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Hello mARSMicrobial Antarctic Resource System
Wednesday 18 July 12
Hello mARSMicrobial Antarctic Resource System
Wednesday 18 July 12
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
What’s ANTABIF?
David B, Danis B, Griffiths HJWednesday 18 July 12
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
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
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
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
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
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
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
progress: ANTABIF Architecture
Wednesday 18 July 12
• www.biodiversity.aq
progress: ANTABIF Architecture
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq
progress: ANTABIF Architecture
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq
progress: ANTABIF Architecture
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq
progress: ANTABIF Architecture
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq
progress: ANTABIF Architecture
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• mars.biodiversity.aq
progress: ANTABIF Architecture
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• mars.biodiversity.aq
progress: ANTABIF Architecture
Promote)the)communityEdriven)development)of)NPT)
• GBIF)promotes)training)and)use)of)NPT)
ANTABIF
MODULAR ARCHITECTURE
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• mars.biodiversity.aq
progress: ANTABIF ArchitectureNodes)Investment)in)new)func@onality)
• Nodes)extend)the)plaGorm)with)new)modules)
A)module)I)need)A)module)we)all)need)
Data discovery
Promote)the)communityEdriven)development)of)NPT)
• GBIF)promotes)training)and)use)of)NPT)
ANTABIF
MODULAR ARCHITECTURE
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• mars.biodiversity.aq
progress: ANTABIF ArchitectureNodes)Investment)in)new)func@onality)
• Nodes)extend)the)plaGorm)with)new)modules)
A)module)I)need)A)module)we)all)need)
Data discovery
Promote)the)communityEdriven)development)of)NPT)
• GBIF)promotes)training)and)use)of)NPT)
ANTABIF
MODULAR ARCHITECTURENodes)Investment)in)new)func@onality)
• Nodes)extend)the)plaGorm)with)new)modules)
A)module)I)need)A)module)we)all)need)
Data visualization
Wednesday 18 July 12
• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• mars.biodiversity.aq
progress: ANTABIF ArchitectureNodes)Investment)in)new)func@onality)
• Nodes)extend)the)plaGorm)with)new)modules)
A)module)I)need)A)module)we)all)need)
Data discovery
Promote)the)communityEdriven)development)of)NPT)
• GBIF)promotes)training)and)use)of)NPT)
ANTABIF
MODULAR ARCHITECTURENodes)Investment)in)new)func@onality)
• Nodes)extend)the)plaGorm)with)new)modules)
A)module)I)need)A)module)we)all)need)
Data visualization
NPT)can)be)extended)by)crea@ng)and)installing)Modules)
Data products
Wednesday 18 July 12
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
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 studies
Wednesday 18 July 12
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 language
Wednesday 18 July 12
DarwinCore Archive
meta.xml describes the mappings in thecore data file (species.txt)
Darwin Core Archive (two files)
Wednesday 18 July 12
DarwinCore Archive
Columns in extensions are mapped to Darwin Core using the meta.xml file
Multiple extensions are available
Wednesday 18 July 12
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
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
Database tool features
Wednesday 18 July 12
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; protocols
Wednesday 18 July 12
mars.biodiversity.aq
Wednesday 18 July 12
• Integrate Antarctic microbial DNA sequence data in ANTABIF
mars.biodiversity.aq
Wednesday 18 July 12
• Integrate Antarctic microbial DNA sequence data in ANTABIF
• Phased approach:
mars.biodiversity.aq
Wednesday 18 July 12
• Integrate Antarctic microbial DNA sequence data in ANTABIF
• Phased approach:
Step 0: data description and discovery
mars.biodiversity.aq
Wednesday 18 July 12
• Integrate Antarctic microbial DNA sequence data in ANTABIF
• Phased approach:
Step 0: data description and discovery
Step 1: microbial sequence and habitat metadata
mars.biodiversity.aq
Wednesday 18 July 12
• 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
mars.biodiversity.aq
Wednesday 18 July 12
• 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
mars.biodiversity.aq
Wednesday 18 July 12
• 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 processing
mars.biodiversity.aq
Wednesday 18 July 12
mars.biodiversityaq
image © NY Times
Thanks and questions?
Wednesday 18 July 12