Christopher J.O. Baker Greg Butler Igor Jurisica (Eds.) 0 Data Integration 7 9 7 I in the Life Sciences B N L 9th International Conference, DILS 2013 Montreal, QC, Canada, July 2013 Proceedings 123 Lecture Notes in Bioinformatics 7970 EditedbyS.Istrail,P.Pevzner,andM.Waterman EditorialBoard: A.Apostolico S.Brunak M.Gelfand T.Lengauer S.Miyano G.Myers M.-F.Sagot D.Sankoff R.Shamir T.Speed M.Vingron W.Wong Subseries of Lecture Notes in Computer Science Christopher J.O. Baker Greg Butler Igor Jurisica (Eds.) Data Integration in the Life Sciences 9th International Conference, DILS 2013 Montreal, QC, Canada, July 11-12, 2013 Proceedings 1 3 VolumeEditors ChristopherJ.O.Baker UniversityofNewBrunswick DepartmentofComputerScienceandAppliedStatistics SaintJohn,NBE2L4L5,Canada E-mail:[email protected] GregButler ConcordiaUniversity DepartmentofComputerScienceandSoftwareEngineering Montreal,QCH3G1M8,Canada E-mail:[email protected] IgorJurisica UniversityofToronto OntarioCancerInstitute Toronto,ONM5G1L7,Canada E-mail:[email protected] ISSN0302-9743 e-ISSN1611-3349 ISBN978-3-642-39436-2 e-ISBN978-3-642-39437-9 DOI10.1007/978-3-642-39437-9 SpringerHeidelbergDordrechtLondonNewYork LibraryofCongressControlNumber:2013941943 CRSubjectClassification(1998):H.3,J.3,I.2,H.4,C.2,H.2,H.5 LNCSSublibrary:SL8–Bioinformatics ©Springer-VerlagBerlinHeidelberg2013 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerptsinconnection withreviewsorscholarlyanalysisormaterialsuppliedspecificallyforthepurposeofbeingenteredand executedonacomputersystem,forexclusiveusebythepurchaserofthework.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheCopyrightLawofthePublisher’slocation, initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Permissionsforuse maybeobtainedthroughRightsLinkattheCopyrightClearanceCenter.Violationsareliabletoprosecution undertherespectiveCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Whiletheadviceandinformationinthisbookarebelievedtobetrueandaccurateatthedateofpublication, neithertheauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityforanyerrorsor omissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,withrespecttothe materialcontainedherein. Typesetting:Camera-readybyauthor,dataconversionbyScientificPublishingServices,Chennai,India Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface DILS was established in 2004 as a new bioinformatics workshop focusing on topics related to data management and integration. Now in its ninth year the conference continues to attract researchers from across a range of disciplines all of whom recognize the challenges faced by life scientists in managing and reusing data. Stakeholders involved in digital ecosystems and data ownership are able to generate large volumes of high-quality data and want to publish it to the widest possible audience for prospecting by scientists. And yet, data are not knowledge. The real value is the translation of the data into actionable knowledge. The methodologies and frameworks we depend on to facilitate this translation are still evolving, and the challenges in data management and reuse have grownrather than diminished overthe lastdecade andare common across many disciplines. Life scienceremainsoneofthe leadingdomainsandcontinuesto createmas- sive amounts of diverse data needing validation, curation, and annotation with meaningful descriptions and formatting according to open standards to ensure it is sharable between interoperable distributed systems and accessible by end users. Practitioners are, however, continually experimenting and the forum for discussingwhichmethodologieshavesucceeded,whichnewtechnologiesarenow being adopted, for which particular tasks, and how they are used to integrate data for subsequent bioinformatic analysis is DILS. This year, DILS received 23 papers to the main research track (both long andshortpapers).Fourpaperswereacceptedunconditionally.Afurthersixwere acceptedwiththeprovisionthatauthorsrevisedtheirpapersinaccordancewith reviewers’ comments and provided detailed and itemized responses. All papers were subsequently verified by the ProgramCommittee (PC) Chair and General Chairs. Accepted papers cover a range of important topics including: algorithms for ontology matching, interoperable frameworks for text mining using Semantic Web services, pipelines for genome-wide functional annotation, automation of pipelinesprovidingdatadiscoveyandaccesstodistributedresources,knowledge- driven querying-answer systems, prizms, nanopublications, electronic health records and linked data. This year we opted to also offer an Early Career and Systems Track at the DILS workshop.At the time of writing, papers submitted to each track were still under review. These papers are not published in the researchtrack proceedings. DILS 2013 featured two keynote speakers. Firstly, Dr. Erich Gombocz, co- founderandCSOofIOInformaticsadecadeago,isaveteraninapplyingsystems biology approachesto pharmaceutical and clinical decision making based on se- manticdataintegrationandknowledgemanagementtechnologies.Dr.Gombocz VI Preface presentedtherationaleforrethinkingoldproblems,retoolingwithnew method- ologies and revisiting the process models that underpin our existing knowledge discovery in pharma and clinical practice in healthcare. Specifically, he advo- cates new patient-centric, precision-medicine healthcare models to change how drugs are developed, how trials are performed, and how patients are treated. His manuscript is included in the proceedings. Our second keynote speaker was Dr. Paolo Ciccarese, Assistant in Neuroscience at Massachusetts General Hos- pital and Instructor in Neurology at Harvard Medical School. He is known for his pioneering work on the Annotation Ontology, an RDF model for exchang- ing annotation. In his talk, Dr. Ciccarese introduced annotation as a form of “micro-integration,” in which typed, versioned, and provenance links are as- signed between text and schema, text and data, or data and data. He showed howthe OpenAnnotationstandardfacilitates bothshort-andlonger-termdata integration efforts, transforming content into smart and connected data. DILS 2013 was held at Concordia University in Montreal, Canada, and was organized as part of a series of three co-located events known as the Semantic Trilogy. The two co-located events were the 4th International Conference on Biomedical Ontology and the 4th Canadian Semantic Web Symposium. As the event co-chairs and editors of this volume, we would like to thank all authors who submitted papers, as well as the PC members and additional refereesfortheirexcellentworkinevaluatingthe submissions.Specialthanksgo toConcordiaUniversityforprovidinguswiththefacilitiestorunthe event,and the Semantic Trilogy organization team. Finally, we would like to thank Alfred HofmannandhisteamatSpringerfortheircooperationandhelpinputtingthis volume together. May 2013 Christopher J.O. Baker Greg Butler Igor Jurisica Organization General Chairs Christopher J.O. Baker University of New Brunswick, Saint John, Canada Greg Butler Concordia University, Montreal, Canada Program Committee Chair Igor Jurisica University of Toronto, Canada Program Committee Adam Lee University of Maryland, USA Adrien Coulet Loria - INRIA Nancy Grand Est, France Amar K. Das Stanford University, USA Artjom Klein University of New Brunswick, Canada Asif M. Khan National University of Singapore, Singapore Bastien Rance NIH, Bethesda, USA Brad Malin Vanderbilt University, USA Christian Sch¨onbach Kyushu Institute of Technology, Japan David De Roure Oxford e-ResearchCenter, UK Dietrich Rebholz-Schuhmann EBI, UK Erhard Rahm University of Leipzig, Germany Fatima Al-Shahrour Broad Institute of MIT and Harvard, USA Fleur Mougin University of Bordeaux Segalen, France Guo-Qiang Zhang Case Western Reserve University, USA Hasan Jamil University of Idaho, USA James Cimino NIH/CC/OD, USA J¨org Hakenberg Arizona State University, USA Jerven Bolleman Swiss Institute of Bioinformatics, Switzerland Jong Park Korea Advanced Institute of Science and Technology, Korea Karen Eilbeck University of Utah, USA Karin Verspoor National ICT, Australia, NISTA Lawrence Hunter University of Colorado, USA Marco Masseroli Politecnico di Milano, Italy Marco Roos LUMC, University of Amsterdam, The Netherlands Maria Esther Vidal Universidad Simo´n Bol´ıvar, Venezuela Matthew Hindle Synthetic and System Biology, Edinburgh, UK VIII Organization Michael Krauthammer Yale University, USA Mong Li Lee National University of Singapore, Singapore Neil Sarkar University of Vermont, USA Nigam Shah Stanford Center for Biomedical Informatics Research, USA Paolo Missier Newcastle University, UK Paolo Romano Institute of Genoa, Italy Peter Mork Noblis, USA Radhakrishnan Nagarajan University of Kentucky, USA Rainer Winnenburg NIH, USA Satya Sahoo Case Western Reserve University, USA Tammy Cheng Cancer Research UK London, UK Vasant Honavar Iowa State University, USA DILS Steering Committee Sarah Cohen-Boulakia LRI, University of Paris-Sud 11, France Graham Kemp Chalmers University of Technology, Sweden Ulf Leser Humboldt-Universita¨t zu Berlin, Germany Paolo Missier Newcastle University, UK Norman Paton University of Manchester, UK Louiqa Raschid University of Maryland, USA Erhard Rahm University of Leipzig, Germany Organizing Committee Greg Butler Concordia University, Montreal, Canada Christopher J.O. Baker University of New Brunswick, Saint John, Canada Michel Dumontier Carleton University, Ottawa, Canada Webmaster Artjom Klein University of New Brunswick, Saint John, Canada Table of Contents Changing the Model in Pharma and Healthcare – Can We Afford to Wait Any Longer? ............................................... 1 Erich Alfred Gombocz Ibidas: Querying Flexible Data Structures to Explore Heterogeneous Bioinformatics Data.............................................. 23 Marc Hulsman, Jan J. Bot, Arjen P. de Vries, and Marcel J.T. Reinders From Questions to Effective Answers: On the Utility of Knowledge-Driven Querying Systems for Life Sciences Data ........................................................... 38 Amir H. Asiaee, Prashant Doshi, Todd Minning, Satya Sahoo, Priti Parikh, Amit Sheth, and Rick L. Tarleton OmixAnalyzer – A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets .............................. 46 Thomas Stoltmann, Karin Zimmermann, Andr´e Koschmieder, and Ulf Leser The RDF Pipeline Framework: Automating Distributed, Dependency-Driven Data Pipelines................................. 54 David Booth TowardsInteroperableBioNLP Semantic Web Services Using the SADI Framework...................................................... 69 Ahmad C. Bukhari, Artjom Klein, and Christopher J.O. Baker Optimizing Similarity Computations for Ontology Matching - Experiences from GOMMA ....................................... 81 Michael Hartung, Lars Kolb, Anika Groß, and Erhard Rahm Semi-automatic Adaptation of Mappings between Life Science Ontologies ...................................................... 90 Anika Groß, Julio Cesar Dos Reis, Michael Hartung, C´edric Pruski, and Erhard Rahm Next GenerationCancer Data Discovery, Access, and IntegrationUsing Prizms and Nanopublications...................................... 105 James P. McCusker, Timothy Lebo, Michael Krauthammer, and Deborah L. McGuinness X Table of Contents Putting It All Together: The Design of a Pipeline for Genome-Wide Functional Annotation of Fungi in the Modern Era of “-Omics” Data and Systems Biology ............................................. 113 Greg Butler Mining Anti-coagulant Drug-Drug Interactions from Electronic Health Records Using Linked Data ....................................... 128 Jyotishman Pathak, Richard C. Kiefer, and Christopher G. Chute Author Index.................................................. 141