Mars Workshop

450 views

Published on

Presentation given at the Microbial Antarctic Resource System (mARS), during the SCAR Open Science Conference 2012, in Portland. Presented by Alison Murray and Bruno Danis.

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
450
On SlideShare
0
From Embeds
0
Number of Embeds
3
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Mars Workshop

  1. 1. Hello mARS Microbial Antarctic Resource SystemWednesday 18 July 12
  2. 2. Hello mARS Microbial Antarctic Resource SystemWednesday 18 July 12
  3. 3. Why are we here? • Update on mARS initiative • synk on data flows and standards • integrate microbial information into the Antarctic Biodiversity Information Facility (ANTABIF)Wednesday 18 July 12
  4. 4. What’s ANTABIF? David B, Danis B, Griffiths HJWednesday 18 July 12
  5. 5. What’s ANTABIF? • Born as Census of Antarctic Marine Life as the data, visualization and analysis component David B, Danis B, Griffiths HJWednesday 18 July 12
  6. 6. What’s ANTABIF? • Born as Census of Antarctic Marine Life as the data, visualization and analysis component • Free and open access to biodiversity data: taxonomy and biogeography David B, Danis B, Griffiths HJWednesday 18 July 12
  7. 7. What’s ANTABIF? • Born as Census of Antarctic Marine Life as the data, visualization and analysis component • Free and open access to biodiversity data: taxonomy and biogeography • SCAR-MarBINand ANTABIF projects David B, Danis B, Griffiths HJWednesday 18 July 12
  8. 8. What’s ANTABIF? • Born as Census of Antarctic Marine Life as the data, visualization and analysis component • Free and open access to biodiversity data: taxonomy and biogeography • SCAR-MarBINand ANTABIF projects • Science, conservation and management David B, Danis B, Griffiths HJWednesday 18 July 12
  9. 9. What’s ANTABIF? • Born as Census of Antarctic Marine Life as the data, visualization and analysis component • Free and open access to biodiversity data: taxonomy and biogeography • SCAR-MarBINand ANTABIF projects • Science, conservation and management • Networked community developments David B, Danis B, Griffiths HJWednesday 18 July 12
  10. 10. What’s ANTABIF? • Born as Census of Antarctic Marine Life as the data, visualization and analysis component • Free and open access to biodiversity data: taxonomy and biogeography • SCAR-MarBINand ANTABIF projects • Science, conservation and management • Networked community developments • Scientific impact: Citations : 423, Publications: 58, H-Index: 11 David B, Danis B, Griffiths HJWednesday 18 July 12
  11. 11. What’s ANTABIF? • Born as Census of Antarctic Marine Life as the data, visualization and analysis component • Free and open access to biodiversity data: taxonomy and biogeography • SCAR-MarBINand ANTABIF projects • Science, conservation and management • Networked community developments • Scientific impact: Citations : 423, Publications: 58, H-Index: 11 David B, Danis B, Griffiths HJWednesday 18 July 12
  12. 12. progress: ANTABIF ArchitectureWednesday 18 July 12
  13. 13. progress: ANTABIF Architecture • www.biodiversity.aqWednesday 18 July 12
  14. 14. progress: ANTABIF Architecture • www.biodiversity.aq • data.biodiversity.aqWednesday 18 July 12
  15. 15. progress: ANTABIF Architecture • www.biodiversity.aq • data.biodiversity.aq • ipt.biodiversity.aqWednesday 18 July 12
  16. 16. progress: ANTABIF Architecture • www.biodiversity.aq • data.biodiversity.aq • ipt.biodiversity.aq • afg.biodiversity.aqWednesday 18 July 12
  17. 17. progress: ANTABIF Architecture • www.biodiversity.aq • data.biodiversity.aq • ipt.biodiversity.aq • afg.biodiversity.aq • atlas.biodiversity.aqWednesday 18 July 12
  18. 18. progress: ANTABIF Architecture • www.biodiversity.aq • data.biodiversity.aq • ipt.biodiversity.aq • afg.biodiversity.aq • atlas.biodiversity.aq • mars.biodiversity.aqWednesday 18 July 12
  19. 19. progress: ANTABIF Architecture Promote)the)communit • www.biodiversity.aq MODULAR development)of)N ARCHITECTURE • data.biodiversity.aq •  GBIF)promotes)training)and)us • ipt.biodiversity.aq • afg.biodiversity.aq • atlas.biodiversity.aq • mars.biodiversity.aq ANTABIFWednesday 18 July 12
  20. 20. progress: ANTABIF Architecture Nodes)Investment)in)new)func@onality) Promote)the)communit • •  www.biodiversity.aq MODULAR development)of)N Nodes)extend)the)plaGorm)with)new)modules) ARCHITECTURE • data.biodiversity.aq •  GBIF)promotes)training)and)us Data discovery A)module)we)all)need) • ipt.biodiversity.aq A)module)I)need) • afg.biodiversity.aq • atlas.biodiversity.aq • mars.biodiversity.aq ANTABIFWednesday 18 July 12
  21. 21. progress: ANTABIF Architecture Nodes)Investment)in)new)func@onality) Promote)the)communit Nodes)Investment)in)new)func@ona • •  www.biodiversity.aq MODULAR development)of)N Nodes)extend)the)plaGorm)with)new)modules) ARCHITECTURE •  Nodes)extend)the)plaGorm)with)new)mod •  GBIF)promotes)training)and)us • data.biodiversity.aq Data discovery A)module)we)all)need) • ipt.biodiversity.aq A)module)I)need) Data visualization A)module)we)all)need) A)module)I)need) • afg.biodiversity.aq • atlas.biodiversity.aq • mars.biodiversity.aq ANTABIFWednesday 18 July 12
  22. 22. progress: ANTABIF Architecture Nodes)Investment)in)new)func@onality) NPT)can)be)extended)by)crea@ng)an Promote)the)communit Nodes)Investment)in)new)func@ona • •  www.biodiversity.aq installing)Modules) MODULAR development)of)N Nodes)extend)the)plaGorm)with)new)modules) ARCHITECTURE •  Nodes)extend)the)plaGorm)with)new)mod •  GBIF)promotes)training)and)us • data.biodiversity.aq Data discovery Data products A)module)we)all)need) • ipt.biodiversity.aq A)module)I)need) Data visualization A)module)we)all)need) A)module)I)need) • afg.biodiversity.aq • atlas.biodiversity.aq • mars.biodiversity.aq ANTABIFWednesday 18 July 12
  23. 23. Benefits • Provide  a  centralized  data  access  point  to  metadata  and   sequence-­‐based  informa9on  for  Antarc9c  biodiversity   studies • Facilitate  scien9fic  cross-­‐comparisons  within  and   between  habitats  in  Antarc9ca • Facilitate  conserva9on-­‐based  decision  making  in  order  to   assess  human  and  climate  impacts  to  numerous   environments  in  which  the  microbial  community  may  be   the  only  reporter  of  ecosystem  status • Serve  as  an  example  for  other  biodiversity  research   communi9es   • Serves  Na9onal  Antarc9c  program  requirements  for  data  Wednesday 18 July 12
  24. 24. Challenges  with  storing  and  accessing   microbial  diversity  informa9on • Many  scales  of  informa/on – Culture  collec9ons  (1  –  hundreds)   – Clone  libraries  &  Sanger  Sequences  (10’s  to  hundreds) – Next  genera9on  sequencing  (454,  Illumina,  Ion  Torrent)  (1000’s  to   hundreds  of  millions) • Different  gene  markers  studied – Bacteria:  16S  rRNA,  gyrB,  func9onal  genes  (ie.  Nitrogen  cycling  genes   nifH,  nirK,  nirS,  amoA) – Archaea:  16S  rRNA…  func9onal  genes – Eukarya:  18S  rRNA,  ITS,  mt:  COI  –  for  barcoding • Many  regions  of  the  same  marker  gene  studied • Metagenome  studies  on  the  rise!   – replace/in  tandem  with  marker  gene  studiesWednesday 18 July 12
  25. 25. Data  standards • Genome  Standards  Consor9um –MIGS  –  Field  et  al.  2008  Nature  Biotechnology –MIMARKS  –  Yilmaz  et  al.  2011  Nature  Biotechnology –Biological  observa9on  matrix  -­‐  BIOM;  biom-­‐format.org   (candidate  project  for  GSC) • Environment  Ontology  -­‐  hbp:// environmentontology.org/ • DarwinCore  Archives • EML:  ecological  markup  languageWednesday 18 July 12
  26. 26. DarwinCore Archive Darwin Core Archive (two files) meta.xml  describes  the  mappings  in  the core  data  file  (species.txt)Wednesday 18 July 12
  27. 27. DarwinCore Archive Multiple extensions are available Columns  in  extensions  are  mapped  to  Darwin  Core  using  the  meta.xml  fileWednesday 18 July 12
  28. 28. How  is  the  challenge  handled  currently:   state  of  the  art • Where  is  microbial  diversity  informa9on   currently  stored? • Are  there  current  resources  to  access  geo-­‐ referenced  microbial  diversity  data?   • Are  there  resources  to  access  data  sets  for   compara9ve  study?  Wednesday 18 July 12
  29. 29. Current  data  storage  solu9ons  for  geo-­‐ referenced  marker  gene  studies 1.  GenBank –Typical  marker  gene-­‐centric  submissions –Single  read  archive  (SRA  -­‐  holds  SFF  dqtq  files;  can  also   accept  MIMARKS  metadata) –  EMBL  also  suppor9ng  SRA  equivalent 2.  Data  resources  (database  driven  vs.  user  driven) –See  chart  Wednesday 18 July 12
  30. 30. Database  tool  featuresWednesday 18 July 12
  31. 31. DISCUSSION… • Missed  items? • Further  explana9ons  or  examples?   • Ideal  needs  of  community  vs.  realis9c  ability  to   provide  resources? • Other  challenges?   • Standards  –  suggest  16S  rRNA  region  for   Antarc9c  microbial  community;  protocolsWednesday 18 July 12
  32. 32. mars.biodiversity.aqWednesday 18 July 12
  33. 33. mars.biodiversity.aq • Integrate Antarctic microbial DNA sequence data in ANTABIFWednesday 18 July 12
  34. 34. mars.biodiversity.aq • Integrate Antarctic microbial DNA sequence data in ANTABIF • Phased approach:Wednesday 18 July 12
  35. 35. mars.biodiversity.aq • Integrate Antarctic microbial DNA sequence data in ANTABIF • Phased approach: Step 0: data description and discoveryWednesday 18 July 12
  36. 36. mars.biodiversity.aq • Integrate Antarctic microbial DNA sequence data in ANTABIF • Phased approach: Step 0: data description and discovery Step 1: microbial sequence and habitat metadataWednesday 18 July 12
  37. 37. mars.biodiversity.aq • Integrate Antarctic microbial DNA sequence data in ANTABIF • Phased approach: Step 0: data description and discovery Step 1: microbial sequence and habitat metadata Step 2: sequence dataWednesday 18 July 12
  38. 38. mars.biodiversity.aq • Integrate Antarctic microbial DNA sequence data in ANTABIF • Phased approach: Step 0: data description and discovery Step 1: microbial sequence and habitat metadata Step 2: sequence data Step 3: batch sequence data processingWednesday 18 July 12
  39. 39. mars.biodiversity.aq • Integrate Antarctic microbial DNA sequence data in ANTABIF • Phased approach: Step 0: data description and discovery Step 1: microbial sequence and habitat metadata Step 2: sequence data Step 3: batch sequence data processing Step 4: customized sequence data processingWednesday 18 July 12
  40. 40. Thanks and questions? mars.biodiversityaq image  ©  NY  Times  Wednesday 18 July 12

×