WBConfCall 2012.04.19-Agenda and Minutes

From WormBaseWiki
Jump to navigationJump to search


1. Model changes (Hinxton)

1a) Variation model sign off

Chris Grove (Caltech)

I would like to remove the tags "Antibody" and "Remark" from the
#Interactor_info hash and add an "Antibody_remark" field with a "?Text"
entry to the main ?Interaction model.

Also, I would like to change the name of the tag "Antibody_info" to simply
"Antibody" in the #Interactor_info hash.

2. HelpDesk Status update

3. Review of available data; reassess menu items (Todd)

4. Formalize modENCODE data transfer strategy: data priority, integration plan, timeline (Todd)

5. Accounts (again; Todd)

6. User guide progress; timeline

7. AOB


1. Model changes (Hinxton)

1a) Interaction model sign off

Paul has working version of new model and tested.

  • Action Item: Paul will commit to sanger CVS and forward link to Chris to check prior to Models tagging on Friday.

2. HelpDesk Status update

No unanswered questions or issues...Great

Staff have been very responsive, WB 2.0 release seems to have reinvigorated staff.

3. Review of available data; reassess menu items (Todd)

  • In response to Matt B.'s email discussion thread.

Primarily centered around the Species menu -> Resources

Web team had a 1st stab at only identifying data that is available for each species but they need help from others to look through all of the species and really identify the issues that remain to avoid confusing users.

Action Point: Michael P. said he would volunteer to look into this

If he is feeling daring he is welcome to edit the config directly!

-- sent a patch for the config this morning (Apr 20) Mh6

  • Kevin H. also composed an eloquent email (T. Harris)

a) Really need to Unify disconnect between the ACeDB or Not ACeDB species

1st proposed solution.

Index gff files so that any gene can be searched for from the main search facility.

This should aid the promotion of parasite genomes and the species that are non-core through their lack of manual curation.

Also allow population of faceted menu view.

Actoion item: Abby to investigate additional indexing of gff files to get data for mock gene pages.

b) Address disconnect between the search and the genome browser.

Possibly introduce search links so that you can skip the gene page and go directly to the genome browser or other displays.

Linking properly will be a big step forward

  • Action Item: Abby can you look into writing an indexer to interface with the MySQL Dbs.

Don't need co-ordinate data as you can pass an object to the genome browser to achieve the display result.

-- URLs look like that: http://www.wormbase.org/tools/genome/gbrowse/c_elegans/?name=PCR_product%3Asjj_B0019.1 (feature_type / id) Mh6

?? Gene pages would require ACeDB integration ??

Or could re-visit the genome browser pseudo gene page views.

Could sub sets of non-core genes be fully integrated?? - Paul S.

Currently there are 200,000 genes in ACeDB and most functional annotation is on C. elegans so could Orthology provide the route to transferring context/added value.

Matt B. pointed out that species that are evolutionarily divergent from elegans will have many 1000s of genes that will not be covered by this strategy.

Is there an middle ground measure that could be adopted?

Overloading gff has been trialed, but could this be extended? Interpro data and gene data/orthology has/is included for non-core.

Paul S. said would be good to have a strategy outlined within next 5 months because of grant schedule.

Options available that don't need full ACeDB integration.

OICR as a proof of concept have explored a NoSQL? solution CouchDB (very flexible and fast). They feel that they are 1 step away from running the website off a database called AceCouch instead of the OICR ACeDB.

Build will require more technical discussion - what can realistically be done in a 2 month release cycle.

aceCouch code is on github so interested parties can take a look.

4. Formalize modENCODE data transfer strategy: data priority, integration plan, timeline (Todd)

Todd opened

Sorry on the agenda again but need to make sure that the bases are covered.

The wiki document is a great summary of the modENCODE project data sets.

This covers the current state of play.

1st June appears to be a milestone that will aid the further integration of data that has been shelved because of the constant flux.

Post June there will be a real push to get data in.

2 main areas that are lacking/haven't had full attention.

1) Data describing binding and genome interaction (500,000 features at least)- really waiting for freeze.

2) Tiling array data - expression data so need Caltech involvement.

  • Action Item: Raymond, Wen and Gary to look at this.
  • Action Item: June 1st freeze should allow decent move forward.
  • Action Item: Everyone is encouraged to check out the document

ModENCODE Integration status

RNASeq for other organisms.....how can we deal with this

Gary W. - Alignment is easy

Display is easy

Gene model changes -> Manual with some auto possible.

Even best elegans set cannot just swap in, Gary W. corresponding to get issues resolved.

Hinxton have bam files of aligned read data.

  • Action Item: Need to work on file transfer HX -> OICR.

Raymond: Is it possible to go backwards from a Wormbase modENCODE data boint to the modENCODE source?

Gary W. is possible going via ?Evidence back to ?Analysis and retrieve modENCODE ID.

Action Point: Ensure we have modENCODE id's in analysis objects consistently.

modENCODE will be long term repository for the data.....in "the cloud" so limited cost.

Gary W. said that he had asked Lincoln about what is expected and he confirmed

    Raw data = modENCODE
    Derived data sets = Mod.

5. Accounts (again; Todd)

  • Action Item: Staff should all have a @wormbase.org account

This gets you special perks on the site

  • Action Item: All staff should have a github account

This will enable report and tracking and get notification of issues.

  • Action Item: Tell Todd your github account username so he can link it to repo etc.
  • What can be edited by approved users and staff

Report pages X no edit as there is ACeDB content, but you can add widgets

/about - anything under this stub can be edited and you can create and edit widgets and pages.

6. User guide progress; timeline

Tool tips can be edited

Todd created a user guide link and stub.

Can link out to wiki but not so good, better to integrate into website as this adds the pages to the search box (WS231 www.wormbase.org release).

Need to formulate an action plan.

7. AOB

1) Chris wants to talk to Todd about Interaction data and web display

Todd stayed on call for Caltech meeting.

2) Karen wants to discuss Variation data with Mary Ann

Mary Ann, stayed on call for a short time
  • Action Item: Mary Ann, Karen Y. set up call or something off line.