PomBase Planning Meeting 09 Oct 2013

Cambridge - Meeting Room ???, EBI

Action item review

Postponed Action Items

• Demo of curation tool (postponed)
• Dan and Mark to see what files downloadable from PomBase? have previously been generated by Ensembl. These should be easy to create automatic updates for (In progress?)
• making Artemis applet available
• Sort out display for gene captions/summaries on gene pages (Mark)
• Paul to see to that the restriction enzyme mappings get calculated (if REBASE doesn’t work out) and/or get included as a track.

Outstanding action items carried forward from previous meeting

• AI Curators to draw up a script for the curation video. What steps do we want to show on the video? Discuss at next curator meeting. (Part Done)
• AI: Need to document how users can visualize their data privately (Ensembl ​https://www.ebi.ac.uk/panda/jira/browse/PB-1409)
• AI: Mark needs to know when new SO qualifiers (like TR box) are added (open jira item for Kim to generate a list) (​https://www.ebi.ac.uk/panda/jira/browse/PB-1343).. also NOTE: TR box is a gene feature not a transcript feature
• AI:? Discussed moving to similar schema for proteins as for transcripts, so proteins are named systematic_ID.1 .2 matching alternative transcripts and only differentiated by "type" Any changes related to this are postponed until after 2013 which gives us time to think if this is what we really want to do (Kim sounded not keen)
• AI: Val to find assembly files pre-dating 2007, ​https://sourceforge.net/p/pombase/curation-tasks/24/

Action items from

• AI: send instructions to Val about how to submit data to ftp site? (Mark) (what file format for what data-types. Using accession numbers or uploading data files, genome assembly date, PMID) (Ensembl ​https://www.ebi.ac.uk/panda/jira/browse/PB-1411) rest is in ​https://www.ebi.ac.uk/panda/jira/browse/PB-1407)
• AI: Sort out display of reciprocal interactions, this should be done post-chado (as part of loading into ensembl), at the moment they are just mirrored (?) so take care with assymetrical ones (Mark)
• AI: find examples for phenotype graph relations missing (Val) relationships for graph generation, actions rolled into ​https://www.ebi.ac.uk/panda/jira/browse/PB-1311
• AI: do next step for SRA studies (Val)
• AI: Discussion about grant, Preproposal deadline 2 Dec, arrange meeting with WT

New (and continuing) Agenda items

Hosting high throughput datasets

• Mark demo htp data sets from Marc Bühler DAM 1 D data (discuss display pulled through to PomBase? page, and details displayed)
• ditto Juan's poly A data

Chado

Kim add a summary of changes (loader for phenotype screens etc)

Usage stats

​http://tinyurl.com/7qs2zap

• Corrupted stats EVERY month

Versioning

Website

• User reported intermittent browser speed issues
• Mark demo reciprocal "targetis" annotation

Phenotype ontology

2700 terms; cell cycle phenotypes overhauled

Canto

Kim add summary update

Helpdesk

Antonia add summary op open ticket status

Survey

Survey, look at results so far and address related jira priorities (many moans are ticketed)

Priority Jira tickets and setting priorities for next couple of releases

Based on survey feedback we should look at browser and blast related issues:

• Resolution problem with region in detail view ​https://www.ebi.ac.uk/panda/jira/browse/PB-1429
• add others

Grant

• Decide overall grant aims

Other general issues

Curation

Update on community curation

• Good quality curation, usually improving for second papers
• Some users providing annotation extensions

Literature (triage) status

Item	March meeting	April meeting	May meeting	July 3	Aug 18	Oct ??
All publications	9755	9761	9773	9935	9989	10025
Un-triaged publications	0	4	2	1	0	0
Curatable publications	4735	4740	4780	4877	4896	4909
Publications with Approved sessions	580	600	647	674	712	791
Publications with active sessions	245	247	265	249	246	209
Publications with session needing approval	14	4	4	16	18	35
community curatable publications	-	-	-	262	351	385
community curated publications with approved sessions	-	-	-	31	58	80

Canto annotations (from 2013-??-??)

name	March count	April count	May count	July count	August
PSI-MOD	77	77	77	78	78
molecular_function	167	173	182	204	222
cellular_component	211	245	272	353	376
biological_process	838	893	927	944	975
fission_yeast_phenotype	3519	3820	3879	4464	4971
Total	4812	5208	5337	6043	6622

All annotation types

name	count
	DNA_binding_specificity
	cat_act
	ex_tools
	pathway
	subunit_composition
	m_f_g
	complementation
	genome_org
	misc
	disease_associated
	name_description
	EC numbers
	sequence
	warning
	PomBase? family or domain
	PSI-MOD
	PomBase? gene characterisation status
	PomBase? gene products
	molecular_function
	biological_process
	cellular_component
	fission_yeast_phenotype
	species_dist
	gene_ex
Total

Last month was 133102

Next priorities

Publications

• Canto nearly ready for submission
• Annotation extensions (Racheal Huntley et al) nearly ready for submission

Meetings

• Val attnded GO meeting
  • feedback on "regulates" relationship

News and Outreach

Next planning meeting

AOB

• students