Changes between Initial Version and Version 1 of PombasePlanningMeetingAgenda20120126


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Timestamp:
Jan 26, 2012, 7:17:54 PM (9 years ago)
Author:
val_wood
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  • PombasePlanningMeetingAgenda20120126

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     1
     2 == Action items from technical meeting ==
     3 
     4Incomplete actions from technical meetings are included with new issues below
     5
     6
     7== Action items carried forward from 3rd October planning meeting ==
     8
     9 * Need to coordinate dataset for regular public release with Ensembl genomes release cycle after the preview (Kim/Mark/Dan)
     10
     11 * FYPO will be submitted to OBO foundry shortly which should trickle through to OLS in due course (Midori)
     12
     13DONE
     14
     15 * Ensembl group tell us which format specification for various HTP datasets. Val will draft an announcement to be approved by Paul/Mark/Dan
     16
     17DONE
     18
     19 * Load external GO data into Chado as a priority (Kim)
     20  * GO data is now loaded, but filters are not implemented (complicated by annotation extensions. Kim will prioritise this when he starts back in October)
     21
     22DONE and filters implemented, waiting for data to filter through to check but sounds promising based on numbers
     23
     24 * Follow up desktop sharing software (circulate possibilities, do free trial?) (Midori)
     25
     26Carried Forward
     27
     28 * 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.
     29
     30Carried Forward
     31
     32== General ==
     33
     34 * Usage stats http://tinyurl.com/7qs2zap
     35
     36 * pombelist posting from Bioneer (val)
     37
     38 * OriDB (val)
     39  From Conrad Nieduszynski: The database is SQL based. There is a low tech browser as part of OriDB and all of the data is available for users to either download or to visualise in genome browsers as custom tracks. Let's look at how to share the data. (Conrad has evaluated the origin datasets and classified origins)
     40
     41 * RT: Curators have agreed on a procedure for handling helpdesk queries (brief report) (Val)
     42   * Outline procedure/ immediate response
     43
     44 * FAQ: Drupal module now deployed. Common helpdesk queries will generate FAQ entries as needed. (Midori)
     45
     46 * Versioning, need somewhere where we can see which Ensembl and which Chado data version is currently displayed on dev and www (and what is the current Chado version)...Midori suggest how this should happen (automated...)
     47  * See also http://www.ebi.ac.uk/panda/jira/browse/PB-517 http://www.ebi.ac.uk/panda/jira/browse/PB-483 (Midori)
     48
     49 * curation tool sub domain (Kim) (AI from 1st October, notes Mark hasn't heard anything yet. Needs input from Paul, and probably will involve EBI External Services)
     50
     51 * Intermittent speed issues (as reported by Robin Allshire (Midori)
     52
     53 * Any progress on setting up focused user testing? (AI from 1st Oct)
     54
     55
     56== Review "post-preview" criteria & progress ==
     57
     58=== Search issues ===
     59(Midori)
     60
     61 * Document what Simple Search searches; also Advanced Search keyword filter (should be quick)
     62 * Curators test fixes Mark has done to address serious Advanced Search problems
     63  * http://www.ebi.ac.uk/panda/jira/browse/PB-430
     64  * http://www.ebi.ac.uk/panda/jira/browse/PB-521
     65  * http://www.ebi.ac.uk/panda/jira/browse/PB-535
     66 * Mark make changes discussed in curator meeting 24th Jan.; then curators test
     67  * http://www.ebi.ac.uk/panda/jira/browse/PB-583
     68 
     69=== Blast related ===
     70
     71  * Blast giving no hits for some searches http://www.ebi.ac.uk/panda/jira/browse/PB-556 (val)
     72  * Difficult to link output back to genomic regions based on descriptions provided
     73   *  http://www.ebi.ac.uk/panda/jira/browse/PB-339 (val)
     74
     75=== Misc Data problems (wrong/missing data) ===
     76
     77  Unlikely to discuss any of these in detail, just wanted to flag them
     78  *  GO slim related  http://www.ebi.ac.uk/panda/jira/browse/PB-485 (Val)
     79  *  Status totals discrepany http://www.ebi.ac.uk/panda/jira/browse/PB-530 (Val)
     80  *  Curated ortholog display, wrong data http://www.ebi.ac.uk/panda/jira/browse/PB-481 (Val)
     81  *   Incorrect numbers for "others" links http://www.ebi.ac.uk/panda/jira/browse/PB-463 (Val)
     82
     83== Tasks before GeneDB decommissioned ==
     84
     85=== Ensembl related ===
     86
     87   
     88=== Blast related ===
     89 
     90   * Blast is incredibly slow by comparable MOD standards. Could we have a !PomBase-specific Blast queue?
     91    http://www.ebi.ac.uk/panda/jira/browse/PB-557 (val)
     92
     93   * Blast option, Databases http://www.ebi.ac.uk/panda/jira/browse/PB-375 (val)
     94
     95   * Blast results presentation (Midori) Needs jira items linking
     96    * find 'run' button http://www.ebi.ac.uk/panda/jira/browse/280
     97    * results on one page http://www.ebi.ac.uk/panda/jira/browse/281 (exists, but not on main results page, and link is barely detectable)
     98    * better links to results http://www.ebi.ac.uk/panda/jira/browse/340
     99    * improve descriptions http://www.ebi.ac.uk/panda/jira/browse/339
     100    * karyotype map http://www.ebi.ac.uk/panda/jira/browse/558
     101
     102   
     103=== Misc Data problems (wrong/missing data) ===
     104
     105  Unlikely to discuss any of these in detail, just wanted to flag them, there may be a few other items but these seem fairly straightforward.
     106  *  Missing data sno/snRNA http://www.ebi.ac.uk/panda/jira/browse/PB-475 (val)
     107  *  Missing data for protein sequence features http://www.ebi.ac.uk/panda/jira/browse/PB-499 (Val)
     108
     109 
     110== Things which are not crucial for preview removal, or GeneDB decommissioning but we would like to discuss , if time permits ==
     111
     112=== Usability issues/ issues reported by users ===
     113
     114   * problems switching on tracks (like ESTs) is very cryptic http://www.ebi.ac.uk/panda/jira/browse/PB-548 (val)
     115    * when tracks are enabled they will be visible on gene page context map http://www.ebi.ac.uk/panda/jira/browse/PB-408 (val I would definitely like to touch on this one briefly even if none of the others)
     116    * Discussed with Mark on 24th; Val raising tickets to go to Ensembl group; !PomBase to try linking to "location" tab from gene pages
     117
     118  * Ability to browse left and right in browser is only available in "location" tab
     119    http://www.ebi.ac.uk/panda/jira/browse/PB-547
     120
     121
     122=== Integration (Better integration between the Ensembl part of the site and the Gene pages) especially: ===
     123 
     124    * Linking between the browser and the gene pages (discuss button option  position/size/text etc) http://www.ebi.ac.uk/panda/jira/browse/PB-435
     125
     126    *  curator contact http://www.ebi.ac.uk/panda/jira/browse/PB-511
     127
     128    * tools
     129      * http://genomebrowser.pombase.org/tools.html
     130      Q are all of these tools relelvant?  remove which are not, add relevent ones to Pombase tools menu
     131
     132    * helpdesk/help http://www.ebi.ac.uk/panda/jira/browse/PB-409
     133      * The "Ensembl help" link leads to a general help page for Ensembl genomes, this won't mean much to our users
     134      * We need an intermediate Pombe specific help page under  PomSase needs to be Pombase specific (it can include items here which are relevant to Pombase but should exclude items which are not related to Pombase (e.g. eHIVE production system for honeybee,  Annotation of Ig/Tcr Segment Genes, and other links in jira item)
     135     
     136    *  download
     137  http://genomebrowser.pombase.org/downloads.html
     138       * Need an intermediate page for site wide download options linked from main page menus
     139
     140General note for all of the above, it is important that we remove things which are net relevant. There are so many new  and hidden features that users should only be presented with the relevant items or they will stop exploring.
     141
     142
     143    * search http://www.ebi.ac.uk/panda/jira/browse/PB-513
     144
     145    * Entry level text http://www.ebi.ac.uk/panda/jira/browse/PB-497
     146
     147== AOB ==
     148
     149 * next technical meeting?
     150
     151== Lower priority so bump to next meeting ? ==
     152
     153 * Re-visit Online Meeting software
     154
     155 * AmiGO2 demo
     156  * Need to contact Chris and Seth to make sure stable URL for meeting
     157
     158Notes: 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.....
     159
     160I'll put this for discussion, demo at a future planning meeting. (Quickgo issues include: different gene product names and IDs; only protein; not representing all annotation; how are term names displayed and accessed; update frequency )