!
                                             !
                           Proceedings!
                                of

                    THE!SECOND!
             INTERNATIONAL!WORKSHOP
                        ON
             DEFINITIONS!IN!ONTOLOGIES
                   (IWOOD!2014)
                          !
                          !
                          !
                             Proceedings
                              edited,by
                                   ,
                            Selja,Seppälä
                             Patrick,Ray
                           Alan,Ruttenberg
                                   !
!
!
!
!
                IWOOD%2014%was%held%in%conjunction%with%
                                   the%
    5th%International%Conference%on%Biomedical%Ontology%(ICBO%2014)
                            Houston,%TX,%USA
                            October%6K7,%2014
!
                      !




                                	
  32	
  
Preface
!
The! IWOOD! 2014*! 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!
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! own! 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.!
!
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.
!
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.!Diehl
Defining,'sign',and,'symptom'
!
Werner!Ceusters
An,alternative,terminology,for,pain,assessment
!

1! We!changed!the!acronym!of!the!workshop!from!DO!2014!to!IWOOD!2014!to!avoid!any!confusion!with!the!Disease!Ontology!acronym,!
    also!DO.!

!



                                                          	
  33	
  
Acknowledgements !
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/.
!
!
Organizing5Committee
Selja!Seppälä!(University!at!Buffalo,!USA)
Patrick!Ray!(University!at!Buffalo,!USA)
Alan!Ruttenberg!(University!at!Buffalo,!USA)
5
Program5Committee
Nathalie!AussenacSGilles!(National!Center!for!Scientific!Research!(CNRS),!France)
Mélanie!Courtot!(MBB!Department!Simon!Fraser!University!and!BC!Public!Health!
Microbiology!&!Reference!Laboratory,!Canada)
Natalia!Grabar!(Université!de!Lille!3,!France)
Janna!Hastings!(European!Bioinformatics!Institute,!Cambridge,!UK)
James!Malone!(European!Bioinformatics!Institute,!Cambridge,!UK)
Alexis!Nasr!(Aix!Marseille!Université,!France)
Richard!Power!(The!Open!University,!UK)
Allan!Third!(The!Open!University,!UK)




                                             	
  34