mobedac - microbiome of the built environment data analysis core

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?