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.

1. Hello mARS
Microbial Antarctic Resource System
Wednesday 18 July 12

2. Hello mARS
Microbial Antarctic Resource System
Wednesday 18 July 12

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. What’s ANTABIF?
David B, Danis B, Griffiths HJ
Wednesday 18 July 12

5. What’s ANTABIF?
• Born as Census of Antarctic Marine Life
as the data, visualization and analysis
component
David B, Danis B, Griffiths HJ
Wednesday 18 July 12

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 HJ
Wednesday 18 July 12

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 HJ
Wednesday 18 July 12

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 HJ
Wednesday 18 July 12

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 HJ
Wednesday 18 July 12

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 HJ
Wednesday 18 July 12

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 HJ
Wednesday 18 July 12

12. progress: ANTABIF Architecture
Wednesday 18 July 12

13. progress: ANTABIF Architecture
• www.biodiversity.aq
Wednesday 18 July 12

14. progress: ANTABIF Architecture
• www.biodiversity.aq
• data.biodiversity.aq
Wednesday 18 July 12

15. progress: ANTABIF Architecture
• www.biodiversity.aq
• data.biodiversity.aq
• ipt.biodiversity.aq
Wednesday 18 July 12

16. progress: ANTABIF Architecture
• www.biodiversity.aq
• data.biodiversity.aq
• ipt.biodiversity.aq
• afg.biodiversity.aq
Wednesday 18 July 12

17. progress: ANTABIF Architecture
• www.biodiversity.aq
• data.biodiversity.aq
• ipt.biodiversity.aq
• afg.biodiversity.aq
• atlas.biodiversity.aq
Wednesday 18 July 12

18. progress: ANTABIF Architecture
• www.biodiversity.aq
• data.biodiversity.aq
• ipt.biodiversity.aq
• afg.biodiversity.aq
• atlas.biodiversity.aq
• mars.biodiversity.aq
Wednesday 18 July 12

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
ANTABIF
Wednesday 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)us
Data discovery
A)module)we)all)need)
• ipt.biodiversity.aq
A)module)I)need)
• afg.biodiversity.aq
• atlas.biodiversity.aq
• mars.biodiversity.aq
ANTABIF
Wednesday 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)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
ANTABIF
Wednesday 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)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
ANTABIF
Wednesday 18 July 12

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. 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

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
language
Wednesday 18 July 12

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. DarwinCore Archive
Multiple extensions are available
Columns
in
extensions
are
mapped
to
Darwin
Core
using
the
meta.xml
file
Wednesday 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
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. Database
tool
features
Wednesday 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;
protocols
Wednesday 18 July 12

32. mars.biodiversity.aq
Wednesday 18 July 12

33. mars.biodiversity.aq
• Integrate Antarctic microbial DNA sequence data in ANTABIF
Wednesday 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 discovery
Wednesday 18 July 12

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 metadata
Wednesday 18 July 12

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 data
Wednesday 18 July 12

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 processing
Wednesday 18 July 12

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 processing
Wednesday 18 July 12

40. Thanks and questions?
mars.biodiversityaq
image
©
NY
Times
Wednesday 18 July 12