Difference between revisions of "Managers 11Oct06"

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[[Category:GO_Managers_Meetings]]
 
=MINUTES=
 
=MINUTES=
  

Latest revision as of 09:29, 30 June 2014

MINUTES

minute taker: Jane

  • Present: David, Judy, Jennifer, Midori, Eurie, Jane, Michael, Chris, Mike, Suzi
  • Absent: Rex

Review previous Action Items from previous meeting

a. John and Jen to put together a spreadsheet on requirements and evaluate WebEx

Stanford have an arrangement with WebEx that costs 38 dollars usd a month, but the downside is that a Stanford person needs to be present at each meeting. John is looking into other systems e.g. MegaMeeting which costs around 75-150/month and WebEx costs 300 dollars/month.

Judy: conference calls already costing 200 dollars/month, so these costs probably okay.

  • Action item: Jen, Midori and John to look into web conference options more fully and report back.

b. (ALL): evaluate BaseCamp project management s/w - http://www.basecamphq.com

Not many people have looked at it yet. Jen says it lacks a shared calendar. Can we use Google calendar in conjunction with a management system? Next Mac OS update iCal calendars which can be published, but iCal okay for Mac users but not cross-platform.

  • Action item: Suzi to find out whether BaseCamp has shared task manager/calendar

c. User Advocacy group come up with a proposal for users meetings in January

Proposal still being drafted - defer until next week.

d. Suzi: OWL loader for oboedit

e. Judy and Chris: send draft report on caBIG vocabulary review collaboration to go-top and Chris; Chris will look at section on formal definitions

Judy has sent report. caBIG is a project for evaluating the quality of controlled vocabularies. Two contracts to evaluate GO, also NCI thesaurus. They used metrics of what controlled vocabulary should contain. GO came out pretty well by the criteria used. (not sure what the formal definitions bit is about here, Chris)

Individual Manger reports

a. Ontology Development

David came to Cambridge on October 2-3rd in an effort to complete the is_a graph for biological process with Jane, Jen, Midori and Tanya on Skype. Many is_a orphans were rehoused, but approx. still remain. The process for re-housing the terms is to go through the remaining orphans one by one and find or add an appropriate parent term, and often improve the definition of the term. Most of the high-level grouping terms now in place. Jane and Jen are going to continue going through the terms and house them under the new grouping terms. The graph will then be dividing up, and different people will check different sections. The current file is kept in go/scratch and is called IsaComplete.obo - people are encouraging to look at it. Hoping to be complete by the Jan meeting. The group is also adding 'rules' to the wiki about how the ontology should be structured - people should also look at those. When everything is complete, the file will be sent to whole list.

There will be a conference call with Jonathan Liu this week about improving the ontology (David, Judy, Suzi, Jane, Chris calling in from GO). David has spoken to Jonathan beforehand and he explained how they looked at where annotations fell in graph - identifying areas where annotations 'clumped' e.g. heart dev which has 500 annotations, no children. This could be a good way of identifying areas of the ontology that need development.

Content development group are to have a weekly group meeting. The first one will be tomorrow at 5.30pm BST. The group of people attending the meeting will change from week to week, sometimes including outside experts. Idea to bring more consortium people in to editing ontology - TAIR annotators have already started editing again. Need to check cvs access, see who needs adding. Also to train other members of consortium to add terms on their own. Perhaps have a training session in conjunction with the next consortium meeting of how to use cvs and OE. We also need to write a SOP for editing the ontology. John may also want to stay on after Jan meeting for OE training/feedback?

We're moving to using OBO 1.2 format for the edit file at 5pm today. The file for editing will be go/ontology/gene_ontology.obo.

  • Action item: David, Judy, Suzi, Jane and Chris to report back to managers about meeting with Jonathan Liu
  • Action item: Mike to send list of people with cvs write-access

b. Outreach

Jen went to the ARK Genomics meeting - they are waiting to hear about funding for chicken annotation, if they get that then they will use the chicken project as a model for other farm animal species. Atlantic salmon may be the next model organism species - Jen trying to make contact with them. Michael says they're not a cohesive community which might cause problems.

Jane and Jennifer went to Royal Society Chemistry (RSC) in Cambridge to teach them about using GO - they will be marking up the papers in their journals with GO, SO and soon CL terms. Interesting feedback from OBO-Edit searches e.g. exact searches on 'enzyme' don't bring anything back - OE needs to use more intelligent searching. They all searched on their favourite gene/process and many of the results were obsolete - we need to get OE to bring up the replacement terms. The 'use term'/'consider term' tags to replace structured comments need to go in the new 1.2 file to make this easier. RSC have agreed to add a 'request a GO term button' to their tool. There was an issue with some SO terms being used by the text mining software out of context.

  • Action item: Jane and Jen to feedback OE issues to OE WG

c. Software

The OBO to OWL mapping is currently being finalised. Nigam and Dilvan at NCBO are active contributors

Adding post-co-ordinated (aka: structured annotations) annotations to database. MGI and TAIR already doing this type of annotation. Big demand for this contextual information. Just needs an extra column in the annotation file.

OBO-Edit paper submitted. AmiGO II development continues.

Developing ways of generating metrics from the database. Do we want these run regularly, or just as needed? Run with database dumps to separate file in the first place.

d. Reference Genomes

Rex away.

f. User Advocacy

Working on new AmiGO hub development first meeting Users meeting specification

  • Action item: Jane and Eurie to send out proposal for users meeting before next meeting

Meetings

For Jan Consortium meeting we need proposals from people - to be added to wiki. Suzi has created the wiki page. It is divided into different sections:

Status reports needed from group leaders Thorny issues Proposals/new ideas

[note: wiki will be down for a while this week whilst server being upgraded]

  • Action item: Everyone to add agaenda items for Jan meeting to wiki

Collaborations and Interactions, active and new

ChEBI have approached us because they have been asked by BioModels to work on a reaction ontology for InTenz, the enzyme database. A reaction ontology already exists which is part of OBO (REX ontology, written by Kirill - not Rex the person!) and they were thinking about further developing this. Want to know whether this ontology would be useful to GO, how GO could contribute. Yes, it would be useful to GO - contains more granular reactions than in GO function - could eventually make GO cross-products. We could help them develop the more biological areas of the ontology. May also be worth checking BioPax.

  • Action item: Jane to feed this back to ChEBI, see where they want to go next

Operations and Procedures

Suggestion from Evelyn to send out agenda for these meetings to remind the larger group that they are happening and allow them to contribute. We decided a better way would be to send the email saying the minutes are available to the whole group, and to contact the appropriate manager if they want to add something to the agenda. There is also an onus on the managers to feed back what is discussed in these meetings to their groups. Difficulty is that not all people necessarily in a group, and some groups don't have mailing lists. We need to make sure all people involved in consortium are in at least one WG.

  • Action item: Jane to write a message template to say managers meeting minutes available, and send around.

Staffing and Personnel (i.e. new hires, departures, leave, vacations...)

Midori away for the next couple of weeks.

Budget issues

At farm animals meeting someone from BBSRC said that GO grants have had too many letters of support - hard to find reviewers. Not our problem.

Publications

Instance paper from Barry, David and Judy now going to Computational Biology because too long for last journal it was submitted to.

Other Current Topics and Concerns

none.

  • Next meeting: 25th October

Action Items:

  • Action item: Jen, Midori and John to look into web conference options more fully and report back.
  • Action item: Suzi to find out whether BaseCamp has shared task manager/calendar
  • Action item: David, Judy, Suzi, Jane and Chris to report back to managers about meeting with Jonathan Liu
  • Action item: Mike to send list of people with cvs write-access
  • Action item: Jane and Jen to feedback OE issues from RSC workshop to OE WG
  • Action item: Jane and Eurie to send out proposal for users meeting before next meeting
  • Action item: Everyone to add agaenda items for Jan meeting to wiki
  • Action item: Jane to feed this back to ChEBI, see where they want to go next
  • Action item: Jane to write a message template to say managers meeting minutes available, and send around.

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