January 2009 GMOD Meeting

Jan2009MtgLogoNoText.png January 2009 GMOD Meeting
January 15-16, 2009

Following PAG 2009
San Diego, California, USA
San Diego Convention and Visitors Bureau

This GMOD community meeting was held January 15-16, 2009, in San Diego, immediately following Plant and Animal Genome (PAG 2009). There were over 50 participants at the meeting.

Jan 2009 Meeting



Thursday, January 15

| Time | Topic | Presenter(s) | Links | |—-|—-|—-|—-| | 10:00 AM | Registration | | | | 10:30 AM | Introductions | Scott Cain | | | 11:00 AM | The State of GMOD | Scott Cain | PPT, Summary | | 11:30 AM | A variety of GMOD Help Desk stuff | Dave Clements | PDF, Summary | | 12:00 PM | Lunch | one hour 30 minutes | | | 1:30 PM | Drupal and | Stephen Ficklin | PDF, Summary | | 2:00 PM | Artemis and Chado at GeneDB | Robin Houston | PPT, PDF, Summary | | 2:30 PM | modENCODE: extending Chado, BIR-TAB, & GBrowse for automating data validation & display | Nicole Washington | PDF, Summary | | 3:00 PM | Break | | | | 3:30 PM | A RESTful interface for MODs? | Josh Goodman | PPT, PDF, Summary, Discussion | | 4:00 PM | Metadata Input and Submission Tool and GIS linked metagenomic database | Iddo Friedberg and Christopher Condit | PDF, Summary | | 4:30 PM | Data Representation in Chado: Best Practices | Joshua Orvis and/or Scott Cain | Summary, Discussion | | 5:00 PM | Dinner (on your own) | | |

Friday, January 16

Time Topic Presenter(s) Links
9:00 AM Chado and GUS at SBRI Dhileep Sivam and Isabelle Phan PPT, PDF, Summary, Discussion
9:30 AM BioMart Arek Kasprzyk PDF, Summary
10:00 AM BeeSpace Barry Sanders, Dave Arcoleo PPT, Summary
10:30 AM Break
11:00 AM WebGBrowse GBrowse configuration management, Summary Ram Podicheti PPT, PDF, Summary
11:30 AM JBrowse (aka GBrowse 3.0) Mitch Skinner ODP, PDF, Summary
12:00 PM Lunch one hour 30 minutes
1:30 PM EcoliWiki and TableEdit Daniel Renfro I tried, but all I get is errors.
And PowerPoint makes a 10MB pdf,
which is way too big to upload.
Contact me if you want a copy.
, Summary
2:00 PM Generic Gene Page XML Scott Cain PPT, PDF, Summary, Discussion
2:30 PM GMODWeb and package management Brian O'Connor PPT, PDF, Summary
3:00 - 5:00 PM MIGS and MIMS Iddo Friedberg Summary
Bovine Genome Database Justin Reese and Chris Childers PPT, PDF, Summary
GNPAnnot Pierre Larmande ChadoControler, Summary

Themes and Discussions

Several themes ran throughout the meeting

Data Sharing

Several presentations touched on this:

A common question during these talks was how much should we do? Should we implement a comprehensive data sharing protocol or start with very modest goals, or should we aim for a sweet spot in the middle? Should we emphasize robustness or ease of implementation? Should GMOD support semantic web efforts?

Josh Goodman argued that RESTful interfaces provide the highest payoff for the least amount of effort – that RESTful was both useful and the easiest to implement.

The semantic web in general and SSWAP in particular was discussed. Ren Nelson of SoyBase pointed out that SoyBase’s map data is now available through SSWAP. RDF, the Bio2RDF projct, and the Swoogle semantic web search engine were also mentioned.

Josh Goodman, Rob Buells, Rex Nelson, and Kevin Clancy formed the Web services working group and will continue and expand this discussion with the GMOD community.

Joshua Orvis’s “Data Representation in Chado: Best Practices” session dealt with the same issue, this time in the context of representing biology within Chado in the same way across organizations. In this session we proposed converging on common representations by having organizations post their current Chado practices to the wiki, discussing them on the wiki or on the GMOD-Schema mailing list, and then converging on a common set of Chado best practices. Common practices would enable both data sharing and common tools. Joshua got the ball rolling by describing IGS’s Chado practices on the IGS Data Representation page.

RDF got additional discussion during Dhileep Sivam and Isabelle Phan’s session on Chado and GUS at SBRI. Uniprot uses RDF to represent their data. XML gives you a tree representation, while RDF gives you a graph of RDF files. Graphs more often better reflect what is being described. Sparql is the standard query language for accessing RDF.


The presentations are listed here in a very approximate order:

The State of GMOD