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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…
- 6. Right now…
- 7. Right now…
- 8. Right now…
- 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?
- 15. Such a nice monkey…
- 16. Err wait, is it a walrus?
- 19. A local…
- 20. Or… a dolphin?
- 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
- 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