SWUG:Meeting 2007-05-30: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
(One intermediate revision by one other user not shown) | |||
Line 1: | Line 1: | ||
[[Category:SWUG_Meetings]] | |||
== Agenda Notes == | == Agenda Notes == | ||
Sohel can't make it this week, so we won't be having an in-depth discussion of refgenomes - Mary will give us an update. | Sohel can't make it this week, so we won't be having an in-depth discussion of refgenomes - Mary will give us an update. | ||
Line 92: | Line 93: | ||
* cgi-client currently + arbitrary xml clients. | * cgi-client currently + arbitrary xml clients. | ||
* set up on toy server - will send URL | * set up on toy server - will send URL | ||
== Reference Genomes (Mary) = | == Reference Genomes (Mary) == | ||
* Requirements | * Requirements |
Latest revision as of 18:01, 14 July 2014
Agenda Notes
Sohel can't make it this week, so we won't be having an in-depth discussion of refgenomes - Mary will give us an update.
Dan - I have volunteered you for SWUG outreach - can you check the emails to the software-group from gohelp and make sure everything has been answered adequately & is in the FAQ?
Present at meeting
Chris, Gail, Amelia, John, Mary, Seth
Agenda Preamble
This will be our regular meeting time, every 2 weeks. I realise it's not ideal for everyone, Stan won't be able to consistently make it. But it's the best that can be done given our constraints. Let's try it for a while; we can try an alternating slot later in the year.
AGENDA
Review of previous action items
- ACTION: documentation
- Finally done. Will review.
- ACTION: discuss time for reg meetings
- Ben will probably have to cut out at 9:45 (but not today)
- ACTION: Suzi is to send out description of requirements for protein family annotation tool and see if anyone is interested in working on this
- Whiff.
- ISSUE: Identifier tracking. Matching ref. genome ids to MOD ids. Stan says that EBI has a tool we might be able to use.
- Stan sent an interpro mapping file but we are not sure if this is what we need or if it's the same as gp2protein.
- TODO Set up a phone call with Chris, Stan, Ben, Sohel, Mary to discuss this.
- ACTION: Chris & Mary are to send requirements to this list.
- On wiki
- ACTION: Chris, Seth, and Amelia to document GO-dev by next meeting and rest of group will critique then.
- Done?
- ACTION: Amelia will be moving GO FAQ to wiki pages.
- Done
Reports and Discussion
OBO-Edit (John)
- 2.0 beta release
- installer won't work, need CVS?
- plans
- many internal arch. changes
- new bulk intersection editor
- graph-based editing (draw it!) - integrated with reasoner
- graph-based DAG viewer - replaces tree view
- not finished state - more features will be added:
- flex doc library (drag-and-drop interface)
- reasoner improvement
- auto-complete components added to library (is anyone using it)
- reasoner great for x-products (chebi, etc.)
- Amelia wants to know about search algorithms for AmiGO.
AmiGO (Amelia)
- latest changes
- release in June/July -
- rewritten search to make it efficient.
- return results in a more intuitive way
- "special intelligence" - tries selected fields first, then other fields
- does this use go-dbi API? by-passed, but not in templates
- relevance score does fractions of terms in match
- might not be efficient to use John's algorithm
- AmiGO feature meeting?
- (Seth)
- Is Amigo 2.0 a re-write of amigo 1.0 code, or we will reuse?
- We will reuse and replace piecemeal.
- Is Amigo 2.0 a re-write of amigo 1.0 code, or we will reuse?
- Integrate term finder and mapper for June/July release
ORB (Seth)
- service for obo foundry.org - makes term requests simple.
- cgi-client currently + arbitrary xml clients.
- set up on toy server - will send URL
Reference Genomes (Mary)
- Requirements
- Discussion on the wiki - ensuring consistent use of identifiers.
- Sohel looking at use cases
- curators have to enter genes, keep track of curation.
- schema changes
- did not discuss
- integrating visualisation with AmiGO
- Ref geneome graphs - interactive tool.
Documentation & Outreach (Dan via Chris)
- EBI & ensembl mirror
- documentation
- gohelp emails
- need to add answers to faq when you answer a question
- Mirroring script to capture older versions of database - seth to look at.
Production Databases (Ben)
- Working on loading slowly. Next project is getting fully taxonomy data.
Software Architecture (Chris)
- db presentation
Papers
- John submitting paper on graph-based editing.
- draft of amigo paper (Seth) ready to review