= !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 on 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 = * Kim asked if it is possible for every access to curation.pombase.org to go (transparently) via an EBI server which could show a message if sysbiol/oliver0 is offline (more detail from Kim) * Are we still not doing somthing we are supposed to. (Re e-mail Mark was surprised about ne features appearing, I think we were supposed to give prior notice, biut I don't think there are procedures in place for this? * In noticed in a thread about gff3 specification "Can anyone think of a valid case where multiple feature lines might have the same ID, but different SO types" "I've seen nasty GFF files which do this by having the same ID for the gene and CDS records (etc), which I think is invalid and wrong" ...I think we do this (at least we have always used the same IDs for both historically) * Problems with overnight synching of drupal site. Are these resolved? * multiple alignment related * is it possble to generate alignements on the sequence set selected only * what is used to generate the multiple alignements? * UniProt trying to generate uniprot -> pombase mappings using PomBAse, this is NOT going to work. ...Need to liaise with UniProt to figure out what they are trying to do. 2 helpdesk tickets: * Query from a user we can't answer: * "Resolved: definition of feature types" * basically appear to be reporting problems with the gff file * 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 * Mark to explain drupal work == Chado == * Nothing of note == Usage stats == http://tinyurl.com/7qs2zap * Nov 10859 unique users * Dec 8512 unique users == Versioning == == Website == == Phenotype ontology == == Canto == * Paper submitted * GMOD compliance granted * video preontation at GMOD meeting well received * presenting demo to some plant communities this week possibly? == Other general issues == == Helpdesk == == Curation == === Update on community curation === * Sent the second reminders for teh first batch of communiyt curation sessions, resulted in an increase in submitted sessions. Curators are still approving these. * Once we have on top of this I'll send out more reminders, and more new sessions * Will make video for community shortly (in next couple of weeks, now have egs. and script) === Literature (triage) status === ||Item||March meeting||April meeting|| May meeting || July 3|| Aug 18|| Oct ??||Nov 20|| Jan 20 ||All publications||9755||9761||9773|| 9935 ||9989|| 10025 ||10120||10133|| ||Un-triaged publications||0||4||2|| 1 ||0 || 0 ||0|| 3 || ||Curatable publications||4735||4740|| 4780|| 4877 || 4896 ||4909 ||4951|| 4963 || ||Publications with Approved sessions||580||600|| 647|| 674|| 712|| 791 ||884|| 928 || ||Publications with active sessions||245||247|| 265|| 249|| 246|| 209 ||225|| 228 || ||Publications with session needing approval||14||4|| 4||16|| 18|| 35 ||23|| 20 || || community curatable publications ||- ||-||-|| 262 ||351|| 385 ||433|| 446|| || community curated publications with approved sessions||- ||-||-|| 31 || 58|| 80 ||94|| 110|| || curatable publications without sessions||-||-||-||-||3730||?||3542|| 3515 || * aiming to keep "curatable publications without sessions" in decline === 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 ) == Next priorities == == Publications == == Meetings == == News and Outreach == == Next planning meeting == = AOB =