76F7FD6CEDDC47CEBF3B9E7747EF264D GROBID - A machine learning software for extracting information from scholarly documents

This! workshop! would! not! have! been! possible! without! the! thorough! reviews! of! the! international!scholars!who!accepted!to!be!part!of!the!program!committee.!We!would!like!to! thank! them! for! their! participation! and! support! to! this! workshop.! We! would! also! like! to! thank!the!participants!for!helpful!insights!and!thoughtful!discussions.!Finally,!we!thank!the! ICBO!organizers!for!hosting!the!workshop!and!providing!assistance!with!logistics,!as!well!as! the!Swiss!National!Science!Foundation!and!the!State!University!of!New!York!at!Buffalo!for! their!support. ! October!2014 IWOOD!organizers ! ! ! ! ! More!information!is!available!on!the!workshop's!website:! https://sites.google.com/site/definitionsinontologies/. ! !

!The! communications! published! in! these! proceedings! address! the! theoretical,! methodological,!and!pragmatic!criteria!one!should!consider!before!engaging!in!the!activity! of! defining! terms! in! ontologies.! The! main! goals! of! the! first! article! are! to! shed! light! on! the! nature! of! logical! and! textual! definitions,! to! explore! the! relationship! that! exists! between! them,! and! to! make! recommendations! for! an! improvement! between! the! two.! The! second! paper!addresses!issues!related!to!the!general!activity!of!defining!terms!as!illustrated!by!the! definition!of!'sign'!and!'symptom':!asking!preliminary!questions;!looking!up!and!comparing! existing! definitions;! considering! one's! ontological! framework! (BFO,! other…);! taking! or! not! into!account!actual!usages!of!the!terms;!discussing!the!relevance!of!alternative!definitions;! etc.!The!last!communication!describes!how!definitions!can!be!used!to!assess!the!coherence! and! overall! quality! of! an! ontology! according! to! some! prerequisites,! and! proposes! a! systematic!methodology!for!revising!and!updating!existing!definitions!to!conform!to!the!set! quality!criteria. ! Selja!Seppälä,!Yonatan!Schreiber!and!Alan!Ruttenberg Textual,and,logical,definitions,in,ontologies ! Alexander!P.!Cox,!Patrick!Ray,!Mark!Jensen!and!Alexander!D.!changed!the!acronym!of!the!workshop!from!DO!2014!to!IWOOD!2014!to!avoid!any!confusion!with!the!Disease!Ontology!acronym,! also!DO. ! !
! workshop! was! the! second! workshop! on! definitions! in! ontologies! in! as! many! years.! The! first! workshop! (DO! 2013)! was! held! last! year! in! Montreal! in! conjunction! with! ICBO! 2013.! The! focus! of! this! second! workshop! was! on! definition! practices! in! either! ! field! well,! but! may! only! have! limited! knowledge! of! adjacent! disciplines.! Good! definitions! make! it! possible! for! nonSexperts! to! understand! unfamiliar! terms! and! thereby!make!it!possible!for!more!confident!reuse!of!terms!by!external!ontologies,!which!in! turn!facilitates!data!integration.!Preface!The! IWOOD! 2014 human!or!machineSassisted!ontology!development.!Explicit! definitions! of! terms! in! ontologies! serve! a! number! of! purposes.! Logical! definitions!allow! reasoners! to! create! inferred! hierarchies,! lessening! the! burden! of! asserting! and!checking! the! validity! of! subsumptions.! Natural! language! definitions! help! to! ameliorate! the!pervasive! problem! of! low! interSannotator! agreement.! In! specialized! domains,! experts! will!know! their! ownProceedingsedited,by,Selja,SeppäläPatrick,RayAlan,Ruttenberg!!!!!IWOOD%2014%was%held%in%conjunction%with%the%5th%International%Conference%on%Biomedical%Ontology%(ICBO%2014)Houston,%TX,%USAOctober%6K7,%2014!!
* ! The! goal! of! this! workshop! was! to! bring! together! researchers! and! developers! in! the! biomedical!domain!to!discuss!difficulties!that!arise!in!definition!construction!with!a!view!to! sharing! strategies.! Even! within! the! narrow! domain! of! definition! construction,! crossS fertilization! of! ideas! from! related! disciplines! should! yield! benefits! in! quality! and! help! reinforce!common!approaches!and!identify!novel!ones.
Acknowledgements!
Selja!Seppälä!
Buffalo,!USA
 University!at! <author> <persName><forename type="first">Ray</forename><surname>Patrick</surname></persName> </author> <imprint> <pubPlace>Buffalo,!USA</pubPlace> </imprint> <respStmt> <orgName>University!at!</orgName> </respStmt> </monogr> </biblStruct> <biblStruct xml:id="b2"> <monogr> <title/> <author> <persName><forename type="first">Alan</forename><forename type="middle">!</forename><surname>Ruttenberg</surname></persName> </author> <imprint> <biblScope unit="volume">5</biblScope> <pubPlace>Buffalo,!USA</pubPlace> </imprint> <respStmt> <orgName>University!at!</orgName> </respStmt> </monogr> </biblStruct> <biblStruct xml:id="b3"> <monogr> <title level="m">National!Center!for!Scientific!
France
 Research!(CNRS) Nathalie!AussenacSGilles! MBB!Department!Simon!Fraser!University!and!BC!Public!Health! Microbiology!&! !Mélanie Courtot Reference!Laboratory,!Canada Natalia!Grabar!
France
 3 Université!de!Lille! Janna!Hastings European!Bioinformatics!Institute
Cambridge,!UK
 James!malone European!Bioinformatics!Institute
Cambridge,!UK
 Alexis!Nasr Aix!Marseille!
!France
 Université Richard!Power!
!UK
 University The!Open! Allan!Third!(The!Open!
!UK
 University