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Research resources: curating the new eagle-i discovery system

Poster presentation at the International Society for Biocuration Conference in Washington, DC in 2012.

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Research resources: curating the new eagle-i discovery system

  1. 1. Research  resources:  cura,ng  the  new  eagle-­‐i  discovery  system   Nicole  Vasilevsky1,  Tenille  Johnson2,  Karen  Corday2,  Carlo  Torniai1,  Ma:hew  Brush1,  Sco:  Hoffmann1,  Erik  Segerdell1,     Melanie  L.  Wilson1,  Christopher  J.  Shaffer1,  David  Robinson1,  and  Melissa  A.  Haendel1**   1  Oregon  Health  &  Science  University,  Library,  Portland,  Oregon   2  Harvard  Medical  School,  Center  for  Biomedical  InformaTcs,  Cambridge,  Massachuse:s   The  Ideal  Scholarly  Research  Cycle     o  Researchers  produce  data  and   resources  that  lead  to   publicaTons.     Resources     and  data   1   Public  repositories   •  eagle-­‐i   •  MODs   •  NIF   •  Entrez  Gene...   Researcher 2   Professional     networking:   •  VIVO   •  Harvard  Profiles   •  LinkedIn…     o  Published  data  informs   researchers  of  new   experimental  designs.     Publica,ons   Public  repositories   •  PubMed   •  Google  Scholar   •  Mendeley…   3   o  InformaTon  about  researchers,   resources,    data,  and  published   papers  is  stored  in  various   public  repositories.   How  can  we  make  this  cycle  more  efficient?     Provide  scien,sts  with  the  tools  they  need     to  record  their  resources  during  the  course  of  research   During  the  course  of  collecTng  informaTon  about  research  resources,  which  many   laboratories  were  willing  to  share,  we  discovered  that  while  larger  core  faciliTes  rouTnely   have  resource  and  workflow  organizaTon  strategies,  primary  research  labs  very  rarely  do.   This  creates  barriers  to  reproducing  experiments  as  well  as  to  publishing  and  sharing   resources.  Giving  labs  organizaTonal  tools  can  help  address  these  issues.   The  eagle-­‐i  workflow   Seman,c  Web  Entry  and  Edi,ng  Tool   Data  Cura,on  at  eagle-­‐i   Data  collecTon   CuraTon   guidelines   Decision  trees   BiocuraTon   User  interface   design   SWEET   Search   applicaTon   Components  of  the  eagle-­‐i   annotaTon  tool,  known  by   the  acronym  SWEET,  are   generated  directly  from   the  eagle-­‐i  ontology.  The   SWEET  contains  both   annotaTon  fields  that  are   auto-­‐populated  using  the   ontology  (purple  box)  and   free  text  (orange  box).   Entrez  Gene  ID  links  out  to   the  NCBI  database  (red   box).  Fields  in  the  SWEET   can  also  link  records  to   other  records  in  the   repository,  such  as  related   publicaTons  or   documentaTon  (blue  box).   Users  can  request  new   terms  be  added  to  the   ontology  using  the  Term   Request  field.       SPARQL  query  tool   for  QA   Ontology   development   Google   code   Ontology   Browser   Development  of  data  curaTon  pracTces  at  eagle-­‐i  depended  on  the  Resource  NavigaTon   team  for  data  collecTon,  the  CuraTon  team  for  ontology  development  and  data  QA,  and  the   SoWware  team  for  user  interface  design  in  an  iteraTve  process.  Tools  and  documentaTon   were  developed  to  assist  users  and  team  members  with  each  of  these  processes.   Ontological  modeling  of  research  resources   Decision  trees  assist  with  data  entry     and  annota,on  of  resources   Denotes  quesTons  eliciTng   informaTon  for  annotaTon.   AnnotaTon  tool   InsTtuTonal  repositories   Denotes  required  annotaTons.       Denotes  redirecTon  to    a   different  decision  tree.       Denotes  drop  down  or   annotaTon  field  examples.   Denotes  higher  value/priority   annotaTons.       Denotes  medium  value/ priority  annotaTons.       Denotes  lower  value/priority   annotaTons.       erms    new  t Biocurator   t eques R Ontology   Request  resources   Researcher   Search  applicaTon   Lessons  Learned   eagle-­‐i   parTcipaTng  lab   The  goal  of  eagle-­‐i  is  to  make  scienTfic  research  resources  more  visible  via  a   federated  network  of  insTtuTonal  repositories.  Using  an  ontology-­‐driven   approach  for  biomedical  resource  annotaTon  and  discovery,  the  Network   currently  includes  resources  from  23  insTtuTons.   www.eagle-­‐i.net   Open  source  so;ware  available  at:     h=ps://open.med.harvard.edu/display/eaglei/So;ware   eagle-­‐i  Ontology  GoogleCode:     h=p://code.google.com/p/eagle-­‐i/     Major  eagle-­‐i  resource  types  are  shown  as  dark  boxes.  Persons  and   laboratories  play  a  central  role  in  eagle-­‐i.    Classes  and  properTes  are  reused   from  pre-­‐exisTng  ontologies  or  created  de  novo.  Examples  of  some  of  the   relaTons  between  the  classes  are  indicated.     New  ini,a,ves  with  eagle-­‐i   NCATS  has  funded  two  new  projects  that  leverage  eagle-­‐i  to  further   translaTonal  science.  The  first  project  aims  to  expand  the  breadth,  quality,  and   discoverability  of  data  about  people  and  resources  by  harmonizing  the   ontologies  of  VIVO,  eagle-­‐i,  and  ShareCenter  (www.ctsaconnect.org).  The   second  project  aims  to  expand  the  eagle-­‐i  plakorm  to  new  CTSA  insTtuTons,   and  to  publish  resources  as  Linked  Open  Data.   • Balance  the  data  you  need  with  the  data  you  can  get   • Documenta,on  and  quality  assurance  are  itera,ve   • Tools  and  technology  choices  depend  on  the  above   Acknowledgements   **We,  the  authors,  represent  the  members  and  leaders  of  the  eagle-­‐i  CuraTon   team,  and  describe  some  of  the  efforts  and  products  of  all  teams  involved  in  the   development  of  the  eagle-­‐i  discovery  system.  We  would  like  to  thank  the   Resource  NavigaTon  team,  led  by  Richard  Pearse;  SoWware  Build  team,  led  by   Daniela  Bourges;  and  Project  Management  team,  led  by  Julie  McMurry.  We   would  also  like  to  thank  Jackie  Wirz.  We  gratefully  acknowlege  NIH  award   #U24RR029825.  

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Poster presentation at the International Society for Biocuration Conference in Washington, DC in 2012.

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