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Proceedings   of  

 

THE  FIRST    

INTERNATIONAL  WORKSHOP   ON  

DRUG  INTERACTION  KNOWLEDGE  REPRESENTATION     (DIKR  2014)  

 

 THE  SECOND    

INTERNATIONAL  WORKSHOP   ON  

DEFINITIONS  IN  ONTOLOGIES   (IWOOD  2014)  

 

THE  WORKSHOP     ON    

STARTING  AN  OBI-­‐BASED  BIOBANK  ONTOLOGY     (OBIB  2014)  

Proceedings   edited  by  

 

Richard  D.  Boyce   Mathias  Brochhausen  

Philip  E.  Empey   Melissa  Haendel   William  R.  Hogan  

Daniel  C.  Malone   Patrick  Ray   Alan  Ruttenberg  

Selja  Seppälä   Christian  J.  Stoeckert  

Jie  Zheng  

The  workshops  were  held  in  conjunction  with    the    5th  International  Conference  on  Biomedical   Ontology  (ICBO  2014)  

Houston,  TX,  USA   October  6-­‐7,  2014  

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Preface  

This  volume  collects  the  papers  of  three  workshops  held  at  the   International  Conference  on  Biomedical  Ontologies  (ICBO  2014)  in   Houston,  TX.  For  more  detailed  information  about  the  First  

International  Workshop  on  Drug  Interaction  Knowledge  Management   (DIKR  2014),  the  Second  International  Workshop  on  Definitions  in   Ontologies  (IWOOD  2014)  and  the  Workshop  on  Starting  an  OBI-­‐Based   Biobank  Ontology  please  refer  to  the  individual  workshop  prefaces.  

The  editors  would  like  to  thank  the  ICBO  organizers,  the  members  of  all   three  scientific  committees,  the  authors  and,  of  course,  the  participants   of  the  workshops.  In  addition,  we  would  like  to  thank  Mark  Jensen  for   his  advice  regarding  the  creation  of  CEUR-­‐WS  submissions.  

 

December  2014   The  editors    

   

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TABLE  OF  CONTENTS    

The  First  International  Workshop  on  Drug  Interaction  Knowledge       1   Representation  (DIKR  2014)  

R.  D.  Boyce,  M.  Brochhausen,  P.  E.  Empey,  W.  R.  Hogan,  D.  C.  Malone    

Redesign  of  a  clinical  decision  support  system  for  a  drug  –  drug       3   interaction  alert  

D.  Luna,  C.  Otero,  F.  G.  Bernaldo  de  Quiros    

Towards  a  foundational  representation  of  potential  drug  -­‐  drug       16   interaction  knowledge  

M.  Brochhausen,  J.  Schneider,  D.  C.  Malone,  P.  E.  Empey,  W.  R.  Hogan,  R.  D.  Boyce    

The  Second  International  Workshop  on  Definitions  in  Ontologies     32     (IWOOD  2014)  

S.  Seppälä,  P.  Ray,  A.  Ruttenberg  

 Textual  and  logical  definitions  in  ontologies           35   S.  Seppälä,  Y.  Schreiber,  A.  Ruttenberg  

 

Defining  ‘sign’  and  ‘symptom’               42  

A.  P.  Cox,  P.  L.  Ray,  M.  Jensen,  A.  D.  Diehl    

An  alternative  terminology  for  pain  assessment           49   W.  Ceusters  

 

The  Workshop  on  Starting  an  OBI-­‐based  Biobank  Ontology  (OBIB  2014)   55   M.  Brochhausen,  M.  Haendel,  C.  J.  Stoeckert,  J.  Zheng  

 

Penn  Medicine  Biobank  Informatics             57  

H.  Williams,  D.  Birtwell    

Towards  a  Common  Semantic  Representation  of  Informed  Consent  for     61     Biobank  Specimens  

F.  J.  Manion,  Y.  He,  E.  Eisenhauer,  Y.  Lin,  A.  Karnovsky,  M.  R.  Harris    

A  Specimen-­‐based  View  of  the  World  -­‐  Using  the  Biological       64     Collections  Ontology  to  Model  Biodiversity  Collections  

R.  Walls,  R.  Guralnick,  J.  Deck,  A.  Matsunaga    

       

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