Mars Workshop

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)


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


What’s ANTABIF?


• Free and open access to biodiversity data: taxonomy and biogeography


What’s ANTABIF?



• SCAR-MarBINand ANTABIF projects


What’s ANTABIF?




• Science, conservation and management


What’s ANTABIF?





• Networked community developments


What’s ANTABIF?





• Networked community developments

• Scientific impact: Citations : 423, Publications: 58, H-Index: 11


progress: ANTABIF Architecture


http://data.biodiversity.aq










• www.biodiversity.aq



http://www.biodiversity.aq












• www.biodiversity.aq• data.biodiversity.aq















• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq















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• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq















• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• mars.biodiversity.aq

















Promote)the)communityEdriven)development)of)NPT)

•  GBIF)promotes)training)and)use)of)NPT)

ANTABIF

MODULAR ARCHITECTURE















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



ANTABIF

MODULAR ARCHITECTURE


















Data discovery



ANTABIF

MODULAR ARCHITECTURENodes)Investment)in)new)func@onality)



Data visualization


















Data discovery



ANTABIF

MODULAR ARCHITECTURENodes)Investment)in)new)func@onality)



Data visualization

NPT)can)be)extended)by)crea@ng)and)installing)Modules)

Data products














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


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


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


http://environmentontology.org




DarwinCore Archive

meta.xml describes the mappings in thecore data file (species.txt)

Darwin Core Archive (two files)


DarwinCore Archive

Columns in extensions are mapped to Darwin Core using the meta.xml file

Multiple extensions are available


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?


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


Database tool features


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


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 3: batch sequence data processing

Step 4: customized sequence data processing



mars.biodiversityaq

image © NY Times

Thanks and questions?




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