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PomBase Planning Meeting 09 Oct 2013
Cambridge - Meeting Room ???, EBI
Action item review
Postponed Action Items
- Demo of curation tool (postponed)
- Mark to liaise with Giulietta to help with making a pombe community curation video (postponed until curators have script)
- 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: Document how to submit data to ftp directory (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: Need to document how users can visualize their data privately (Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1409)
- AI: relationships for graph generation, actions rolled into https://www.ebi.ac.uk/panda/jira/browse/PB-1311
- 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: Remove ':pep' from identifiers in cDNA FASTA file (Kim) https://sourceforge.net/p/pombase/chado/200/
- AI:? Discussed moving to similar schema 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/
- AI: Kim to check if interactions are reciprocally represented in chado? revisit PB-873 at next planning meeting
Action items from
- AI: send instructions to Val about how to submit data to ftp site? (Mark)
- 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)
- 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
Priority Jira tickets
Chado
Usage stats
Versioning
Website
Phenotype ontology
Canto
Other general issues
Helpdesk
Curation
Update on community curation
Literature (triage) status
| Item | March meeting | April meeting | May meeting | July 3 |
| All publications | 9755 | 9761 | 9773 | 9935 |
| Un-triaged publications | 0 | 4 | 2 | 1 |
| Curatable publications | 4735 | 4740 | 4780 | 4877 |
| Publications with Approved sessions | 580 | 600 | 647 | 674 |
| Publications with active sessions | 245 | 247 | 265 | 249 |
| Publications with session needing approval | 14 | 4 | 4 | 16 |
| community curatable publications | - | - | - | 262 |
| community curated publications with approved sessions | - | - | - | 31 |
Canto annotations (from 2013-??-??)
| name | March count | April count | May count | July count |
| PSI-MOD | 77 | 77 | 77 | 78 |
| molecular_function | 167 | 173 | 182 | 204 |
| cellular_component | 211 | 245 | 272 | 353 |
| biological_process | 838 | 893 | 927 | 944 |
| PomBase annotation extension terms | 1448 | 1605 | 1651 | 1938 |
| fission_yeast_phenotype | 3519 | 3820 | 3879 | 4464 |
| Total | 6260 | 6813 | 6988 | 7981 |
All annotation types
| name | count |
| 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 )
