MoBeDAC - Microbiome of the Built Environment Data Analysis Core

MoBeDACMicrobiome 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

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

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: apple b: bunny c: 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  Microbe.net  http://mobedac.org  http://www.microbe.net/ VAMPS  GSC  http://vamps.mbl.edu  http://gensc.org MG-RAST  BE Package Terms  http://metagenomics.anl.gov  http://www.microbe.net/wp- content/uploads/2012/05/built_environm Qiime ent-metadata-terms-v51.xls  http://microbio.me/qiime http://www.qiime.org/  Sloan Foundation  http://www.sloan.org/ FungiDB  http://fungidb.org/fungidb.b2

Thanks! Questions?

MoBeDAC - Microbiome of the Built Environment Data Analysis Core

by douginator2000 on Jul 30, 2012

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