| | 17 | * 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 |
| | 18 | * 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) |
| | 19 | * AI EBI Direct all !PomBase feedback to !PomBase helpdesk "helpdesk@…" http://www.ebi.ac.uk/panda/jira/browse/PB-511 |
| | 20 | * 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 |
| | 21 | * AI EBI Change entry level text http://www.ebi.ac.uk/panda/jira/browse/PB-497 |
| | 22 | * ftp site migration (see e-mail to !PomBase internal) |
| | 23 | * 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) |
| | 24 | |
| | 25 | == Action items from May == |
| | 26 | |
| | 27 | * 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. |
| | 28 | * AI EBI to contact Conrad (Arnaud has looked into this and we could potentially load these as a BAM file). |
| | 29 | (tranfer this to jira item) |
| | 30 | * AI EBI to action selenium testing and check server is sufficiently powered |
| | 31 | * AI Mark/Dan Difficult to link back to genomic regions with output provided |
| | 32 | * Mark will provide some examples for the next meeting |
| | 33 | * 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) |
| | 34 | * AI EBI Linking between browser and gene page http://www.ebi.ac.uk/panda/jira/browse/PB-435 |
| | 35 | * provide a "button" to link to Ensembl from Gene pages and vice versa |
| | 36 | * reduce number of linked up/downstream genes |
| | 37 | * 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?) |
| | 38 | * 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?) |
| | 39 | |
| | 40 | |
| | 41 | == General == |
| | 42 | |
| | 43 | Have not done stats updates as will need to redo at month end: |
| | 44 | |
| | 45 | * Usage stats http://tinyurl.com/7qs2zap |
| | 46 | |
| | 47 | * Hosting data on tracks (e.g Buck example) .... what is the plan for hosting these types of datasets? |
| | 48 | Was there an action item here? |
| | 49 | |
| | 50 | * Item from Mark determine the functionality of the dev site going forward. |
| | 51 | |
| | 52 | |
| | 53 | == Curation update (Val) == |
| | 54 | |
| | 55 | * Skipped, will do update for next meeting |
| | 56 | |
| | 57 | |
| | 58 | == Focused User testing == |
| | 59 | |
| | 60 | Mark - outcomes from user testing |
| | 61 | Q did all issues get logged (didn't get follow up from 2nd part) |
| | 62 | |
| | 63 | == Review "post-preview" and "GeneDB decommissioning" criteria & progress == |
| | 64 | |
| | 65 | === Preview removal === |
| | 66 | |
| | 67 | Discuss preview removal, see email from earlier in week with new propsed priorites, discuss |
| | 68 | |
| | 69 | * Update notice about preview removal on GeneDB website |
| | 70 | * Inform users of changes/ pending changes (like, new annotation will only go into !PomBase) |
| | 71 | * Explain differences in GO totals (later) |
| | 72 | |
| | 73 | === Discuss items required for GeneDB decommissioning === |
| | 74 | |
| | 75 | * Will do this next meeting |
| | 76 | |
| | 77 | === Other jira items (Val or Midori) === |
| | 78 | |
| | 79 | Current jira status: |
| | 80 | |
| | 81 | * Open 125 Closed 577 (was 200/511 last meeting) |
| | 82 | |
| | 83 | |
| | 84 | |
| | 85 | == Usability issues/ issues reported by users (anyone? any not covered above?) == |
| | 86 | |
| | 87 | |
| | 88 | |
| | 89 | == Meetings Attended/ Upcoming == |
| | 90 | |
| | 91 | |
| | 92 | * proposed Workshop for 2103 (International meeting) straw poll? |
| | 93 | * Proposed Pombase 1-2 hour workshop at CRUK, with 1-2 hour curation tool demo and or jamboree (to precede EMBO) |
| | 94 | * EMBO course (Val teaching) July |
| | 95 | * Others ? (Steve mentioned a yeast meeting but not minuted?) |
| | 96 | |
| | 97 | |
| | 98 | == AOB == |
| | 99 | |
| | 100 | |
| | 101 | * Next meeting (doodle) |
| | 102 | |
| | 103 | == PIs meeting (10 minutes) == |
| | 104 | |
| | 105 | Postpone until next inperson? |
| | 106 | |
| | 107 | |
| | 108 | == Lower priority /Later? == |
| | 109 | |
| | 110 | === Integration === |
| | 111 | * tools |
| | 112 | * http://genomebrowser.pombase.org/tools.html |
| | 113 | Q are all of these tools relevant? remove which are not, add relevant ones to !PomBase tools menu |
| | 114 | * download http://genomebrowser.pombase.org/downloads.html |
| | 115 | * Need an intermediate page for site wide download options linked from main page menus |
| | 116 | |
| | 117 | === Browsing Ontologies === |
| | 118 | * AmiGO2 demo |
| | 119 | * Need to contact Chris and Seth to make sure stable URL for meeting |
| | 120 | |
| | 121 | Notes: 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..... |
| | 122 | |
| | 123 | I'll put this for discussion, demo at a future planning meeting. (QuickGO issues include: different gene product names) |
| | 124 | |
| | 125 | |
| | 126 | |
| | 127 | |
| | 128 | |
| | 129 | |
