![Page 1: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/1.jpg)
MoBeDAC
Microbiome of the Built Environment Data Analysis Core
![Page 2: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/2.jpg)
Background
Rob Knight’s group, University of Colorado at Boulder
Since we’re talking about air quality…
![Page 3: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/3.jpg)
Boulder, Colorado
![Page 4: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/4.jpg)
Boulder, Colorado
![Page 5: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/5.jpg)
Boulder, Colorado
![Page 6: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/6.jpg)
Right now…
![Page 7: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/7.jpg)
Right now…
![Page 8: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/8.jpg)
Right now…
![Page 9: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/9.jpg)
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
![Page 10: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/10.jpg)
Why do we need standards?
Everyone likes the idea
Everyone uses their own standard
Problem: Leads to situations such as this…
![Page 11: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/11.jpg)
It’s a cat.
![Page 12: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/12.jpg)
Or maybe a shark?
![Page 13: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/13.jpg)
![Page 14: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/14.jpg)
![Page 15: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/15.jpg)
Such a nice monkey…
![Page 16: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/16.jpg)
Err wait, is it a walrus?
![Page 17: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/17.jpg)
![Page 18: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/18.jpg)
![Page 19: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/19.jpg)
A local…
![Page 20: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/20.jpg)
Or… a dolphin?
![Page 21: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/21.jpg)
![Page 22: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/22.jpg)
![Page 23: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/23.jpg)
Unexpected Results
Different tools can (and do!) lead to different results
Answer: speak the same language
![Page 24: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/24.jpg)
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
![Page 25: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/25.jpg)
MoBeDAC Overview
![Page 26: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/26.jpg)
Metadata: GSC Checklists
![Page 27: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/27.jpg)
Metadata: GSC Checklists
![Page 28: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/28.jpg)
The Technology
Platform Agnostic – keep it really simple
REST API for communication
JSON for encoding
![Page 29: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/29.jpg)
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
![Page 30: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/30.jpg)
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
![Page 31: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/31.jpg)
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/
![Page 32: MoBeDAC - Microbiome of the Built Environment Data Analysis Core](https://reader033.vdocuments.us/reader033/viewer/2022061300/54c8ae594a795945148b45f8/html5/thumbnails/32.jpg)
Thanks!
Questions?