WHAT IS THE ALPINE MICROBIAL OBSERVATORY

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WHAT IS THE ALPINE MICROBIAL OBSERVATORY?

• The Alpine Microbial Observatory (AMO) is a
  5-year, 1.5 million dollar NSF project
• AMO goal is to study seasonal dynamics of soil
  microbes across an extreme environmental gradient
  in the alpine
• Focus on community composition changes
  utilizing phylogenetic measures of diversity
• Importance of scaling from local diversity to
  potentially global patterns

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WHY INFORMATICS FOR AMO?

• Need mechanism for storing and linking large
  quantities of genetic AND environmental data
• Such a mechanism crucial for downstream analyses
  of community composition in relation to
  environment
• Mechanism allows scaling of analyses from local
  to global patterns of diversity

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• The core database for the Alpine Microbial
  Observatory (AMO) captures information about the
  site where soils are collected (eg. geospatial
  and temporal data), the characteristics of the
  soil sample itself (eg. bio-geochemical data),
  and the microbial sequences generated from those
  soil samples (eg. 16S rRNA data).

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Core Data Model
Location x,y,z
(Soil) Samples
Sequence Data
Environ-mental Data
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• Query
• Location
• Proximity
• Time
• Chemistry
• Gene
• Sequence
• Environment
• etc

Database Query
Location x,y,z

• Results
• Requested sequences, integrated with
• environmental data
• Spatial/temporal distrivbution
• Project or methods

• Data
• Relational DBMS
• Entities reflect real-world objects

(Soil) Samples
Sequence Data
Environ-mental Data
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Query Destinations
Location x,y,z
Web Interface

• amo.colorado.edu
• AMOdv private site

Output file / External db Interface
(Soil) Samples

• Fasta
• XML
• (more )

Integrated Applications
Sequence Data
Environ-mental Data

• GIS Mapping,
• Phylogenetic Reconstruction, Tree Visualization

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Data Upload(fasta)
Location x,y,z
Secure, web-based data upload

• Location, Sample, BGC
• data entry plus automation
• GPS, GIS
• field observations measurements

(Soil) Samples
Fasta-formatted sequence data (GenBank)
Sequence Data
Environ-mental Data
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MIGS/MIMS Schema (partial)
XML Inter-change
ltBiomaterialgt ltsedimentgt ltsediment_depthgt ltporosit
ygt ltpermeabillitygt ltgrain_size_distributiongt ltsedi
ment_pore_watergt lteHgt ltwater_bodygt lttemperaturegt lt
pHgt ltsalinitygt ltpressuregt ltchlorophylgt ltconductivi
tygt ltlight_intensitygt ltalkalinitygt ltdissolved_oxyg
engt ltphosphategt ltnitrategt ltTip Sequencegt ltcomplete
_genetic_lineagegt ltploidy_levelgt ltnumber_of_replic
onsgt ltextrachromosomal_elementsgt ltestimated_sizegt
ltgeographical_locationgt ltgeographical_regiongt ltdat
egt lttimegt ltlatitudegt ltlongitudegt . . .
Location x,y,z
Samples
Query
XML parse
Sequence Data
Environ-mental Data
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Tip Sequence 1
Tip Sequence 2
Tip Sequence 3
Tip Sequence 4
Tip Sequence 5
Tip Sequence 6
Click on a node to select and highlight a clade.
Tip Sequence 7
Tip Sequence 8
Tip Sequence 9
Tip Sequence 10
Tip Sequence 11
Tip Sequence 12
Tip Sequence 13
Tip Sequence 14
Tip Sequence 15
Tip Sequence 16
Tip Sequence 17
Tip Sequence 18
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Tip Sequence 1
Tip Sequence 2
Tip Sequence 2
Tip Sequence 3
Tip Sequence 4
Tip Sequence 5
Click on a selected node to open a window that
displays biogeochemistry information for the
selected sequences.
Tip Sequence 6
Tip Sequence 7
Tip Sequence 8
Tip Sequence 9
Tip Sequence 10
Tip Sequence 11
Tip Sequence 12
Tip Sequence 13
Tip Sequence 14
Tip Sequence 15
Tip Sequence 16
Tip Sequence 17
Tip Sequence 18
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Tip Sequence 1
Tip Sequence 2
Tip Sequence 3
The specific data elements to display in this
table are open to design. Depends on what is
available in the database. Enhancements to
current data can bring more data into this
table. Each column can be sortable. Some data
will be linked - i.e., click on data (such as
gene, library, location ) to open a window with
more detail, or to link to pages with similar
data.
Tip Sequence 4
All displays of BGC data will include units of
measure (left out here to simplify the
example). Which BGC entities to include in the
table (e.g., NO3-, DOC) can be selectable will
be limited by what is available for the given
location.
Micro Tip Sequence 4
Tip Sequence 5
Tip Sequence 6
Tip Sequence 7
Tip Sequence 8
Tip Sequence 9
Tip Sequence 10
Tip Sequence 11
Tip Sequence 12
Tip Sequence 13
Tip Sequence 14
Tip Sequence 15
Tip Sequence 16
Tip Sequence 17
Tip Sequence 18
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Milestones / Accomplishments

• Great minds mapping of MIGS/MIMS to our data
  model shows broad overlap
• Implemented database with needed core functions
  upload new environmental sequence data
  download data to user or informatics tools
• Mechanism allows scaling of analyses from local
  to global patterns of diversity

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What Next An idea, an invitation and a question

• Workshop idea add an attribute to the .xsd for
  mapping to this data model
• Invitation requirements sought from those whose
  concern is importing biogeochem data
• What is the strategic context for information
  managament and science/discovery?