholz-Schuhmann in putting this supplement together.
This article has been published as part of Journal of Biomedical Semantics Volume 3 Supplement 1, 2012: Proceedings
of the Bio-Ontologies Special Interest Group Meeting 2012. The full contents of the supplement are available online at
http://www.jbiomedsem.com/supplements/3/S1
Author details
1Aberystwyth University, Wales, UK. 2University of Oxford, Oxford e-Research Centre, UK. 3Carleton University, Ottawa,
Canada. 4Stanford University, CA, USA.
Published: 24 April 2012
References
1. Ciccarese Paolo, Ocana Marco, Clark Tim: DOMEO: a web-based tool for semantic annotation of online documents.
[http://www.jbiomedsem.com/supplements/3/S1/S1].
2. Tsatsaronis George, Macari Natalia, Torge Sunna, Dietze Heiko, Schroeder Michael: A maximum entropy approach for
accurate document annotation. [http://www.jbiomedsem.com/supplements/3/S1/S2].
3. Jupp Simon, Stevens Robert, Hoehndorf Robert: Exploring Gene Ontology annotations with OWL. [http://www.
jbiomedsem.com/supplements/3/S1/S3].
4. Beisswanger Elena, Hahn Udo: Towards valid and reusable reference alignments – ten basic quality checks for
reference alignments and their application to three different reference data sets. [http://www.jbiomedsem.com/
supplements/3/S1/S4].
5. Le Pendu Paea, Racunas Stephen, Iyer Srinivasan, Liu Yi, Fairon Cédrick, Shah Nigam: Annotation analysis for testing
drug safety signals. [http://www.jbiomedsem.com/supplements/3/S1/S5].
Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1
http://www.jbiomedsem.com/supplements/3/S1/I1
Page 3 of 4
6. Good Benjamin, Loguercio Salvatore, Su Andrew: Linking genes to diseases with a SNPedia-Gene Wiki mashup.
[http://www.jbiomedsem.com/supplements/3/S1/S6].
7. Tcheremenskaia Olga, Benigni Romualdo, Nikolova Ivelina, Jeliazkova Nina, Escher Sylvia E, Grimm Helvi, Baier Thomas,
Poroikov Vladimir, Lagunin Alexey, Rautenberg Micha, Hardy Barry: OpenTox predictive toxicology framework:
toxicological ontology and semantic media wiki-based OpenToxipedia. [http://www.jbiomedsem.com/supplements/
3/S1/S7].
doi:10.1186/2041-1480-3-S1-I1
Cite this article as: Soldatova et al.: Selected papers from the 14th Annual Bio-Ontologies Special Interest Group
Meeting. Journal of Biomedical Semantics 2012 3(Suppl 1):I1.
Submit your next manuscript to BioMed Central
and take full advantage of: 
• Convenient online submission
• Thorough peer review
• No space constraints or color figure charges
• Immediate publication on acceptance
• Inclusion in PubMed, CAS, Scopus and Google Scholar
• Research which is freely available for redistribution
Submit your manuscript at 
www.biomedcentral.com/submit
Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1
http://www.jbiomedsem.com/supplements/3/S1/I1
Page 4 of 4


Aberystwyth UniversitySelected papers from the 14th Annual Bio-Ontologies Special Interest GroupMeetingSoldatova, Larisa N; Sansone, Susanna-Assunta; Dumontier, Michel; Shah, Nigam HPublished in:Journal of Biomedical SemanticsDOI:10.1186/2041-1480-3-S1-I1Publication date:2012Citation for published version (APA):Soldatova, L. N., Sansone, S-A., Dumontier, M., & Shah, N. H. (2012). Selected papers from the 14th AnnualBio-Ontologies Special Interest Group Meeting. Journal of Biomedical Semantics, 3(Suppl 1), [I1].https://doi.org/10.1186/2041-1480-3-S1-I1General rightsCopyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) areretained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by thelegal requirements associated with these rights.            • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study orresearch.            • You may not further distribute the material or use it for any profit-making activity or commercial gain            • You may freely distribute the URL identifying the publication in the Aberystwyth Research PortalTake down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.tel: +44 1970 62 2400email: is@aber.ac.ukDownload date: 03. Oct. 2019INTRODUCTION Open AccessSelected papers from the 14th Annual Bio-Ontologies Special Interest Group MeetingLarisa N Soldatova1*, Susanna-Assunta Sansone2, Michel Dumontier3, Nigam H Shah4From Bio-Ontologies 2011Vienna, Austria. 15-16 July 2011* Correspondence: lss@aber.ac.uk1Aberystwyth University, Wales, UKAbstractOver the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum fordiscussion of the latest and most innovative research in the bio-ontologiesdevelopment, its applications to biomedicine and more generally the organisation,presentation and dissemination of knowledge in biomedicine and the life sciences.The seven papers selected for this supplement span a wide range of topicsincluding: web-based querying over multiple ontologies, integration of data fromwikis, innovative methods of annotating and mining electronic health records,advances in annotating web documents and biomedical literature, quality control ofontology alignments, and the ontology support for predictive models about toxicityand open access to the toxicity data.Summary of selected papersIn 2011, the SIG received 29 paper submissions, 5 flash updates and 4 poster abstracts.18 papers and 11 flash updates (some papers were converted to flush updates) wereselected for presentation at the meeting, out of which 7 appear in this supplement.The seven papers selected for this supplement are extended versions of the originalpapers presented at the 2011 SIG. The papers include research on web-based queryingover multiple ontologies [3], integration of data from wikis into a meta semantic wiki[6], advances in the annotation of electronic health records [5], web documents [1] andbiomedical literature [2], quality control of ontology alignments [4], and the ontologybased support for the toxicity predictive models and access to the toxicity data [7].Paolo Ciccarese et al in the paper titled “DOMEO: a web-based tool for semanticannotation of online documents” describe work to date on an advancement in scienti-fic document automated annotation and collaborative curation using integrated ontolo-gies and frameworks in bioscience. The authors report on a user-friendly web basedinterface Domeo for the implementation of annotations of existing web resources.Domeo is an extensible web application enabling users to visually and efficiently createand share ontology-based stand-off annotation on HTML or XML document targets.The Domeo annotation tool supports manual, fully automated, and semi-automatedannotation with complete provenance records, as well as personal or community anno-tation with access authorization and control.Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1 JOURNAL OFBIOMEDICAL SEMANTICS© 2012 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.Domeo has been deployed in beta release as part of the NIH Neuroscience Informa-tion Framework (http://www.neuinfo.org). The Domeo annotation tool is available athttp://annotationframework.org/.The paper titled “A maximum entropy approach for accurate document annotation”by George Tsatsaronis et al addresses the critical task of document tagging for annota-tion of biomedical literature against ontologies of medical concern such as anatomy,disease and phycology. The authors present an automated and robust method, basedon maximum-entropy approach, for annotating biomedical literature documents withterms from Medical Subject Headings (MeSH). The suggested approach has increasedF-measure results when tested against title, journal and abstract text even using asmall number of documents. The work demonstrates the potential benefit of usingontologies to address the problem of information retrieval/extraction given the expo-nential growth of biomedical literature.Simon Jupp et al in the paper titled “Exploring Gene Ontology annotations withOWL” demonstrate that the controlled vocabulary annotations of gene products usingGO terms can be engineered to represent logical property restrictions on classes andindividuals in the OWL language such that it becomes possible to execute rich, logicalqueries over genes utilizing both the semantics of the gene annotations, as well as thesemantics of the GO itself. To do multi-perspective rich querying, the authors createdthe GOAL (Logical Gene Ontology) that combines the Gene ontology, Human DiseaseOntology, and the Mammalian Phenotype Ontology, together with classes for mousegene products. Defined classes were used to query these protein classes through auto-mated reasoning. This was presented through a Web interface that allows rich queriesand displays results. The GOAL ontology is available at http://owl.cs.manchester.ac.uk/goal.The paper “Towards valid and reusable reference alignments – ten basic qualitychecks for reference alignments and their application to three different reference datasets” by Elena Beisswanger and Udo Hahn outlines work in the area of ontology align-ment and highlights different checks that should be completed to assess whether align-ment is valid.The basic quality checks maybe of help to editors and curators evaluating the align-ment of ontologies, focusing on the reliability and reusability aspects.The checks are applied to the anatomy reference alignment datasets (the anatomybranch of the NCI Thesaurus and the Mouse adult gross anatomy ontology), also usedin the yearly Ontology Alignment Evaluation Initiative (OAEI); to the alignments ofLinked Open Data schemes; and for assessing upper ontology-based alignmentapproaches. The results reveal incorrect and missing correspondences, classes, andmissing or invalid relations between classes in the input ontologies. The basic checkscontribute to the quality of alignments. This is an area of growing importance.In “Annotation analysis for testing drug safety signals” by Paea LePendu et aldescribe a novel approach for leveraging resources for biomedical computing, such asthe NCBO Annotator tool and public biomedical ontologies for mining electronichealth records and to test drug safety signals. The authors analyzed over 9 millionunstructured clinical notes to compute the risk of having a myocardial infarction aftertaking Vioxx prescribed for rheumatoid arthritis. Their analysis reveals significant ele-vated risk for myocardial infarction in rheumatoid arthritis patients taking Vioxx asSoldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 2 of 4early as 2003 (2 years before the actual recall of the drug). The results demonstrate theutility of applying ontology based annotation analysis for detecting the relationshipsbetween drugs and health conditions in general. The results also demonstrate the feasi-bility of text-mining based approach for early detection of drug associated adverseevents by exploring a corpus of electronic health records.In the paper titled “Linking genes to diseases with a SNPedia-Gene Wiki mashup”,Benjamin Good et al present a semantic meta-wiki called the Gene Wiki+ that auto-matically integrates data from Gene Wiki and SNPedia. The Gene Wiki provides con-tinuously updated review articles for human genes, including descriptions of the rolethe gene may play in disease, and SNPedia provides textual information about linksbetween variations in human genes and human phenotypes. The Gene Wiki+ exposessubstantially more evidence of links between genes and diseases than either resourcecontains independently. Currently, it captures >8,000 distinct gene-disease relation-ships. The authors created an open source program SyncBot that continuously moni-tors the source wikis for changes and ensures that the Gene Wiki+ stays up-to-date.The content of the Gene Wiki+ is exported as RDF. The Gene Wiki+ is available athttp://genewikiplus.org.Olga Tcheremenskaia et al in the paper titled “OpenTox predictive toxicology frame-work: toxicological ontology and semantic media wiki-based OpenToxipedia” report ona suite of ontologies developed for the OpenTox project (http://www.opentox.org). TheOpenTox framework aims at providing access to toxicity data, predictive models, andvalidation procedures. Interoperability of resources is based on the OpenTox ontolo-gies describing predictive algorithms, models, and toxicity data. These ontologies havebeen developed following the OBO Foundry principles. The authors also report onwiki for the OpenTox predictive toxicology framework. The described project is ofmajor importance and likely to lead to many results in toxicology. The OpenToxontologies are available at http://www.opentox.org/dev/ontology.AcknowledgementsAs editors of this supplement, we thank all the authors who submitted papers, the Program Committee members andthe reviewers for their excellent work. We are grateful for help from Isobel Peters from BioMed Central as well as Dr.Goran Nenadic and Dr. Dietrich Rebholz-Schuhmann in putting this supplement together.This article has been published as part of Journal of Biomedical Semantics Volume 3 Supplement 1, 2012: Proceedingsof the Bio-Ontologies Special Interest Group Meeting 2012. The full contents of the supplement are available online athttp://www.jbiomedsem.com/supplements/3/S1Author details1Aberystwyth University, Wales, UK. 2University of Oxford, Oxford e-Research Centre, UK. 3Carleton University, Ottawa,Canada. 4Stanford University, CA, USA.Published: 24 April 2012References1. Ciccarese Paolo, Ocana Marco, Clark Tim: DOMEO: a web-based tool for semantic annotation of online documents.[http://www.jbiomedsem.com/supplements/3/S1/S1].2. Tsatsaronis George, Macari Natalia, Torge Sunna, Dietze Heiko, Schroeder Michael: A maximum entropy approach foraccurate document annotation. [http://www.jbiomedsem.com/supplements/3/S1/S2].3. Jupp Simon, Stevens Robert, Hoehndorf Robert: Exploring Gene Ontology annotations with OWL. [http://www.jbiomedsem.com/supplements/3/S1/S3].4. Beisswanger Elena, Hahn Udo: Towards valid and reusable reference alignments – ten basic quality checks forreference alignments and their application to three different reference data sets. [http://www.jbiomedsem.com/supplements/3/S1/S4].5. Le Pendu Paea, Racunas Stephen, Iyer Srinivasan, Liu Yi, Fairon Cédrick, Shah Nigam: Annotation analysis for testingdrug safety signals. [http://www.jbiomedsem.com/supplements/3/S1/S5].Soldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 3 of 46. Good Benjamin, Loguercio Salvatore, Su Andrew: Linking genes to diseases with a SNPedia-Gene Wiki mashup.[http://www.jbiomedsem.com/supplements/3/S1/S6].7. Tcheremenskaia Olga, Benigni Romualdo, Nikolova Ivelina, Jeliazkova Nina, Escher Sylvia E, Grimm Helvi, Baier Thomas,Poroikov Vladimir, Lagunin Alexey, Rautenberg Micha, Hardy Barry: OpenTox predictive toxicology framework:toxicological ontology and semantic media wiki-based OpenToxipedia. [http://www.jbiomedsem.com/supplements/3/S1/S7].doi:10.1186/2041-1480-3-S1-I1Cite this article as: Soldatova et al.: Selected papers from the 14th Annual Bio-Ontologies Special Interest GroupMeeting. Journal of Biomedical Semantics 2012 3(Suppl 1):I1.Submit your next manuscript to BioMed Centraland take full advantage of: • Convenient online submission• Thorough peer review• No space constraints or color figure charges• Immediate publication on acceptance• Inclusion in PubMed, CAS, Scopus and Google Scholar• Research which is freely available for redistributionSubmit your manuscript at www.biomedcentral.com/submitSoldatova et al. Journal of Biomedical Semantics 2012, 3(Suppl 1):I1http://www.jbiomedsem.com/supplements/3/S1/I1Page 4 of 4

Clark Tim: DOMEO: a web-based tool for semantic annotation of online documents.

Fairon Cédrick, Shah Nigam: Annotation analysis for testing drug safety signals.

Hahn Udo: Towards valid and reusable reference alignments – ten basic quality checks for reference alignments and their application to three different reference data sets. [http://www.jbiomedsem.com/ supplements/3/S1/S4].

Hoehndorf Robert: Exploring Gene Ontology annotations with OWL.

Torge Sunna, Dietze Heiko, Schroeder Michael: A maximum entropy approach for accurate document annotation.

file:///data/core-remote/dit/data/Springer-OA/pdf/a4a/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvMjA0MS0xNDgwLTMtUzEtSTEucGRm.pdf

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Abstract

Similar works

Full text

Available Versions

Brunel University Research Archive

Maastricht University Research Portal

Aberystwyth Research Portal

Springer - Publisher Connector

Aberystwyth Research Portal

Maastricht University Research Portal