© 2013 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.Over the 15 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 and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes

Dumontier, M

Sansone, SA

Shah, NH

Soldatova, LN

Journal of Biomedical Semantics

English

PubMed

Over the 15 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 and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes.</p

Soldatova, Larisa N.

Sansone, Susanna-Assunta

Dumontier, Michel

Shah, Nigam Haresh

Maastricht University Research Portal

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting

Brunel University Research Archive

INTRODUCTION Open AccessSelected papers from the 15th AnnualBio-Ontologies Special Interest Group MeetingLarisa N Soldatova1*, Susanna-Assunta Sansone2, Michel Dumontier3, Nigam H Shah4From Bio-Ontologies 2012Long Beach, CA, USA. 13-14 July 2012* Correspondence: larisa.soldatova@brunel.ac.uk1Brunel University, London, UKAbstractOver the 15 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 and the commentary selected for this supplement span a widerange of topics including: web-based querying over multiple ontologies, integrationof data, annotating patent records, NCBO Web services, ontology developments forprobabilistic reasoning and for physiological processes, and analysis of the progressof annotation and structural GO changes.Summary of selected papersIn 2012, the SIG received 20 paper submissions and 9 flash updates. 15 papers and allthe flash updates were selected for presentation at the meeting, out of which 7 papersand 1 commentary appear in this supplement.The seven papers and the commentary selected for this supplement are extended ver-sions of the original papers presented at the 2012 SIG. The papers include research onweb-based querying over multiple ontologies [1,2,7], analysis of the Gene Ontology [3],reports on advances in knowledge representations, e.g. the representation of physiologicalprocesses [4] and probabilistic reasoning [6], advances in the annotation of patent records[5], and Web services from the National Center for Biomedical Ontology [8].The paper titled “Ontology-Based Querying with Bio2RDF’s Linked Open Data” by Call-ahan et al reports on an update to Bio2RDF [1]. Nineteen new and updated RDF datasetshave been mapped to the Semanticscience Integrated Ontology (SIO) to enable federatedqueries across multiple Bio2RDF endpoints. The new datasets include BioModels—an EBIresource providing details on published computational models primarily from systemsbiology, BioPortal—a collection of over 300 bio-ontologies from multiple providers, NDC(the National Drug Code Directory)—a Food and Drug Administration (FDA) resourceproviding a current list of all drugs produced or otherwise processed for distribution bydrug companies, and others. Each dataset in the Bio2RDF network is linked to all theother datasets. Federated queries make it possible to formulate a query across connecteddatasets that reside in separate SPARQL endpoints. Several example SPARQL queries areSoldatova et al. Journal of Biomedical Semantics 2013, 4(Suppl 1):I1http://www.jbiomedsem.com/content/4/S1/I1 JOURNAL OFBIOMEDICAL SEMANTICS© 2013 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.discussed in the paper and Bio2RDF conversion scripts are available at a GitHub reposi-tory http://github.com/bio2rdf/bio2rdf-scripts.The paper “Biotea: RDFizing PubMed Central in Support for the Paper as an Interface tothe Web of Data” by Castro et al demonstrates an approach to the generation of intero-perable, interlinked, and self-describing documents in the biomedical domain [2]. Theproposed semantic processing approach has been applied to the full-text, open-access sub-set of PubMed Central. The resulting RDF dataset exploits existing ontologies and seman-tic enrichment services. The semantic processing of biomedical literature presented in thispaper embeds documents within the Web of Data and facilitates the execution of con-cept-based queries against the entire digital library. The proposed approach delivers a setof tools for metadata declaration and semantic processing of biomedical documents.The model, services, prototype, and datasets are available at http://biotea.idiginfo.org/.Clarke et al in the paper titled “A task-based approach for Gene Ontology (GO) eva-luation” introduce a method for evaluating the GO annotations based on the impactthey have on gene set enrichment analysis [3]. The proposed framework uses enrich-ment analysis to determine the effectiveness of the GO annotations in providing biolo-gically accurate results. As a use case of the evaluation the authors examine how wellthe GO annotations perform at reproducing biological expectations for a dataset. Theydemonstrate that the proposed framework enabled the analysis of the progress ofannotation and structural GO changes from 2004 to 2012. The authors were also ableto determine that the quality of annotations and structure have been improving interms of their ability to recall underlying biological traits.The paper titled “Representing physiological processes and their participants with Phy-sioMaps” by Cook et al presents computable knowledge networks of biological processesand their participants—PhysioMaps [4]. PhysioMaps have originated from the large-scaleprojects such as the Physiome, the Virtual Physiological Human, and the Virtual Physiolo-gical Rat. PhysioMap and SemSim (semantic simulation) models are based on the Ontol-ogy of Physics for Biology (OPB). The simulation models are XML files that specify a setof dynamical processes and their participants. Currently the proposed approach supportstwo types of processes, physical flows and modulation processes. Illustrative examples areprovided. The key result is the semi-automatic parsing of biosimulation model code intoPhysioMaps that can be displayed and interrogated for qualitative responses to hypotheti-cal perturbations. SemSim project materials are available at http://sbp.bhi.washington.edu/projects/semsim. A tool for creating, annotating, composing and decomposing SemSimmodels SemGen is available at http://sbp.bhi.washington.edu/projects/semgen.Eisinger et al in the paper titled “Automated Patent Categorization and GuidedPatent Search using IPC as Inspired by MeSH and PubMed” provide a comparativeanalysis of the Medical Subject Headings ontology (MeSH) and the main patent classi-fication system, the International Patent Classification (IPC) [5]. MeSH supports andimproves the document search on PubMed, while patent documents are considerablyless accessible. The analysis shows a strong structural similarity of the MeSH and IPChierarchies, but also some significant differences. The use of IPC to support the patentsearch comes with two serious disadvantages: complexity of the classification systemand sparse class assignments. The low number of IPC class assignments and the lackof occurrences of class labels in patent texts result in the limitations in the patentsearch. To overcome these limits, the authors propose a system for guided patentSoldatova et al. Journal of Biomedical Semantics 2013, 4(Suppl 1):I1http://www.jbiomedsem.com/content/4/S1/I1Page 2 of 4search based on the use of class co-occurrence information and the assigning of addi-tional classes to patents.The paper “Representation of probabilistic scientific knowledge” by Soldatova et al dis-cusses the probabilistic nature of biomedical knowledge and the necessity for an ontolo-gical support for probabilistic reasoning with scientific knowledge [6]. The authorspropose an ontology HELO (HypothEses and Laws Ontology) to model the key entitiesof the theory of probability. HELO is designed to consistently accommodate scientifichypotheses and laws collected from different sources: interviews with scientists, webpages, research papers, databases, program codes. The authors demonstrate the utility ofHELO on three worked examples: changes in the probability of the hypothesis that sir-tuins regulate human life span; changes in the probability of hypotheses about genefunctions in the S. cerevisiae aromatic amino acid pathway; and the use of active learningin drug design, where a strategy for the selection of compounds with the highest prob-ability of improving on the best known compound was used. HELO is available athttps://github.com/larisa-soldatova/HELO.Vita et al in the commentary “Query enhancement through the practical application ofontology: the IEDB and OBI” outline their experiences in utilizing bio-medical ontologiesto provide enhanced database search functionality [7]. The authors analyse the benefits ofthe information captured by a formal ontology implemented directly into the user webinterface for querying databases. The authors discuss the long-term goal of enabling a truesemantic integration of data and knowledge in the biomedical domain. Vita et al describetheir progress towards this goal and the main obstacles. The discussed approach is consid-ered on the example of the Immune Epitope Database (IEDB, www.iedb.org) that utilizesthe Ontology for Biomedical Investigations (OBI) and several additional ontologies torepresent immune epitope mapping experiments.Whetzel on behalf of the NCBO Team in the review paper “NCBO Technology:Powering semantically aware applications” provides an overview of technology devel-oped by the National Center for Biomedical Ontology (NCBO), a National Center forBiomedical Computing created under the NIH Roadmap [8]. The NCBO developesWeb services, which provide access to one of the largest repositories of biomedicalontologies. This overview describes typical services provided by NCBO for theresearch community. For example, the Ontology Web services provide access to ontol-ogies, navigation of the class hierarchy and details of each term and the NCBO Anno-tator Web service “tags” text automatically with terms from ontologies in BioPortal.The NCBO Widgets package enables the Ontology Web services to be used directly inweb sites. The functionality of the NCBO Web services and widgets are incorporatedinto semantically aware applications for ontology development and visualization, dataannotation, and data integration. The NCBO Web services are documented at: http://www.bioontology.org/wiki/index.php/NCBO _REST_services.Competing interestsThe authors have no competing interests to declare.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 Sarah Headley from BioMed Central in puttingthis supplement together.Soldatova et al. Journal of Biomedical Semantics 2013, 4(Suppl 1):I1http://www.jbiomedsem.com/content/4/S1/I1Page 3 of 4DeclarationsThis article has been published as part of Journal of Biomedical Semantics Volume 4 Supplement 1, 2013: Proceedingsof the Bio-Ontologies Special Interest Group 2012. The full contents of the supplement are available online at http://www.jbiomedsem.com/supplements/4/S1Author details1Brunel University, London, UK. 2University of Oxford, Oxford e-Research Centre, UK. 3Carleton University, Ottawa,Canada. 4Stanford University, CA, USA.Published: 15 April 2013References1. Callahan A, Cruz-Toledo J, Dumontier M: Ontology-Based Querying with Bio2RDF’s Linked Open Data.[http://www.jbiomedsem.com/supplements/4/S1/S1].2. Castro LJG, McLaughlin C, Garcia A: Biotea: RDFizing PubMed Central in Support for the Paper as an Interface to theWeb of Data. [http://www.jbiomedsem.com/supplements/4/S1/S2].3. Clarke EL, Loguercio S, Good BM, Su AI: A task-based approach for Gene Ontology (GO) evaluation.[http://www.jbiomedsem.com/supplements/4/S1/S3].4. Cook DL, Neal ML, Hoehndorf R, Gkoutos JV, Gennari JH: Representing physiological processes and their participantswith PhysioMaps. [http://www.jbiomedsem.com/supplements/4/S1/S4].5. Eisinger D, Tsatsaronis G, Bundschus M, Wieneke Ul, Schroeder M: Automated Patent Categorization and GuidedPatent Search using IPC as Inspired by MeSH and PubMed. [http://www.jbiomedsem.com/supplements/4/S1/S5].6. Soldatova LN, Rzhetsky A, De Grave K, King RD: Representation of probabilistic scientific knowledge.[http://www.jbiomedsem.com/supplements/4/S1/S6].7. Vita R, Overton JA, Greenbaum JA, Sette A, OBI consortium, Peters B: Query enhancement through the practicalapplication of ontology: the IEDB and OBI. [http://www.jbiomedsem.com/supplements/4/S1/S7].8. Whetzel PL, NCBO Team: NCBO Technology: Powering semantically aware applications. [http://www.jbiomedsem.com/supplements/4/S1/S8].doi:10.1186/2041-1480-4-S1-I1Cite this article as: Soldatova et al.: Selected papers from the 15th Annual Bio-Ontologies Special Interest GroupMeeting. Journal of Biomedical Semantics 2013 4(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 2013, 4(Suppl 1):I1http://www.jbiomedsem.com/content/4/S1/I1Page 4 of 4

A: Biotea: RDFizing PubMed Central in Support for the Paper as an Interface to the Web of Data.

AI: A task-based approach for Gene Ontology (GO) evaluation.

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed.

Gennari JH: Representing physiological processes and their participants with PhysioMaps.

King RD: Representation of probabilistic scientific knowledge.

OBI consortium, Peters B: Query enhancement through the practical application of ontology: the IEDB and OBI.

Ontology-Based Querying with Bio2RDF’s Linked Open Data.

Powering semantically aware applications. [http://www.jbiomedsem. com/supplements/4/S1/S8]. doi:10.1186/2041-1480-4-S1-I1 Cite this article as: Soldatova et al.: Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.

Selected papers from the 15th Annual Bio-Ontologies special interest group meeting

Larisa N Soldatova

Susanna-Assunta Sansone

Michel Dumontier

Nigam H Shah

Crossref

http://dx.doi.org/10.1186/2041-1480-4-S1-I1

Selected papers from the 15th Annual Bio-Ontologies special interest group meeting

Abstract

Similar works

Full text

Available Versions

Maastricht University Research Portal

Brunel University Research Archive

Maastricht University Research Portal

Crossref