wiki:PombasePlanningMeetingMinutes20141017

Version 12 (modified by vw253, 6 years ago) (diff)

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What is the status of Paco's data?

  • AI Val contact Paco

What is the status of track-hub?

What is the status of track-hub, for "collecting" experiments? This will not happen in the near future, will be done at some point in the future by Ensembl

  • AI Create jira ticket to ensure this is working correctly when it happens

Status of multiple alignments from Compara

What is the status of on the fly multiple alignments from Compara (for gap squashing etc)

Storing ontology synonym scope in Ensembl

Q What is the status of storing ontology synonym scope in Ensembl?

  • AI Mark will find out the details of the Bio-perl module that is used
  • AI Val will contact author to see if synonym scope can be included
  • AI Ticket will be raised with Ensembl to include synonym scope when option is available

Status of Sam's data

  • AI Ask Sam for feedback, Jurg will follow up with Sam (Sam will provide revised data)

Transitivity over the "regulates" relationship for GO BP

What is the status of Ensembl ensuring that annotations are transitive over the "regulates" relationship for biological process?

  • AI Somebody (who?) will create a ticket (where?). We will also need a PomBase? jira tracker ticket for this to list the changes which will need to happen PomBase? side when this is in place (mainly test on query builder and documentation)

A ticket is now raised on the PomBase? tracker, but this needs to be addressed at the Ensembl level

https://www.ebi.ac.uk/panda/jira/browse/PB-2074

Discussion- if Ensembl do this in a generic/modular way it will also provide a solution for https://www.ebi.ac.uk/panda/jira/browse/PB-2027 but this might not be possible....

PomBase? browser suggestions

  • AI Paul will ensure that PomBase? browser suggestions are forwarded to the new point person before browser overhaul begins

Exporting FYPO and GO IDs in GenBank? and EMBL export files

  • AI Dan will remove the PomBase? IDs from this file

Centromere features

Can centromere features be visible in the "detail view"

PomBase? build time

Q How long is a PomBase? build taking from start to finish A Approximately 2-3 days. It takes about 0.5 days of Mark's time

Combining experimental tracks for repeats in the browser track displays

Q Should we be combining experimental tracks for repeats in the browser track displays? A General consensus was yes. Users will be able to refer to publications for details of how the tracks were combined. Only change to track labelling will be to add "combined" or "consensus"

EsyN

Val described that various link outs will be needed from the "GO slim" and the physical and genetic interaction sections of the gene pages.

  • AI Val will open a jira ticket once the teething problems are overcome and the URLs are available ( I will circulate for feedback first).

New high-throughput data

Upcoming dataset from Runge lab

  • AI Mark will contact authors with ftp upload details and check file formats

Discussion about display of variation and phenotypes

Data for 50+ wild strians in Ensembl.

  • AI EG are keen to host this. Dan Jeffares will submit data.

Compact view for FYPO & GO

We spent some time going through Marks mockups of the compact view for phenotypes and GO.

  • AI. Mark to make additional mockups based on discussion outcome