mobedac - microbiome of the built environment data analysis core
DESCRIPTION
MoBeDAC - Microbiome of the Built Environment Data Analysis Core. This slideshow was presented at the Healthy Buildings 2012 conference in Brisbane Australia. Material covers the MoBeDAC and how it integrates various data sources and enables analysis across platforms.TRANSCRIPT
MoBeDAC
Microbiome of the Built Environment Data Analysis Core
Background
Rob Knight’s group, University of Colorado at Boulder
Since we’re talking about air quality…
Boulder, Colorado
Boulder, Colorado
Boulder, Colorado
Right now…
Right now…
Right now…
About the Knight Lab
Rob Knight, PhD, PI, Smartypants
Qiime – Quantitative Insights Into Microbial Ecology
Qiime on the web, data transport, MoBeDAC, etc…
Spend a lot of time on standards and data consistency
Why do we need standards?
Everyone likes the idea
Everyone uses their own standard
Problem: Leads to situations such as this…
It’s a cat.
Or maybe a shark?
Such a nice monkey…
Err wait, is it a walrus?
A local…
Or… a dolphin?
Unexpected Results
Different tools can (and do!) lead to different results
Answer: speak the same language
Presenting MoBeDAC
Central repository for microbial metadata and sequence data
Implements and enforces metadata standards – GSC checklists
Enforces sequence data consistency – quality filtering, trimming
Brings together an array of utilities and resources: VAMPS MG-RAST Qiime FungiDB Microbe.net Future platforms via open API
MoBeDAC Overview
Metadata: GSC Checklists
Metadata: GSC Checklists
The Technology
Platform Agnostic – keep it really simple
REST API for communication
JSON for encoding
REST – Representational State Transfer
Sounds really fancy… but it’s really simple: Usually runs over HTTP Not a standard per-se, a series of guidelines. Flexible.
Only 4 Commands (verbs): GET - List resources or elements of resource PUT - Replace entire collection with new data POST - Add new item to collection DELETE - Remove item or collection
WWW is the largest REST system – everyone uses it without knowing
JSON – JavaScript Object Notation
Sounds fancy too… but it’s: Ubiquitous Simple, human readable If you have data, put lots of brackets around it Send it
For example: If I have a dictionary that looks like:
a: appleb: bunnyc: kitty shark JSON says it should look like:{"a": "apple", "c": "kitty shark", "b": "bunny"}
Current MoBeDAC API specification available at:http://metagenomics.anl.gov/Html/api.html
Resources
MoBeDAC
http://mobedac.org
VAMPS
http://vamps.mbl.edu
MG-RAST
http://metagenomics.anl.gov
Qiime
http://microbio.me/qiimehttp://www.qiime.org/
FungiDB
http://fungidb.org/fungidb.b2
Microbe.net
http://www.microbe.net/
GSC
http://gensc.org
BE Package Terms http://www.microbe.net/wp-content/
uploads/2012/05/built_environment-metadata-terms-v51.xls
Sloan Foundation http://www.sloan.org/
Thanks!
Questions?