Mars Workshop

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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.

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<ul><li>1.Hello mARS Microbial Antarctic Resource SystemWednesday 18 July 12</li></ul> <p>2. Hello mARS Microbial Antarctic Resource SystemWednesday 18 July 12 3. Why are we here? Update on mARS initiative synk on data ows and standards integrate microbial information into the Antarctic Biodiversity Information Facility (ANTABIF)Wednesday 18 July 12 4. Whats ANTABIF?David B, Danis B, Grifths HJWednesday 18 July 12 5. Whats ANTABIF? Born as Census of Antarctic Marine Lifeas the data, visualization and analysiscomponentDavid B, Danis B, Grifths HJWednesday 18 July 12 6. Whats ANTABIF? Born as Census of Antarctic Marine Lifeas the data, visualization and analysiscomponent Free and open access to biodiversity data:taxonomy and biogeography David B, Danis B, Grifths HJWednesday 18 July 12 7. Whats ANTABIF? Born as Census of Antarctic Marine Lifeas the data, visualization and analysiscomponent Free and open access to biodiversity data:taxonomy and biogeography SCAR-MarBINand ANTABIF projects David B, Danis B, Grifths HJWednesday 18 July 12 8. Whats ANTABIF? Born as Census of Antarctic Marine Lifeas the data, visualization and analysiscomponent Free and open access to biodiversity data:taxonomy and biogeography SCAR-MarBINand ANTABIF projects Science, conservation and management David B, Danis B, Grifths HJWednesday 18 July 12 9. Whats ANTABIF? Born as Census of Antarctic Marine Lifeas the data, visualization and analysiscomponent 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, Grifths HJWednesday 18 July 12 10. Whats ANTABIF? Born as Census of Antarctic Marine Lifeas the data, visualization and analysiscomponent Free and open access to biodiversity data:taxonomy and biogeography SCAR-MarBINand ANTABIF projects Science, conservation and management Networked community developments Scientic impact: Citations : 423,Publications: 58, H-Index: 11 David B, Danis B, Grifths HJWednesday 18 July 12 11. Whats ANTABIF? Born as Census of Antarctic Marine Lifeas the data, visualization and analysiscomponent Free and open access to biodiversity data:taxonomy and biogeography SCAR-MarBINand ANTABIF projects Science, conservation and management Networked community developments Scientic impact: Citations : 423,Publications: 58, H-Index: 11 David B, Danis B, Grifths HJWednesday 18 July 12 12. progress: ANTABIF ArchitectureWednesday 18 July 12 13. progress: ANTABIF Architecture www.biodiversity.aqWednesday 18 July 12 14. progress: ANTABIF Architecture www.biodiversity.aq data.biodiversity.aqWednesday 18 July 12 15. progress: ANTABIF Architecture www.biodiversity.aq data.biodiversity.aq ipt.biodiversity.aqWednesday 18 July 12 16. progress: ANTABIF Architecture www.biodiversity.aq data.biodiversity.aq ipt.biodiversity.aq afg.biodiversity.aqWednesday 18 July 12 17. progress: ANTABIF Architecture www.biodiversity.aq data.biodiversity.aq ipt.biodiversity.aq afg.biodiversity.aq atlas.biodiversity.aqWednesday 18 July 12 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. progress: ANTABIF Architecture Promote)the)communit www.biodiversity.aqMODULAR development)of)N ARCHITECTURE data.biodiversity.aq GBIF)promotes)training)and)us ipt.biodiversity.aq afg.biodiversity.aq atlas.biodiversity.aq mars.biodiversity.aqANTABIFWednesday 18 July 12 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)usData discoveryA)module)we)all)need) ipt.biodiversity.aq A)module)I)need) afg.biodiversity.aq atlas.biodiversity.aq mars.biodiversity.aqANTABIFWednesday 18 July 12 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)usdata.biodiversity.aqData discoveryA)module)we)all)need) ipt.biodiversity.aq A)module)I)need)Data visualizationA)module)we)all)need) A)module)I)need) afg.biodiversity.aq atlas.biodiversity.aq mars.biodiversity.aqANTABIFWednesday 18 July 12 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)usdata.biodiversity.aqData discoveryData productsA)module)we)all)need) ipt.biodiversity.aq A)module)I)need)Data visualizationA)module)we)all)need) A)module)I)need) afg.biodiversity.aq atlas.biodiversity.aq mars.biodiversity.aqANTABIFWednesday 18 July 12 23. Benets Provide a centralized data access point to metadata and sequence-based informa9on for Antarc9c biodiversity studies Facilitate scien9c 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. Challenges with storing and accessing microbial diversity informa9on Many scales of informa/on Culture collec9ons (1 hundreds) Clone libraries &amp; Sanger Sequences (10s to hundreds) Next genera9on sequencing (454, Illumina, Ion Torrent) (1000s to hundreds of millions) Dierent 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. 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. DarwinCore Archive Darwin Core Archive (two les) meta.xml describes the mappings in the core data le (species.txt)Wednesday 18 July 12 27. DarwinCore Archive Multiple extensions are available Columns in extensions are mapped to Darwin Core using the meta.xml leWednesday 18 July 12 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. Current data storage solu9ons for geo- referenced marker gene studies 1. GenBank Typical marker gene-centric submissions Single read archive (SRA - holds SFF dqtq les; 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. Database tool featuresWednesday 18 July 12 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. mars.biodiversity.aqWednesday 18 July 12 33. mars.biodiversity.aq Integrate Antarctic microbial DNA sequence data in ANTABIFWednesday 18 July 12 34. mars.biodiversity.aq Integrate Antarctic microbial DNA sequence data in ANTABIF Phased approach:Wednesday 18 July 12 35. mars.biodiversity.aq Integrate Antarctic microbial DNA sequence data in ANTABIF Phased approach:Step 0: data description and discoveryWednesday 18 July 12 36. mars.biodiversity.aq Integrate Antarctic microbial DNA sequence data in ANTABIF Phased approach:Step 0: data description and discoveryStep 1: microbial sequence and habitat metadataWednesday 18 July 12 37. mars.biodiversity.aq Integrate Antarctic microbial DNA sequence data in ANTABIF Phased approach:Step 0: data description and discoveryStep 1: microbial sequence and habitat metadataStep 2: sequence dataWednesday 18 July 12 38. mars.biodiversity.aq Integrate Antarctic microbial DNA sequence data in ANTABIF Phased approach:Step 0: data description and discoveryStep 1: microbial sequence and habitat metadataStep 2: sequence dataStep 3: batch sequence data processingWednesday 18 July 12 39. mars.biodiversity.aq Integrate Antarctic microbial DNA sequence data in ANTABIF Phased approach:Step 0: data description and discoveryStep 1: microbial sequence and habitat metadataStep 2: sequence dataStep 3: batch sequence data processingStep 4: customized sequence data processingWednesday 18 July 12 40. Thanks and questions? mars.biodiversityaqimage NY Times Wednesday 18 July 12 </p>