Changes between Initial Version and Version 1 of PombasePlanningMeetingAgenda20120524


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Timestamp:
Jun 27, 2012, 8:26:25 AM (8 years ago)
Author:
val_wood
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  • PombasePlanningMeetingAgenda20120524

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     2data time
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     4 == Completed action items ==
     5
     6 * DONE AI Jurg/Curators dig out  the !ArrayExpress accession numbers for PMID:18488015
     7   http://www.ebi.ac.uk/panda/jira/browse/PB-573
     8 * DONE AI EBI Action subdomain, now in use
     9 * Midori has forwarded around the minutes from when this was discussed for having !PomBase Ver. x.y where x is the EG release and y is the Chado dump version number.
     10  * DONE Speed of the !PomBase portal
     11    * DONE Currently it is still being hosted via the Hinxton servers due to testing in London.   Dan and Mark are currently in discussions with the ES team about using !PomBase as the test site for moving to London.
     12
     13
     14 == Not done, but logged in jira ==
     15
     16 * AI Mark/Dan Check that all sequence features are available consistently on location and gene tabs See http://www.ebi.ac.uk/panda/jira/browse/PB-548
     17 * AI Mark Add a link from the protein section of the gene page to a PSI Blast (currently we link to NCBI from !PomBase, but any is OK)
     18  * AI EBI Direct all !PomBase feedback to !PomBase helpdesk "helpdesk@…" http://www.ebi.ac.uk/panda/jira/browse/PB-511
     19  * AI EBI Configure search so that !PomBase is optional and EG site-wide is configureable http://www.ebi.ac.uk/panda/jira/browse/PB-513
     20  * AI EBI Change entry level text http://www.ebi.ac.uk/panda/jira/browse/PB-497
     21  * ftp site migration (see e-mail to !PomBase internal)
     22    *  Val is generating a list of files (or tarring them up) ready for transfer (tie this in with discussion about download file options made available, later)
     23
     24 == Outstanding Action items from May ==
     25
     26 * Ask Henning Hermjakob about possibility of OLS as webservice to attach annotations to, we will have the next planning meeting at Hinxton and see if Henning can join us for a while.
     27  * AI EBI to contact Conrad (Arnaud has looked into this and we could potentially load these as a BAM file).
     28    (tranfer this to jira item)
     29  * AI EBI to action selenium testing and check server is sufficiently powered
     30  * AI Mark/Dan Difficult to link back to genomic regions with output provided
     31    * Mark will provide some examples for the next meeting
     32  * AI Mark - EG Browser and the customisation to make it feel more friendly and to aid in the linking between the Drupal and ensembl services (this seems to be same action item as above)
     33  * AI EBI Linking between browser and gene page http://www.ebi.ac.uk/panda/jira/browse/PB-435
     34    * provide a "button" to link to Ensembl from Gene pages and vice versa
     35    * reduce number of linked up/downstream genes
     36    * place link to Ensembl browser underneath the gene list (NOTE, THIS IS STILL NOT CLEAR BUT WILL PROBABLY BE DISCUSSED IN FEEDBACK FROM USER TESTING?)
     37   * AI Currently PK is looking into the interaction between ES and and !PomBase. ( Re Long term will *everything* still need to go through External Services?)
     38
     39
     40 == General ==
     41
     42Have not done stats updates as will need to redo at month end:
     43
     44 * Usage stats http://tinyurl.com/7qs2zap
     45
     46 * Hosting data on tracks (e.g Buck example) .... what is the plan for hosting these types of datasets?
     47  Was there an action item here?
     48
     49 * Item from Mark determine the functionality of the dev site going forward.
     50
     51 * Showing the lates dataset (with filtered IEAs etc), the current dataset ids from September
     52
     53
     54 == Curation update  (Val) ==
     55 
     56 *  Skipped, will do update for next meeting
     57
     58
     59== Focused User testing ==
     60
     61 Mark - outcomes from user testing
     62  Q did all issues get logged (didn't get follow up from 2nd part)
     63
     64== Review "post-preview" and "GeneDB decommissioning" criteria & progress ==
     65
     66 === Preview removal  ===
     67
     68  Discuss preview removal, see email from earlier in week with new propsed priorites, discuss
     69
     70   * Update notice about preview removal on GeneDB website
     71   * Inform users of changes/ pending changes (like, new annotation will only go into !PomBase)
     72   * Explain differences in GO totals (later)
     73
     74 === Discuss items required for GeneDB decommissioning ===
     75 
     76   * Will do this next meeting
     77 
     78 === Other jira items ===
     79
     80 Current jira status:
     81
     82  * Open 125 Closed  577  (was 200/511 last meeting)
     83 
     84
     85
     86 == Usability issues/ issues reported by users (anyone? any not covered above?) ==
     87
     88
     89
     90 == Meetings Attended/ Upcoming ==
     91
     92 
     93 * proposed Workshop for 2103 (International meeting) straw poll?
     94 * Proposed Pombase 1-2 hour workshop at CRUK, with 1-2 hour curation tool demo and or jamboree (to precede EMBO)
     95 * EMBO course (Val teaching) July 
     96 * Others ? (Steve mentioned a yeast meeting but not minuted?)
     97
     98
     99 == AOB ==
     100
     101 
     102 * Next meeting  (doodle)
     103
     104 == PIs meeting (10 minutes) ==
     105
     106  Postpone until next inperson?
     107
     108
     109 == Lower priority /Later? ==
     110
     111 === Integration ===
     112    * tools
     113      * http://genomebrowser.pombase.org/tools.html
     114      Q are all of these tools relevant?  remove which are not, add relevant ones to !PomBase tools menu
     115    *  download http://genomebrowser.pombase.org/downloads.html
     116       * Need an intermediate page for site wide download options linked from main page menus
     117
     118 === Browsing Ontologies ===
     119 * AmiGO2 demo
     120  * Need to contact Chris and Seth to make sure stable URL for meeting
     121
     122Notes: AmiGO2 is generic and can support other ontologies. To get the cool axial, drill down search/filtering working it involved the use of Solr indexes? which need to be built but Chris says it should be relatively straightforward to implement. This should fulfill our requirements which are not met by other available tools (i.e the ability to provide links to gene product at different levels of the heirarchy). It also handles x-products.....
     123
     124I'll put this for discussion, demo at a future planning meeting. (QuickGO issues include: different gene product names)
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