wiki:PombasePlanningMeetingAgenda201406

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PomBase? Planning Meeting Jun 2014

Venue: EBI

May Action item review

  • AI: UniProt? xref script needs to be run each release, Chado42. (Q is there a jira ticket for this?) (Mark) ​https://www.ebi.ac.uk/panda/jira/browse/PB-1864
  • AI: Re-contact Paco's group to fix plus and minus signs in primary database submission (Mark) DONE
  • AI: Circulate Wilhelm and Marguerat data to Jurg, Sam and Brian for feedback, are all tracks useful? Sam’s data: this is only bigwigs, would bam be useful? Still need track descriptions(Mark/curators)
  • AI: Speak to Eugene to group tracks (aka track hub) (Mark) (Q is there an Ensembl jira ticket for this?)
  • AI: Multiple alignments from Compara Check that i) gap squashing and or ii) dynamic alignment generation for subsets of protein in progress (EG, Q check is there a jira ticket for this)

Illustrated by: http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Gene/Compara_Tree?db=core;g=SPBC11B10.09;r=II:1500197-1502095;t=SPBC11B10.09.1

Update related Actions

Outstanding action items carried forward from previous meeting

None

New (and continuing) Agenda items

Update procedures

See action items above.

Progress/discussion from last meeting:

Now have a single repo that sets up config file, downloads chado, update or reload from chado, and a set of script that pulls in uniprot ID’s etc running interpro scan. Healthcheck steps, genemart step (coreDB and ontology mart), caching and updating step, loads onto drupal, generates sup caches such as synonyms, ontology counts (dependent on biomart). And so on. Operationally this means it is smoother to do. This should be break-downable into 2 or 3 scripts. Now there should not be a problem with ontologies being out of synch. Paul advises to have a make file (each time you to things it is not possible to do things out of order). Dependency path. Time to make a release assuming no problems Mark -4 days. Paul wonders if it really takes 4 days if using scripts. Dan also thinks it sounds a lot.

There were still clearly a number of issues this month so V 43 dump from 6th June is not yet live. Health checks are not in place for these issues so we'll see how we go next month.

Inheritance over regulation

(also check other items on last agenda not addressed

This is a big problem. Val will demo why

User feedback on browser

Jurg mentioned getting user feedback on the browser. Are all of the comments from the survey actioned (see e-mail"specific browser comments)"

In general it is difficult to know the progress of Ensembl related tickets see https://www.ebi.ac.uk/panda/jira/browse/PB-1908 "There was an internal RT ticket that was generated notifying their help desk (Ensembl #382459), but this has since been closed as help desk have passed on to the web team."...there does not seem to be an easy way to track an issue.

Antonia raised a number of issues identified from Jurg's group. (Antonia can run through these, see e-mail entitled "ensembl genome browser"

Hosting high throughput datasets

There is a sequence dataset (Gx) data, https://www.ebi.ac.uk/panda/jira/browse/PB-1876 how to convert to wig?

Priority Jira tickets

At the jira ticket review in the last meeting we got as far as going through the next couple chado versions. We left off at sorting the "Unscheduled" tickets

The trac/Wiki issue

We need a replacement for the trac wiki hosted on SF must be i) public ii) able to export existing content (we might need a replacement for SF generally long term.....)

Chado

Usage stats

http://tinyurl.com/7qs2zap

There is a total column for the monthly unique users. This sums the monthly unique users per month. It would be more useful if this were a 'real' culmulative total of unique users (a sum isn't very meaningful here)

Versioning

Website

Small thing:

http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Gene/Compara?db=core;g=SPBC32H8.07;r=II:1463829-1465745;t=SPBC32H8.07.1

Phenotype ontology

Anything?

Canto

Kim is most way through the changes needed for multi gene phenotypes

Other general issues

Helpdesk

Antonia will update us

Curation

Update on community curation

# Literature (triage) status

Item March 2013 April 2013 May 2013 Aug 2013 May7 2014 July 23 2014
All publications 9755 9761 9773 9989 10356 10400
Curatable publications 4735 4740 4780 4896 5017 5070
Publications with Approved sessions 580 600 647 712 1083 1187
Publications with active sessions 245 247 265 246 220 246
Publications with session needing approval 14 4 4 18 6 11
community curatable publications - - - 351 526 613
community curated publications with approved sessions - - - 58 159 178
curatable publications without sessions - - - 3730 3256 3177

We are now curating quite a lot faster than the number of papers (sessions)

Next priorities

Publications

A method for increasing expressivity of Gene Ontology annotations using a compositional approach http://www.biomedcentral.com/1471-2105/15/155 (online only, highly accessed) (incldes Pombase scrrenshots to demo annotation extensions in use)

Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579

  • we should talk about the annotatation set we crated and maintaining it

The NAR database issue paper will be due soon.....

Meetings

News and Outreach

Next planning meeting

# AOB

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