wiki:PombasePlanningMeetingAgenda20140122

Version 2 (modified by val_wood, 7 years ago) (diff)

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PomBase Planning Meeting 22 Jan 2014

Cambridge - ????????

Action item review

Postponed Action Items

None, all are now on relevant trackers

Outstanding action items carried forward from previous meeting

None, all are now pon relevant trackers

Action items from Nov

AI: Ensembl to look toward a better format to represent data which is presented at the single nucleotide level and cannot be indexed AI: Mark put the contig/gene view above the above the data tracks AI: Mark to zoom out detail browser view once to include context around gene AI: MArk Add NCBI blast link with protein sequence submission side by side with ensembl blast (at least until a usable blast facility is available) AI: Midori to email to ask for data resubmissions (DONE). AI: Val to email Paco for nucleosome positioning data (DONE). AI: Val ask Paul Thomas /CJM to explain details of modular/LEGO annotation AI: Val to Summarize tasks need to be done for the grant proposal.

New (and continuing) Agenda items

  • Speed
    • (ETA around a month?) a new track loader where data is combined so that loading is quicker. (progess?)

Hosting high throughput datasets

Quite a few datasets now uploaded ready to host Paco Antequera https://www.ebi.ac.uk/panda/jira/browse/PB-1680 Nick Rhind, replication origins https://www.ebi.ac.uk/panda/jira/browse/PB-1513 have we got this? Jurg's polyA data https://www.ebi.ac.uk/panda/jira/browse/PB-1513 Nick Rhind transcriptome https://www.ebi.ac.uk/panda/jira/browse/PB-1707

Priority Jira tickets

27 tickets open for V 40 https://www.ebi.ac.uk/panda/jira/issues/?jql=project%20%3D%20PB%20AND%20resolution%20%3D%20Unresolved%20AND%20fixVersion%20%3D%20%22Chado%20v40%22%20ORDER%20BY%20priority%20DESC

We should go through these and assess

Chado

Usage stats

http://tinyurl.com/7qs2zap

Versioning

Website

Phenotype ontology

Canto

Other general issues

Helpdesk

Curation

Update on community curation

Literature (triage) status

ItemMarch meetingApril meeting May meeting July 3
All publications975597619773 9935
Un-triaged publications042 1
Curatable publications47354740 4780 4877
Publications with Approved sessions580600 647 674
Publications with active sessions245247 265 249
Publications with session needing approval144 416
community curatable publications - -- 262
community curated publications with approved sessions- -- 31

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

nameMarch countApril countMay countJuly count
PSI-MOD77777778
molecular_function167173182204
cellular_component211245272353
biological_process838893927944
PomBase annotation extension terms1448160516511938
fission_yeast_phenotype3519382038794464
Total6260681369887981

All annotation types

namecount
DNA_binding_specificity
cat_act
ex_tools
subunit_composition
pathway
gene_ex
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
PomBase annotation extension terms
Total

(last month's total was )

Next priorities

Publications

Meetings

News and Outreach

Next planning meeting

AOB