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dkNET Annual Meeting - June 2017

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The dkNET annual meeting provided progress reports on recommendations from 2016. New resources were added to the registry including datasets, centers, and repositories. The dkNET site was improved with updated interfaces for browsing resources and new visualization tools. Efforts to support rigor and reproducibility included expanding RRID adoption and developing API services to integrate dkNET data. Plans are underway to provide more robust tracking of research resources.

Health & Medicine
Related topics:
Data Sharing • Kidney Disease
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dkNET  mtg  06/22/17 http://dknet.org dkNET  Annual  Meeting Progress  Report June  22,  2017
dkNET  mtg  06/22/17 http://dknet.org Summary  of  ESP  Recommendations  2016 Recommendation Prog Comments 1.  Survey  the  community  with  use  cases Next:    Triage  the  user  cases  and  translate  into  work   product 2.    Integration  with  NIH  Commons   Ability  to  interact  with  NIH  Commons  not  defined.     First  Commons  RFA  released  this  month. 3.    Training  courses   4.    Plug  in  architecture Web  services  and  API  keys 5.    Host  NIH  symposium 6.    RRID  resource  validation 7.    Track  resource  utilization 8.    FAIR  data  materials  for  NIDDK  fundees
dkNET  mtg  06/22/17 http://dknet.org Recommendation Prog Comments 10.    RRID  utilization  and  outreach 11.    Better  means  to  integrate  with  dkNET Minimal  information  models   12.    Cross  linking  of  resources 13.    Contextual  help But  much  more  to  be  done 14.    Challenge  project  with  NURSA 15.    Outreach  via  other  centers 16.    Integration  with  Wikipedia Pending  entity  pages 17.    Outreach  to  microbiome  community 18.    Email  campaign 19.    Establish  relationship  with  libraries
dkNET  mtg  06/22/17 http://dknet.org Curation
dkNET  mtg  06/22/17 http://dknet.org Resource  Curation  and  Maintenance: New  Community  Resources Included  more  than  400  NIDDK  centers  and  cores  facilities  in  the  registry Pilot  and  Feasibility  funding  database ISCC  (Intestinal  Stem  Cell  Consortium):  Protocol HIRN:  Antibodies  (with  RRIDs  cross-­reference) Omics  Discovery  Index:  Datasets LIPID  MAPS  proteome  and  structure T1DBase:  Human  Variants  Data NURSA:  Cell  line,  Animal  models Diabetic  Complications  Consortium:  Histology
dkNET  mtg  06/22/17 http://dknet.org Resource  Registry 976 new  resources  added  to  registry Examples: Genomic  Data  Commons  Data  Portal   Pathogen  Portal International  Human  Epigenome  Consortium  Data   Portal Network  for  Pancreatic  Organ  Donors  with   Diabetes ImmunoBase OncoKB Genome  Aggregation  Database Jackson  Laboratory  Clinical  Knowledgebase CDC  Laboratory  Quality  Assurance  and   Standardization  Programs Pituitary  Network  Association National  Adrenal  Diseases  Foundation American  Thyroid  Association Endotext MicrobiomeAnalyst Osteogenesis  Imperfecta  Foundation ALD  Connect And  list  of  metabolomics  and  microbiome  related   resources….
dkNET  mtg  06/22/17 http://dknet.org Dataset  Cross  References ClinicalTrials.gov  and  NIDDK  Central  Repository ClinicalTrials.gov:  dkNET  provides  additional  information  about  whether  the  specimen  or  dataset  was   deposited  in  the  NIDDK  Central  Repository NIDDK  Central  Repository:  dkNET  provides  cross  reference  of  ClinicalTrials.gov  study  registry
dkNET  mtg  06/22/17 http://dknet.org Dataset  Cross  References NURSA  Dataset  and  GEO  Microarray  Data GEO:  dkNET  provides  cross  reference  to  NURSA  annotated  dataset
dkNET  mtg  06/22/17 http://dknet.org dkNET  Site  Updates  and  Improvements
dkNET  mtg  06/22/17 http://dknet.org dkNET.org  Website  History dkNET  1.0 2016  -­ now20152014 dkNET  1.0 dkNET  2.0 Site  Consolidation
dkNET  mtg  06/22/17 http://dknet.org Community  News  and  Social  Media    
dkNET  mtg  06/22/17 http://dknet.org Community  Resources  UI  Improvements   ● Improved  UI   components  based  on   user  feedback  
dkNET  mtg  06/22/17 http://dknet.org Visualization  Tool  and  Modified  Time  Filter Users  can  filter  data  by   clicking  category,   subcategory  or  sources
dkNET  mtg  06/22/17 http://dknet.org Community  Resource  UI  Improvements Click  +  to  see   subcategories Add  table  icon  to  make   each  source  more   clear More  options  for  creating   collections
dkNET  mtg  06/22/17 http://dknet.org Redesign  of  “More  Resources”  Section User  selects  what   he/she  is  looking  for User  can  also  refine   search  by  selecting   categories   Source  list
dkNET  mtg  06/22/17 http://dknet.org Alternate  Source  List  View
dkNET  mtg  06/22/17 http://dknet.org Data  Visualization:  Word  clouds
dkNET  mtg  06/22/17 http://dknet.org Literature  Updates   New  Literature  Page:   Research  resources Data  sets  available Associated  grants Related  publications Share  pages  via  social  media Add  articles  to  collections
dkNET  mtg  06/22/17 http://dknet.org Implemented  Challenge  Module  
dkNET  mtg  06/22/17 http://dknet.org Infrastructure  Updates  and  Improvement Virtual  Machine  /  Cloud  Infrastructure Re-­location  of  virtual  machine  servers  at  hosting  facility Transition  of  virtual  machines  to  newer  hardware Baseline  operating  system  upgrades Service  and  UI  Infrastructure Transitioned  to  NGINX  for  better  request  management Implemented  safeguards  against  overuse  of  services Enable  whitelisting  of  known  users
dkNET  mtg  06/22/17 http://dknet.org dkNET  Support  for  Rigor  and   Reproducibility
Growing  Challenge:  Ensuring  Rigor  and  Reproducibility dkNET  mtg  06/22/17 http://dknet.org
dkNET  mtg  06/22/17 http://dknet.org
What  Does  It  Cost  to  Have  Key  Biological  Resource   Fail  Sometimes? Freeman  et  al,  2017.  Reproducibility  2020:  Progress  and  priorities * dkNET  mtg  06/22/17 http://dknet.org
dkNET  mtg  06/22/17 http://dknet.org dkNET  Supports  Reproducible  Research Journal  editors,  publication  authors,   and  resource  providers  can  find   Research  Resource  Identifiers   (RRIDs)  via  the  dkNET  portal  for   citing  resources  (e.g.,  antibodies,   model  organisms,  software)  in  the   literature.   Using  RRIDs  to  identify  resources   promotes  reuse  and  reproducibility.
dkNET  mtg  06/22/17 http://dknet.org dkNET  Enables  RRID  Ecosystem  Aggregation  of  RRID   Information Cell Lines Organisms Antibodies Software
dkNET  mtg  06/22/17 http://dknet.org Developing    a  Solution  with  Resource  Providers  to  Provide   RRID  Information dkNET  Minimal  Information Metadata  Standards Researcher Researcher Community  Specified  RRID Resource Information
dkNET  mtg  06/22/17 http://dknet.org RRID  Adoption
dkNET  mtg  06/22/17 http://dknet.org More  journals  requiring  RRIDs 2016 American  Journal  of  Human  Genetics Cell Endocrinology eLife eNeuro EBioMedicine Journal  of  Neuroscience Neuron 2017 BioTechniques Cell  Reports Cell  Communication  and  Signaling Cell  Stem  Cell RRID  Adoption
dkNET  mtg  06/22/17 http://dknet.org Star  Methods  Supporting  RRIDs http://www.sciencedirect.com/science/article/pii/S1550413117302176 “STAR  Methods  promote  rigor  and  robustness  with  an   intuitive,  consistent  framework  that  integrates  seamlessly   into  the  scientific  information  flow—making  reporting   easier  for  the  author  and  replication  easier  for  the  reader.”
dkNET  mtg  06/22/17 http://dknet.org Publisher  Integrations http://www.sciencedirect.com/science/article/pii/S1550413117302176
dkNET  mtg  06/22/17 http://dknet.org Resolver/API  Services dkNET  is  more  than  the  “Website” Two  areas  of  focus  from  ESP   recommendations: 1.  Integration  via  APIs 2.  Support  and  Advocacy  for  more   reproducible  methods  via  research   resource  identification  (RRID)  initiative Resolver  Hits  in  May  2017:  110,361 API  Hits  in  May  2017:  2,695,269 Referring  Sites ○ Elifesciences.org ○ Ncbi.nlm.nih.gov ○ Journal.frontiersin.org ○ Antibodycatalog.hirnetwork.org ○ Ebi.ac.uk ○ Europepmc.org ○ Onlinelibrary.wiley.com ○ Libraries.ucsd.edu ○ Orcid.org ○ Nature.com ○ Cell.com ○ Blogs.plos.org ○ f1000research.com
SciBot reads  a  paper   and  brings  back   information  as  an   annotation,  display  is   in  Hypothes.is dkNET  mtg  06/22/17 http://dknet.org
Resource  data  pulled  by   the  RRID  resolver   What  other  papers  used  this   antibody? Data  about  this   paper  is  in Hypothes.is Annotated  Data  is  Used  in  Several  Applications dkNET  mtg  06/22/17 http://dknet.org
dkNET  mtg  06/22/17 http://dknet.org NIH  Rigor  and  Reproducibility  @dknet.org
dkNET  mtg  06/22/17 http://dknet.org Building  on  RRID  Resource  Services dkNET  updates  data  sources  so  that   researchers  are  provided  new   information  on  resources  and  are   informed  of  problematic  resources dkNET  can  assist  grant  submitters  in   creating  an  authentication  plan. Now:    Resource  reports Future:    Add  your  own  validation   data  
Resource   Reports dkNET  mtg  06/22/17 http://dknet.org
Resource  Watch  and  Notifications “Does  the  cell  line   I  use  in  my  lab   have  known   problems?” dkNET  mtg  06/22/17 http://dknet.org
dkNET  mtg  06/22/17 http://dknet.org Resource  Tracking  and   Recommendations
User  Notifications:  Resource  Subscriptions 1.Users  can  track  their  resources 2.Provides  updated  information  on   citations  of  their  resources 3.Resource  mentions  are  retrieved   from  external  data  source,  text   mining,  and  user  submission Subscribe dkNET  mtg  06/22/17 http://dknet.org
Resource  Analytics dkNET  mtg  06/22/17 http://dknet.org
dkNET  mtg  06/22/17 http://dknet.org Tracking  NIDDK  Funded  Resources:  What  Are  the  Most  Mentioned?
dkNET  mtg  06/22/17 http://dknet.org Tracking  NIDDK  Funded  Resources Resource Mentions  count* Worldwide  Protein  Data  Bank 553 Ribosomal  Database  Project 353 T1DBase 62 ToppGene  Suite 44 GUDMAP   35 DiaComp  -­ Diabetic  Complications  Consortium 33 United  States  Renal  Data  System 27 NURSA  -­ Nuclear  receptor  Signaling  Atlas 20 National  Disease  Research  Interchange 19 Madison  Metabolomics  Consortium  Database 15 *  Currently  we  are  able   to  extract  mentions  from   the  open  access  subset   of  Pubmed  Central Also  provide  means  for   mentions  to  be  added   by  resource  owners  and   dkNET  users
dkNET  mtg  06/22/17 http://dknet.org Tracking  Resource  Mentions "We  extracted  clinical  data  on  all  unrelated  index   subjects  with  a  confirmed  diagnosis  of  IBD  from  the   NIDDKIBDGCs  central  repository  database." "DNA  samples  used  for  genotyping  this  SNP  in  the   GoKinD  collection  were  obtained  through  the   National  Institute  of  Diabetes  and  Digestive  and   Kidney  Diseases  Central  Repository   (www.niddkrepository.org/)." "Samples  were  tracked  from  the  point  of   collection,  processed  at  network  laboratories   and  stored  for  deposit  at  National  Institute  for   Diabetes  and  Digestive  and  Kidney   Diseases  (NIDDK)  Central  Repositories."
dkNET  mtg  06/22/17 http://dknet.org Expanding  Outreach  and   Improving  User  Experiences
dkNET  mtg  06/22/17 http://dknet.org Outreach  Activities 1. Interviewed  users  to  improve  UI  and  data  presentation   2. Conferences   Sep.  2016  International  Society  of  Nephrology  (ISN)  Forefronts  Symposium  on  the  Metabolome   and  Microbiome  in  Kidney  Disease:  poster   Mar.  2017  HIRN  Annual  Investigator's  Meeting:  poster  and  booth Apr.  2017  ENDO  Annual  Meeting:  booth,  poster,  big  data  oral  session,  RRID  oral  sessions,   science  hub  oral  sessions 3. Webinars: Sep.  2016  dkNET  @BioCADDIE  Webinar Apr.  2017  dkNET-­NURSA  Challenge  Kick  Off  Webinar May  2017  dkNET  Introductory  Webinar
dkNET  mtg  06/22/17 http://dknet.org Outreach  Activities 4. April-­June,  2017  dkNET-­NURSA  Challenge 5. American  Society  of  Hematology  (ASH)  clinical  prototype 6. Interact  with  users  and  resource  centers 7. Email  campaigns  and  dkNET  Digest 8. June,  2017  dkNET  Searchathon
dkNET  mtg  06/22/17 http://dknet.org Outreach  Activities:    Email  Campaigns April  2017  dkNET  email  list:  challenge,  introductory  webinar,  beta  test April  2017  NIDDK  awardees:  dkNET  introduction,  challenge,  funding  use   cases,  introductory  webinar May  2017  dkNET  email  list  and  NIDDK  awardees:  introductory  webinar,   Monthly  events  and  funding  announcements May  2017  DRC  center  directors,  Resource  centers,  UCSD  postdoc  email  list   and  bioinformatics  graduate  program:  Introductory  and  challenge   information  (no  MailChimp  tracking) dkNET  Email  List 40%  Open  Rate 8%  Clickthrough  Rate Awardee  Email  List 25%  Open  Rate 2.7%  Clickthrough  Rate Mailchimp  2017  Benchmarks 15-­30%  Open  Rate   1-­5%  Clickthrough  Rate  
dkNET  mtg  06/22/17 http://dknet.org dkNET  Highlights  and  News May,  2017:  Pilot  funding  news  and  blog,  new  resources,  new  data,  tissue   sample  use  case,  community  news,  challenge Top  clicks: Funding  (MMPC),  New  resources  (Pituitary  network  association,   American  Thyroid  Association),  Funding  (NURSA) June,  2017:  Same  categories,  clinical  datasets  use  case Top  clicks: New  resources  (MicrobiomeAnalyst),  New  data  (OmicsDI   database),  Events,  Funding  (DiaComp)
dkNET  mtg  06/22/17 http://dknet.org Outcomes  of  Outreach  Activities Increased  traffic  to  dkNET   website Increased  our  mailing  list   subscription   Over  41  new  accounts   opened Saved  searches Resource  subscriptions Increased  social  media   connections Google  analytics  (March  1  -­ June  19,  2017  vs  last  period) ENDO Challenge   Webinar  +   1st  Large   email Intro   Webinar  +   2nd  Large   Email   +postdoc   list Searchathon   +2nd  digest   +postdoc/stud ent  list   HIRN 1st   Small   Email   2nd  Small   Email   1st  digest
dkNET  mtg  06/22/17 http://dknet.org Social  Media  -­ Twitter
dkNET  mtg  06/22/17 http://dknet.org Google  Analytics   Referring  Traffic
dkNET  mtg  06/22/17 http://dknet.org Google  Analytics:  Where  Are  Our  Users?
dkNET  mtg  06/22/17 http://dknet.org Search-­a-­thon Invited  naive  users  to  participate  in  a  searchathon Faculty,  students  and  post-­docs  across  disciplines Bioinformaticians Developers  watched  users  navigate  the  portal Surveyed  users  about  their  use  cases  and  experiences
dkNET  mtg  06/22/17 http://dknet.org dkNET  Searchathon  on  June  9,  2017   Ease  of  dkNET  portal  (1:  very  difficult;;  10:  very  easy) Weighted   Average:   6.55
dkNET  mtg  06/22/17 http://dknet.org Did  you  find  what  you  were  looking  for? 73%
dkNET  mtg  06/22/17 http://dknet.org Recommendations:  Consolidation  of  Search “The  top  row  of  buttons  of  about/community  resources/more  resources/literature  are  confusing.  It  looks   like  just  website  information  but  instead  they  are  three  different  search  engines.  When  I  first  visit  this   webpage,  I  did  not  notice  that  I  can  also  search  for  more  resources  and  literature.” “It  was  difficult  for  me  to  find  some  information  that  I  was  searching  for.  For  example  I  wanted  some  of  the   OMIM  links  but  could  only  see  them  when  I  clicked  on  More  Resources.    I  don't  understand  why   community  resources  and  more  resources  are  split.  I  want  all  the  search  results  to  appear  on  one  page.”   “The  "Community  Resource"  and  "More  Resources"  button  might  be  integrated  into  the  "option"  when   people  do  the  search” “Clearer  divisions  of  search  results  such  as  Reagents  and  Protocols,  Funding  and  Conferences,  Literature   and  Datasets  would  be  nice.  Maybe  having  them  all  displayed  in  side  by  side  columns  or  somehow  more   visible  all  at  once.”
dkNET  mtg  06/22/17 http://dknet.org Recommendations:  Visualizations “I  really  like  some  of  the  graphical  search  features  like  the  word  clouds,  facets,  and  category  graph.  It   would  be  useful  if  I  could  filter  from  the  word  clouds.” “I  like  the  color  circle  feature  when  I  search  literatures,  it  did  catch  my  eye  “ “My  first  impressions  is  that  dkNET  is  very  complicated,  but  contains  many  features.  I  think  the  static   image  tutorials  could  be  improved  by  creating  video  tutorials.”
dkNET  mtg  06/22/17 http://dknet.org Additional  Feedback   “Maybe  add  in  tools  like  Matchmaker  exchange  to  link  researchers  together  who  are  studying  the  same   gene.” “I  found  information  about  another  group  working  with  the  patient  population  I'm  interested  in.” “My  first  impressions  is  that  dkNET  is  very  complicated,  but  contains  many  features.  I  think  the  static   image  tutorials  could  be  improved  by  creating  video  tutorials.” “I  was  looking  for  information  about  a  disease  that  we  study.  I  was  able  to  find  some  of  what  I  was  looking   for,  and  also  some  interesting  datasets  that  I  did  not  know  existed.  This  seems  like  a  good  tool  for   exploratory  searching  (to  see  what  exists  in  terms  of  literature,  reagents,  datasets).  Having  a  clear  header   with  what  diseases  are  searchable  would  be  helpful.  i.e.  For  researchers  in  the  fields  of  kidney  disease,  x,   y,  z.  
dkNET  mtg  06/22/17 http://dknet.org Practical  Use  Cases
dkNET  mtg  06/22/17 http://dknet.org Overview  of  Use  Case  Collection ● Use  cases  from  dkNET  (classic  use  cases,  user  interviews  from   beta  testing,  conferences,  dkNET  survey  via  e-­mail  list,  dkNET   Searchathon) ● Use  cases  from  the  ESP  (survey  ESP  prior  to  the  retreat) ● Use  cases  from  NIH  Staff (obtain  prior  to  the  retreat)
dkNET  mtg  06/22/17 http://dknet.org What  Are  Users  Looking  For  in  dkNET?   Emailed  Use  Case  Survey   Users'  background  and  disease   fields  are  varied;;  they  are   looking  for  different  resources   for  different  use  cases  based   on  their  research  or  areas  of   interest
dkNET  mtg  06/22/17 http://dknet.org Summary  of  Use  Cases  From  dkNET  Users Background Categories/Features  that  dkNET  covers What  users  hope  that  dkNET   can  offer  in  the  future? Basic  Scientist Literature,  Database/Repository,  Tissue  Bank,  Funding,   Resources  (any),  Image  dataset  (Cell,  Mitochondria),  Cell  image   analysis  software,  genes  linked  to  disease Popularity/impact  of  the   resources,  collaborator Clinical  Scientist Funding,  Clinical  Trials  (recruiting  status),  Patient  population  in   clinical  trials.  Dataset/Data  summary  of  Clinical  Trials,  Dataset   (microarray,  RNAseq),  disease  research  information  or  dataset Access  to  several  gene  matrix,   Find  researchers  who  study  the   same  genes  of  interest Bioinformatician Literature,  Software,  Pathways,  Imaging  Dataset,  Beta  testers Faculty Literature,  Database/Repository,  Funding,  Softwares,  New   things,  Open  dataset Ranking  of  open/commercial   resources  in  terms  of  reputation   and  quality,  more  intuitive  page   layouts Trainee   Funding  agency  of  interdisciplinary  field  
dkNET  mtg  06/22/17 http://dknet.org Use  Cases  From  dkNET  Users User  interviews  from  beta  testing A  scientist  who  has  both  basic  research  and  bioinformatics  background  is  looking  for  Literature related   to  how  glucose  regulates  PKA  inhibition  and  Literature  related  to  PKA  Catalytic A  clinical  research  and  image  informatics  faculty  is  looking  for  what's  new or  would  like  to  know  if  there   is  any  new  software related  to  tools  she  currently  uses.  She  is  also  looking  for  funded  grants related  to  a  currently  funded  project. A  basic  science  faculty  is  looking  for  database/repository  to  deposit  the  datasets that  they  generated   A  data  scientist  is  looking  for  image  dataset for  related  to  a  specific  disease A  bioinformatics  faculty  is  looking  for  pathway  analysis  software
dkNET  mtg  06/22/17 http://dknet.org Use  Cases  From  dkNET  Users New  users  at  targeted  conferences A  basic  scientist  is  looking  for  liver  tissue  bank A  PhD  student  is  looking  for  government/non-­profit/profit  agency that  he/she  can  apply  funding  for   microbiome  research A  scientist  (non-­profit  organization)is  looking  for  pituitary  gland relevant  resources  and  fundings A  clinical  scientist  is  looking  for  pediatric  diabetes  clinical  trial  with  open  enrollment A  clinical  scientist  is  looking  for  dataset  or  data  summary  of  clinical  trials A  bioinformatician  is  looking  for  diabetic  kidney  diseases  pathways to  build  a  network A  bioinformatician  is  looking  for  help  in  contacting  beta  testers for  new  developed  tools
dkNET  mtg  06/22/17 http://dknet.org Use  Cases  From  dkNET  Users   Emailed  Use  Case  Survey   A  faculty  member  at  university  whose  research  focused  on  liver  disease  and  obesity  is  looking  for   tissue  banks,  cell  image  datasets,  mitochondria  images,  and  cell  image  analysis  software,   and  hopes  that  dkNET  could  provide  related  resources  of  his/her  interest,  with  links  to  the  resources   and  popularity/impact  estimation  of  the  research  resources. A  basic  scientist  (exercise  physiologist)  at  university  whose  research  focused  on  diabetes,   metabolic  diseases,  nutrition,  and  obesity  is  looking  for  research  ideas  on  the  effects  of   exercise  on  diabetics,  and  hopes  that  dkNET  could  help  him/her  to  find  a  group  to  collaborate   with.  He/She  is  at  a  small  college  so  he/she  has  a  large  teaching  load  and  not  a  ton  of  time  for   research. A  physician  scientist  at  hospital  whose  research  focused  on  emergency  contraception  is  looking  for   microarray  or  RNAseq  gene  expression  data  related  to  endometrial  receptivity,  and  hopes  that   dkNET  could  provide  the  access  to  several  gene  expression  matrix  related  to  the  effects  of   progesterone  receptor  modulators  drugs  used  for  gynecological  diseases.
dkNET  mtg  06/22/17 http://dknet.org Summary  of  Use  Cases  from  ESP   Use  cases 1. I  am  a  researcher  looking  for  genomic  data  sets  about  nuclear  receptors   in  hormone-­dependent  cancers. 2. I'm  a  researcher  looking  for  available  datasets  that  match  a  set  of  criteria   based  on  species,  tissue  type,  cell  line,  cellular  pathway,  etc. Services   1. A  summary  of  the  available  databases  with  links  to  the  relevant   publications. 2. Data  visualization 3. Reproducibility  reporting
dkNET  mtg  06/22/17 http://dknet.org Use  Cases  From  NIH  Staff Validated  probes  (and  validation  reports),  data  on  genes  of  interest I  am  a  researcher  looking  for  datasets  relevant  to  my  research  interest LINKOUT  to  related  resources,  metadata,  and  accessible  digital  resources Aggregated  services  surrounding  enhancement  of  rigor  and  reproducibility,  authentication,  etc. Tutorials  and  best  practices  surrounding  rigor  and  reproducibility  when  it  comes  to  reagents  and   other  research  resources Include  more  omics  data  types Include  highly  relevant  websites    (e.g.  all  the  resources  generating  grants,  consortia;;  other  similar   sites) Include  Relevant  conferences A  discussion  forum.  where  young  scientists  can  ask  for  help  to  find  a  certain  resource,  where  they   can  post  questions  like  “where  I  can  find  ….”    (for  example,  where  I  can  find  humanized  mouse   model,  functional  genomic  datasets,  datasets  with  deep  phenotyping,  data  sets  with  sample   size  larger  than  ***,  etc,...).    

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dkNET Annual Meeting - June 2017

  • 1. dkNET  mtg  06/22/17 http://dknet.org dkNET  Annual  Meeting Progress  Report June  22,  2017
  • 2. dkNET  mtg  06/22/17 http://dknet.org Summary  of  ESP  Recommendations  2016 Recommendation Prog Comments 1.  Survey  the  community  with  use  cases Next:    Triage  the  user  cases  and  translate  into  work   product 2.    Integration  with  NIH  Commons   Ability  to  interact  with  NIH  Commons  not  defined.     First  Commons  RFA  released  this  month. 3.    Training  courses   4.    Plug  in  architecture Web  services  and  API  keys 5.    Host  NIH  symposium 6.    RRID  resource  validation 7.    Track  resource  utilization 8.    FAIR  data  materials  for  NIDDK  fundees
  • 3. dkNET  mtg  06/22/17 http://dknet.org Recommendation Prog Comments 10.    RRID  utilization  and  outreach 11.    Better  means  to  integrate  with  dkNET Minimal  information  models   12.    Cross  linking  of  resources 13.    Contextual  help But  much  more  to  be  done 14.    Challenge  project  with  NURSA 15.    Outreach  via  other  centers 16.    Integration  with  Wikipedia Pending  entity  pages 17.    Outreach  to  microbiome  community 18.    Email  campaign 19.    Establish  relationship  with  libraries
  • 4. dkNET  mtg  06/22/17 http://dknet.org Curation
  • 5. dkNET  mtg  06/22/17 http://dknet.org Resource  Curation  and  Maintenance: New  Community  Resources Included  more  than  400  NIDDK  centers  and  cores  facilities  in  the  registry Pilot  and  Feasibility  funding  database ISCC  (Intestinal  Stem  Cell  Consortium):  Protocol HIRN:  Antibodies  (with  RRIDs  cross-­reference) Omics  Discovery  Index:  Datasets LIPID  MAPS  proteome  and  structure T1DBase:  Human  Variants  Data NURSA:  Cell  line,  Animal  models Diabetic  Complications  Consortium:  Histology
  • 6. dkNET  mtg  06/22/17 http://dknet.org Resource  Registry 976 new  resources  added  to  registry Examples: Genomic  Data  Commons  Data  Portal   Pathogen  Portal International  Human  Epigenome  Consortium  Data   Portal Network  for  Pancreatic  Organ  Donors  with   Diabetes ImmunoBase OncoKB Genome  Aggregation  Database Jackson  Laboratory  Clinical  Knowledgebase CDC  Laboratory  Quality  Assurance  and   Standardization  Programs Pituitary  Network  Association National  Adrenal  Diseases  Foundation American  Thyroid  Association Endotext MicrobiomeAnalyst Osteogenesis  Imperfecta  Foundation ALD  Connect And  list  of  metabolomics  and  microbiome  related   resources….
  • 7. dkNET  mtg  06/22/17 http://dknet.org Dataset  Cross  References ClinicalTrials.gov  and  NIDDK  Central  Repository ClinicalTrials.gov:  dkNET  provides  additional  information  about  whether  the  specimen  or  dataset  was   deposited  in  the  NIDDK  Central  Repository NIDDK  Central  Repository:  dkNET  provides  cross  reference  of  ClinicalTrials.gov  study  registry
  • 8. dkNET  mtg  06/22/17 http://dknet.org Dataset  Cross  References NURSA  Dataset  and  GEO  Microarray  Data GEO:  dkNET  provides  cross  reference  to  NURSA  annotated  dataset
  • 9. dkNET  mtg  06/22/17 http://dknet.org dkNET  Site  Updates  and  Improvements
  • 10. dkNET  mtg  06/22/17 http://dknet.org dkNET.org  Website  History dkNET  1.0 2016  -­ now20152014 dkNET  1.0 dkNET  2.0 Site  Consolidation
  • 11. dkNET  mtg  06/22/17 http://dknet.org Community  News  and  Social  Media    
  • 12. dkNET  mtg  06/22/17 http://dknet.org Community  Resources  UI  Improvements   ● Improved  UI   components  based  on   user  feedback  
  • 13. dkNET  mtg  06/22/17 http://dknet.org Visualization  Tool  and  Modified  Time  Filter Users  can  filter  data  by   clicking  category,   subcategory  or  sources
  • 14. dkNET  mtg  06/22/17 http://dknet.org Community  Resource  UI  Improvements Click  +  to  see   subcategories Add  table  icon  to  make   each  source  more   clear More  options  for  creating   collections
  • 15. dkNET  mtg  06/22/17 http://dknet.org Redesign  of  “More  Resources”  Section User  selects  what   he/she  is  looking  for User  can  also  refine   search  by  selecting   categories   Source  list
  • 16. dkNET  mtg  06/22/17 http://dknet.org Alternate  Source  List  View
  • 17. dkNET  mtg  06/22/17 http://dknet.org Data  Visualization:  Word  clouds
  • 18. dkNET  mtg  06/22/17 http://dknet.org Literature  Updates   New  Literature  Page:   Research  resources Data  sets  available Associated  grants Related  publications Share  pages  via  social  media Add  articles  to  collections
  • 19. dkNET  mtg  06/22/17 http://dknet.org Implemented  Challenge  Module  
  • 20. dkNET  mtg  06/22/17 http://dknet.org Infrastructure  Updates  and  Improvement Virtual  Machine  /  Cloud  Infrastructure Re-­location  of  virtual  machine  servers  at  hosting  facility Transition  of  virtual  machines  to  newer  hardware Baseline  operating  system  upgrades Service  and  UI  Infrastructure Transitioned  to  NGINX  for  better  request  management Implemented  safeguards  against  overuse  of  services Enable  whitelisting  of  known  users
  • 21. dkNET  mtg  06/22/17 http://dknet.org dkNET  Support  for  Rigor  and   Reproducibility
  • 22. Growing  Challenge:  Ensuring  Rigor  and  Reproducibility dkNET  mtg  06/22/17 http://dknet.org
  • 23. dkNET  mtg  06/22/17 http://dknet.org
  • 24. What  Does  It  Cost  to  Have  Key  Biological  Resource   Fail  Sometimes? Freeman  et  al,  2017.  Reproducibility  2020:  Progress  and  priorities * dkNET  mtg  06/22/17 http://dknet.org
  • 25. dkNET  mtg  06/22/17 http://dknet.org dkNET  Supports  Reproducible  Research Journal  editors,  publication  authors,   and  resource  providers  can  find   Research  Resource  Identifiers   (RRIDs)  via  the  dkNET  portal  for   citing  resources  (e.g.,  antibodies,   model  organisms,  software)  in  the   literature.   Using  RRIDs  to  identify  resources   promotes  reuse  and  reproducibility.
  • 26. dkNET  mtg  06/22/17 http://dknet.org dkNET  Enables  RRID  Ecosystem  Aggregation  of  RRID   Information Cell Lines Organisms Antibodies Software
  • 27. dkNET  mtg  06/22/17 http://dknet.org Developing    a  Solution  with  Resource  Providers  to  Provide   RRID  Information dkNET  Minimal  Information Metadata  Standards Researcher Researcher Community  Specified  RRID Resource Information
  • 28. dkNET  mtg  06/22/17 http://dknet.org RRID  Adoption
  • 29. dkNET  mtg  06/22/17 http://dknet.org More  journals  requiring  RRIDs 2016 American  Journal  of  Human  Genetics Cell Endocrinology eLife eNeuro EBioMedicine Journal  of  Neuroscience Neuron 2017 BioTechniques Cell  Reports Cell  Communication  and  Signaling Cell  Stem  Cell RRID  Adoption
  • 30. dkNET  mtg  06/22/17 http://dknet.org Star  Methods  Supporting  RRIDs http://www.sciencedirect.com/science/article/pii/S1550413117302176 “STAR  Methods  promote  rigor  and  robustness  with  an   intuitive,  consistent  framework  that  integrates  seamlessly   into  the  scientific  information  flow—making  reporting   easier  for  the  author  and  replication  easier  for  the  reader.”
  • 31. dkNET  mtg  06/22/17 http://dknet.org Publisher  Integrations http://www.sciencedirect.com/science/article/pii/S1550413117302176
  • 32. dkNET  mtg  06/22/17 http://dknet.org Resolver/API  Services dkNET  is  more  than  the  “Website” Two  areas  of  focus  from  ESP   recommendations: 1.  Integration  via  APIs 2.  Support  and  Advocacy  for  more   reproducible  methods  via  research   resource  identification  (RRID)  initiative Resolver  Hits  in  May  2017:  110,361 API  Hits  in  May  2017:  2,695,269 Referring  Sites ○ Elifesciences.org ○ Ncbi.nlm.nih.gov ○ Journal.frontiersin.org ○ Antibodycatalog.hirnetwork.org ○ Ebi.ac.uk ○ Europepmc.org ○ Onlinelibrary.wiley.com ○ Libraries.ucsd.edu ○ Orcid.org ○ Nature.com ○ Cell.com ○ Blogs.plos.org ○ f1000research.com
  • 33. SciBot reads  a  paper   and  brings  back   information  as  an   annotation,  display  is   in  Hypothes.is dkNET  mtg  06/22/17 http://dknet.org
  • 34. Resource  data  pulled  by   the  RRID  resolver   What  other  papers  used  this   antibody? Data  about  this   paper  is  in Hypothes.is Annotated  Data  is  Used  in  Several  Applications dkNET  mtg  06/22/17 http://dknet.org
  • 35. dkNET  mtg  06/22/17 http://dknet.org NIH  Rigor  and  Reproducibility  @dknet.org
  • 36. dkNET  mtg  06/22/17 http://dknet.org Building  on  RRID  Resource  Services dkNET  updates  data  sources  so  that   researchers  are  provided  new   information  on  resources  and  are   informed  of  problematic  resources dkNET  can  assist  grant  submitters  in   creating  an  authentication  plan. Now:    Resource  reports Future:    Add  your  own  validation   data  
  • 37. Resource   Reports dkNET  mtg  06/22/17 http://dknet.org
  • 38. Resource  Watch  and  Notifications “Does  the  cell  line   I  use  in  my  lab   have  known   problems?” dkNET  mtg  06/22/17 http://dknet.org
  • 39. dkNET  mtg  06/22/17 http://dknet.org Resource  Tracking  and   Recommendations
  • 40. User  Notifications:  Resource  Subscriptions 1.Users  can  track  their  resources 2.Provides  updated  information  on   citations  of  their  resources 3.Resource  mentions  are  retrieved   from  external  data  source,  text   mining,  and  user  submission Subscribe dkNET  mtg  06/22/17 http://dknet.org
  • 41. Resource  Analytics dkNET  mtg  06/22/17 http://dknet.org
  • 42. dkNET  mtg  06/22/17 http://dknet.org Tracking  NIDDK  Funded  Resources:  What  Are  the  Most  Mentioned?
  • 43. dkNET  mtg  06/22/17 http://dknet.org Tracking  NIDDK  Funded  Resources Resource Mentions  count* Worldwide  Protein  Data  Bank 553 Ribosomal  Database  Project 353 T1DBase 62 ToppGene  Suite 44 GUDMAP   35 DiaComp  -­ Diabetic  Complications  Consortium 33 United  States  Renal  Data  System 27 NURSA  -­ Nuclear  receptor  Signaling  Atlas 20 National  Disease  Research  Interchange 19 Madison  Metabolomics  Consortium  Database 15 *  Currently  we  are  able   to  extract  mentions  from   the  open  access  subset   of  Pubmed  Central Also  provide  means  for   mentions  to  be  added   by  resource  owners  and   dkNET  users
  • 44. dkNET  mtg  06/22/17 http://dknet.org Tracking  Resource  Mentions "We  extracted  clinical  data  on  all  unrelated  index   subjects  with  a  confirmed  diagnosis  of  IBD  from  the   NIDDKIBDGCs  central  repository  database." "DNA  samples  used  for  genotyping  this  SNP  in  the   GoKinD  collection  were  obtained  through  the   National  Institute  of  Diabetes  and  Digestive  and   Kidney  Diseases  Central  Repository   (www.niddkrepository.org/)." "Samples  were  tracked  from  the  point  of   collection,  processed  at  network  laboratories   and  stored  for  deposit  at  National  Institute  for   Diabetes  and  Digestive  and  Kidney   Diseases  (NIDDK)  Central  Repositories."
  • 45. dkNET  mtg  06/22/17 http://dknet.org Expanding  Outreach  and   Improving  User  Experiences
  • 46. dkNET  mtg  06/22/17 http://dknet.org Outreach  Activities 1. Interviewed  users  to  improve  UI  and  data  presentation   2. Conferences   Sep.  2016  International  Society  of  Nephrology  (ISN)  Forefronts  Symposium  on  the  Metabolome   and  Microbiome  in  Kidney  Disease:  poster   Mar.  2017  HIRN  Annual  Investigator's  Meeting:  poster  and  booth Apr.  2017  ENDO  Annual  Meeting:  booth,  poster,  big  data  oral  session,  RRID  oral  sessions,   science  hub  oral  sessions 3. Webinars: Sep.  2016  dkNET  @BioCADDIE  Webinar Apr.  2017  dkNET-­NURSA  Challenge  Kick  Off  Webinar May  2017  dkNET  Introductory  Webinar
  • 47. dkNET  mtg  06/22/17 http://dknet.org Outreach  Activities 4. April-­June,  2017  dkNET-­NURSA  Challenge 5. American  Society  of  Hematology  (ASH)  clinical  prototype 6. Interact  with  users  and  resource  centers 7. Email  campaigns  and  dkNET  Digest 8. June,  2017  dkNET  Searchathon
  • 48. dkNET  mtg  06/22/17 http://dknet.org Outreach  Activities:    Email  Campaigns April  2017  dkNET  email  list:  challenge,  introductory  webinar,  beta  test April  2017  NIDDK  awardees:  dkNET  introduction,  challenge,  funding  use   cases,  introductory  webinar May  2017  dkNET  email  list  and  NIDDK  awardees:  introductory  webinar,   Monthly  events  and  funding  announcements May  2017  DRC  center  directors,  Resource  centers,  UCSD  postdoc  email  list   and  bioinformatics  graduate  program:  Introductory  and  challenge   information  (no  MailChimp  tracking) dkNET  Email  List 40%  Open  Rate 8%  Clickthrough  Rate Awardee  Email  List 25%  Open  Rate 2.7%  Clickthrough  Rate Mailchimp  2017  Benchmarks 15-­30%  Open  Rate   1-­5%  Clickthrough  Rate  
  • 49. dkNET  mtg  06/22/17 http://dknet.org dkNET  Highlights  and  News May,  2017:  Pilot  funding  news  and  blog,  new  resources,  new  data,  tissue   sample  use  case,  community  news,  challenge Top  clicks: Funding  (MMPC),  New  resources  (Pituitary  network  association,   American  Thyroid  Association),  Funding  (NURSA) June,  2017:  Same  categories,  clinical  datasets  use  case Top  clicks: New  resources  (MicrobiomeAnalyst),  New  data  (OmicsDI   database),  Events,  Funding  (DiaComp)
  • 50. dkNET  mtg  06/22/17 http://dknet.org Outcomes  of  Outreach  Activities Increased  traffic  to  dkNET   website Increased  our  mailing  list   subscription   Over  41  new  accounts   opened Saved  searches Resource  subscriptions Increased  social  media   connections Google  analytics  (March  1  -­ June  19,  2017  vs  last  period) ENDO Challenge   Webinar  +   1st  Large   email Intro   Webinar  +   2nd  Large   Email   +postdoc   list Searchathon   +2nd  digest   +postdoc/stud ent  list   HIRN 1st   Small   Email   2nd  Small   Email   1st  digest
  • 51. dkNET  mtg  06/22/17 http://dknet.org Social  Media  -­ Twitter
  • 52. dkNET  mtg  06/22/17 http://dknet.org Google  Analytics   Referring  Traffic
  • 53. dkNET  mtg  06/22/17 http://dknet.org Google  Analytics:  Where  Are  Our  Users?
  • 54. dkNET  mtg  06/22/17 http://dknet.org Search-­a-­thon Invited  naive  users  to  participate  in  a  searchathon Faculty,  students  and  post-­docs  across  disciplines Bioinformaticians Developers  watched  users  navigate  the  portal Surveyed  users  about  their  use  cases  and  experiences
  • 55. dkNET  mtg  06/22/17 http://dknet.org dkNET  Searchathon  on  June  9,  2017   Ease  of  dkNET  portal  (1:  very  difficult;;  10:  very  easy) Weighted   Average:   6.55
  • 56. dkNET  mtg  06/22/17 http://dknet.org Did  you  find  what  you  were  looking  for? 73%
  • 57. dkNET  mtg  06/22/17 http://dknet.org Recommendations:  Consolidation  of  Search “The  top  row  of  buttons  of  about/community  resources/more  resources/literature  are  confusing.  It  looks   like  just  website  information  but  instead  they  are  three  different  search  engines.  When  I  first  visit  this   webpage,  I  did  not  notice  that  I  can  also  search  for  more  resources  and  literature.” “It  was  difficult  for  me  to  find  some  information  that  I  was  searching  for.  For  example  I  wanted  some  of  the   OMIM  links  but  could  only  see  them  when  I  clicked  on  More  Resources.    I  don't  understand  why   community  resources  and  more  resources  are  split.  I  want  all  the  search  results  to  appear  on  one  page.”   “The  "Community  Resource"  and  "More  Resources"  button  might  be  integrated  into  the  "option"  when   people  do  the  search” “Clearer  divisions  of  search  results  such  as  Reagents  and  Protocols,  Funding  and  Conferences,  Literature   and  Datasets  would  be  nice.  Maybe  having  them  all  displayed  in  side  by  side  columns  or  somehow  more   visible  all  at  once.”
  • 58. dkNET  mtg  06/22/17 http://dknet.org Recommendations:  Visualizations “I  really  like  some  of  the  graphical  search  features  like  the  word  clouds,  facets,  and  category  graph.  It   would  be  useful  if  I  could  filter  from  the  word  clouds.” “I  like  the  color  circle  feature  when  I  search  literatures,  it  did  catch  my  eye  “ “My  first  impressions  is  that  dkNET  is  very  complicated,  but  contains  many  features.  I  think  the  static   image  tutorials  could  be  improved  by  creating  video  tutorials.”
  • 59. dkNET  mtg  06/22/17 http://dknet.org Additional  Feedback   “Maybe  add  in  tools  like  Matchmaker  exchange  to  link  researchers  together  who  are  studying  the  same   gene.” “I  found  information  about  another  group  working  with  the  patient  population  I'm  interested  in.” “My  first  impressions  is  that  dkNET  is  very  complicated,  but  contains  many  features.  I  think  the  static   image  tutorials  could  be  improved  by  creating  video  tutorials.” “I  was  looking  for  information  about  a  disease  that  we  study.  I  was  able  to  find  some  of  what  I  was  looking   for,  and  also  some  interesting  datasets  that  I  did  not  know  existed.  This  seems  like  a  good  tool  for   exploratory  searching  (to  see  what  exists  in  terms  of  literature,  reagents,  datasets).  Having  a  clear  header   with  what  diseases  are  searchable  would  be  helpful.  i.e.  For  researchers  in  the  fields  of  kidney  disease,  x,   y,  z.  
  • 60. dkNET  mtg  06/22/17 http://dknet.org Practical  Use  Cases
  • 61. dkNET  mtg  06/22/17 http://dknet.org Overview  of  Use  Case  Collection ● Use  cases  from  dkNET  (classic  use  cases,  user  interviews  from   beta  testing,  conferences,  dkNET  survey  via  e-­mail  list,  dkNET   Searchathon) ● Use  cases  from  the  ESP  (survey  ESP  prior  to  the  retreat) ● Use  cases  from  NIH  Staff (obtain  prior  to  the  retreat)
  • 62. dkNET  mtg  06/22/17 http://dknet.org What  Are  Users  Looking  For  in  dkNET?   Emailed  Use  Case  Survey   Users'  background  and  disease   fields  are  varied;;  they  are   looking  for  different  resources   for  different  use  cases  based   on  their  research  or  areas  of   interest
  • 63. dkNET  mtg  06/22/17 http://dknet.org Summary  of  Use  Cases  From  dkNET  Users Background Categories/Features  that  dkNET  covers What  users  hope  that  dkNET   can  offer  in  the  future? Basic  Scientist Literature,  Database/Repository,  Tissue  Bank,  Funding,   Resources  (any),  Image  dataset  (Cell,  Mitochondria),  Cell  image   analysis  software,  genes  linked  to  disease Popularity/impact  of  the   resources,  collaborator Clinical  Scientist Funding,  Clinical  Trials  (recruiting  status),  Patient  population  in   clinical  trials.  Dataset/Data  summary  of  Clinical  Trials,  Dataset   (microarray,  RNAseq),  disease  research  information  or  dataset Access  to  several  gene  matrix,   Find  researchers  who  study  the   same  genes  of  interest Bioinformatician Literature,  Software,  Pathways,  Imaging  Dataset,  Beta  testers Faculty Literature,  Database/Repository,  Funding,  Softwares,  New   things,  Open  dataset Ranking  of  open/commercial   resources  in  terms  of  reputation   and  quality,  more  intuitive  page   layouts Trainee   Funding  agency  of  interdisciplinary  field  
  • 64. dkNET  mtg  06/22/17 http://dknet.org Use  Cases  From  dkNET  Users User  interviews  from  beta  testing A  scientist  who  has  both  basic  research  and  bioinformatics  background  is  looking  for  Literature related   to  how  glucose  regulates  PKA  inhibition  and  Literature  related  to  PKA  Catalytic A  clinical  research  and  image  informatics  faculty  is  looking  for  what's  new or  would  like  to  know  if  there   is  any  new  software related  to  tools  she  currently  uses.  She  is  also  looking  for  funded  grants related  to  a  currently  funded  project. A  basic  science  faculty  is  looking  for  database/repository  to  deposit  the  datasets that  they  generated   A  data  scientist  is  looking  for  image  dataset for  related  to  a  specific  disease A  bioinformatics  faculty  is  looking  for  pathway  analysis  software
  • 65. dkNET  mtg  06/22/17 http://dknet.org Use  Cases  From  dkNET  Users New  users  at  targeted  conferences A  basic  scientist  is  looking  for  liver  tissue  bank A  PhD  student  is  looking  for  government/non-­profit/profit  agency that  he/she  can  apply  funding  for   microbiome  research A  scientist  (non-­profit  organization)is  looking  for  pituitary  gland relevant  resources  and  fundings A  clinical  scientist  is  looking  for  pediatric  diabetes  clinical  trial  with  open  enrollment A  clinical  scientist  is  looking  for  dataset  or  data  summary  of  clinical  trials A  bioinformatician  is  looking  for  diabetic  kidney  diseases  pathways to  build  a  network A  bioinformatician  is  looking  for  help  in  contacting  beta  testers for  new  developed  tools
  • 66. dkNET  mtg  06/22/17 http://dknet.org Use  Cases  From  dkNET  Users   Emailed  Use  Case  Survey   A  faculty  member  at  university  whose  research  focused  on  liver  disease  and  obesity  is  looking  for   tissue  banks,  cell  image  datasets,  mitochondria  images,  and  cell  image  analysis  software,   and  hopes  that  dkNET  could  provide  related  resources  of  his/her  interest,  with  links  to  the  resources   and  popularity/impact  estimation  of  the  research  resources. A  basic  scientist  (exercise  physiologist)  at  university  whose  research  focused  on  diabetes,   metabolic  diseases,  nutrition,  and  obesity  is  looking  for  research  ideas  on  the  effects  of   exercise  on  diabetics,  and  hopes  that  dkNET  could  help  him/her  to  find  a  group  to  collaborate   with.  He/She  is  at  a  small  college  so  he/she  has  a  large  teaching  load  and  not  a  ton  of  time  for   research. A  physician  scientist  at  hospital  whose  research  focused  on  emergency  contraception  is  looking  for   microarray  or  RNAseq  gene  expression  data  related  to  endometrial  receptivity,  and  hopes  that   dkNET  could  provide  the  access  to  several  gene  expression  matrix  related  to  the  effects  of   progesterone  receptor  modulators  drugs  used  for  gynecological  diseases.
  • 67. dkNET  mtg  06/22/17 http://dknet.org Summary  of  Use  Cases  from  ESP   Use  cases 1. I  am  a  researcher  looking  for  genomic  data  sets  about  nuclear  receptors   in  hormone-­dependent  cancers. 2. I'm  a  researcher  looking  for  available  datasets  that  match  a  set  of  criteria   based  on  species,  tissue  type,  cell  line,  cellular  pathway,  etc. Services   1. A  summary  of  the  available  databases  with  links  to  the  relevant   publications. 2. Data  visualization 3. Reproducibility  reporting
  • 68. dkNET  mtg  06/22/17 http://dknet.org Use  Cases  From  NIH  Staff Validated  probes  (and  validation  reports),  data  on  genes  of  interest I  am  a  researcher  looking  for  datasets  relevant  to  my  research  interest LINKOUT  to  related  resources,  metadata,  and  accessible  digital  resources Aggregated  services  surrounding  enhancement  of  rigor  and  reproducibility,  authentication,  etc. Tutorials  and  best  practices  surrounding  rigor  and  reproducibility  when  it  comes  to  reagents  and   other  research  resources Include  more  omics  data  types Include  highly  relevant  websites    (e.g.  all  the  resources  generating  grants,  consortia;;  other  similar   sites) Include  Relevant  conferences A  discussion  forum.  where  young  scientists  can  ask  for  help  to  find  a  certain  resource,  where  they   can  post  questions  like  “where  I  can  find  ….”    (for  example,  where  I  can  find  humanized  mouse   model,  functional  genomic  datasets,  datasets  with  deep  phenotyping,  data  sets  with  sample   size  larger  than  ***,  etc,...).