MoBeDAC - Microbiome of the Built Environment Data Analysis Core

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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.

Tecnología Educación

Background

 Rob Knight’s group, University of Colorado at Boulder

 Since we’re talking about air quality…

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…

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

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

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MoBeDAC - Microbiome of the Built Environment Data Analysis Core

1. MoBeDAC Microbiome of the Built Environment Data Analysis Core

2. Background  Rob Knight’s group, University of Colorado at Boulder  Since we’re talking about air quality…

9. 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

10. Why do we need standards?  Everyone likes the idea  Everyone uses their own standard  Problem: Leads to situations such as this…

11. It’s a cat.

12. Or maybe a shark?

13.

14.

15. Such a nice monkey…

16. Err wait, is it a walrus?

17.

18.

19. A local…

20. Or… a dolphin?

21.

22.

23. Unexpected Results  Different tools can (and do!) lead to different results  Answer: speak the same language

24. 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

25. MoBeDAC Overview

26. Metadata: GSC Checklists

27. Metadata: GSC Checklists

28. The Technology  Platform Agnostic – keep it really simple  REST API for communication  JSON for encoding

29. 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

30. 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

31. 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

32. Thanks!  Questions?

MoBeDAC - Microbiome of the Built Environment Data Analysis Core

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MoBeDAC - Microbiome of the Built Environment Data Analysis Core