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An ELIXIR Perspective Jo McEntyre ELIXIR EMBLEBI ELIXIR Data Platform colead DCIP Publisher Early Adopters workshop, 22 July 2016, London. Carole Goble ELIXIR UK Head of Node ELIXIR Interoperability Platform colead www.elixireurope.org
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An#ELIXIR#Perspective# · An#ELIXIR#Perspective# Jo#McEntyre# ELIXIR#EMBL7EBI# ELIXIR#Data## Platform#co7lead# DCIP#PublisherEarly#Adopters#workshop,#22#July#2016,#London.# Carole#Goble#

Jul 22, 2020

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Page 1: An#ELIXIR#Perspective# · An#ELIXIR#Perspective# Jo#McEntyre# ELIXIR#EMBL7EBI# ELIXIR#Data## Platform#co7lead# DCIP#PublisherEarly#Adopters#workshop,#22#July#2016,#London.# Carole#Goble#

An  ELIXIR  Perspective  

Jo  McEntyre  ELIXIR  EMBL-­‐EBI  

ELIXIR  Data    Platform  co-­‐lead  

DCIP  Publisher  Early  Adopters  workshop,  22  July  2016,  London.  

Carole  Goble  ELIXIR  UK  Head  of  Node  ELIXIR  Interoperability  

Platform  co-­‐lead  

www.elixir-­‐europe.org  

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2  

agriculture  

medicine  

bioindustries  

environment  

ELIXIR  connects  national  centres  and  EMBL-­‐EBI  to  build  a  sustainable    European  infrastructure  for  biological  research  data.  

ELIXIR  underpins  life  science  research  –  across  academia  and  industry.    

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http://www.elixir-­‐europe.org/  

20  ELIXIR  members  2  observers  

major  bioinformatics  service  providers  (~150)  

Co-­‐operation   Long  term  support  

ob  

Germany  

ob  

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Organisa/on  in  a  nutshell  

Data  

Tools  

Interoperability  (Standards)  

Compute  

Training  

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FAIR  Findable  

Accessible  

Interoperable  

Reusable  Intelligible  

Reproducible  

Citable  

Track  &  Countable  

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European  Nucleotide  Archive  

Protein  Data  Bank  

DNA  Variations  (SNPs)  

Gene  Expression  Studies   DOIs  (‘long  tail’)  

Inherited  disease(OMIM)  

KaAas  S,  Kim  JH,  and  McEntyre  JR  Database  Cita/on  in  Full  Text  Ar/cles  (May  2013)  PLoS  One  10.1371/journal.pone.0063184  

“Men/ons”  -­‐>  Cita/ons  

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Data  Cita/on    1.  Impact  of  data  and  data  resources    –  Evidence  to  select,  support  and  sustain  infrastructure    –  “Indicators”  of  community  usage  –  Cited  use  of  resource  

2.  Europe  PubMedCentral  –  Core  ELIXIR  data  resources  –  Integra/on  of  literature  with  data  key  to  inclusive  and  effec/ve  

infrastructure  –  Data  cita/on  (and  consequently  bidirec/onal  linking)  

3.  Cura/on  &  Iden/fier  Services  &  Prac/ces  –  Joined  up  services  for  iden/fiers,  cita/on  and  credit  –  CDL/EBI  iden/fier  harmonisa/on  –  iden/fiers.org,  n2t.net,  ezid,  datacite,  orcid  …  –  Drive  prac/ces,  including  data  cura/on  workflows  

4.  Dataset  metadata  –  Standards,  prac/ces,  indexers,  catalogers,  tools,  adop/on  –  Scaled  up  finding  and  cita/on  using  Search  Engines  

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Indicator:  “Community  served”  

Usage  •  IP  addresses/sessions  on  web  site  per  month  for  past  2/3  years  • Page/data  requests  for  web  site,  FTP,  web  services  per  month                                      for  past  2/3  years  

Use  of  resource  in  research  • No.  times  the  resource  mentioned  in  research  articles  per  year  (in  Europe  PMC)  • No.  times  accession  numbers  from  resource  mentioned  or  cited  in  research  articles  (in  Europe  PMC)  • Key  “database”  papers  (e.g.  published  in  NAR  Database  issue)  and  the  number  of  citations.  

Dependency    

•  on  the  resource  by  others  service  (what  is  the  reach  through)?    

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Cataloguing  and  Indexing  Datasets  (and  their  content)  

Depth  DATS

Reach  Google,  Bing,  Yahoo,  Yandex    

BioSchemas:  Exploitation  of  schema.org    Partnership:  •  ELIXIR  •  NIH  BD2K  •  Google  

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Bonus  Slide  

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https://dx.doi.org/10.1111/febs.13237  

https://doi.org/10.15490/seek.1.investigation.56  

hgp://data.datacite.org/10.15490/seek.1.inves/ga/on.56    

Citation  G.  Penkler;  F.  du  Toit;  W.  Adams;  M.  Rautenbach;  D.  C.  Palm;  D.  D.  van  Niekerk;  J.  L.  Snoep;  (2014):  Glucose  metabolism  in  Plasmodium  falciparum  trophozoites;  FAIRDOMHub.  http://dx.doi.org/10.15490/seek.1.investigation.56  

Data  

Models  

SOPs  

hgp://fair-­‐dom.org  

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Links  

ELIXIR:  http://www.elixir-­‐europe.org/    Bioschemas:  hgp://www.bioschemas.org    NIH  BD2K  bioCADDIE  •  hgps://biocaddie.org/  •  DATS:  hgps://biocaddie.org/workgroup-­‐3-­‐group-­‐links  •  DATAMED:  hgps://datamed.org/  •  hgps://biocaddie.org/datamed-­‐prototype-­‐call-­‐feedback  

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Links  ELIXIR:  http://www.elixir-­‐europe.org/    Bioschemas:  hgp://www.bioschemas.org    NIH  BD2K  bioCADDIE  •  hgps://biocaddie.org/  •  DATS:  hgps://biocaddie.org/workgroup-­‐3-­‐group-­‐links  •  DATAMED:  hgps://datamed.org/  •  hgps://biocaddie.org/datamed-­‐prototype-­‐call-­‐feedback  

FAIRDOM:  hgp://www.fair-­‐dom.org  Research  Objects:  hgp://www.researchobject.org