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.
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…
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
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
