Changes between Version 45 and Version 46 of PombasePlanningMeetingAgenda20130703


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Timestamp:
Jul 3, 2013, 12:24:29 PM (8 years ago)
Author:
danstaines
Comment:

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  • PombasePlanningMeetingAgenda20130703

    v45 v46  
    1313 * AI Check all required files are present and correct on ftp site (Val)
    1414 * AI standard health checks (Mark) - Continual
    15  * AI Selenium testing (Dan) - In progress
    16  * AI manual smoke testing (Dan) - In progress
     15 * AI Selenium testing (Dan) - tests now cover gene page, simple, advanced search, plus existing speed test.
     16 * AI manual smoke testing (Dan) - first draft test sheet completed
    1717 * AI :pep val spotted that this item referred to cDNA fasta, which seems sort of odd that it has a pep ID at all? (val check)
    1818 * AI Report that the GFF "source" column should be the specific data provider (!PomBase? not Ensembl) (dan) DONE
     
    2525
    2626=== Hosting large scale datasets ===
    27  * AI create an incoming Ftp directory to support hosting incoming large scale datasets (EG) - DONE - this is a single username & password for uploading to ftp-private.ebi.ac.uk
     27 * AI create an incoming Ftp directory to support hosting incoming large scale datasets (EG) - DONE - this is a single username & password for uploading to ftp-private.ebi.ac.uk (Dan can supply)
    2828 * AI Curators document use of ftp directory (file naming, required data etc, but this is on hold until the system is running smoothly ...Paul does not want to announce until tested). At the same time we will document the accptable file formats for each data type
    2929
     
    150150     * https://www.ebi.ac.uk/panda/jira/browse/PB-1317
    151151
    152   * question, do Ensembl support GFF (which plavour?) or GTF and where is the file described - GFF3 and GTF FTP dumps provided by EnsemblGenomes.org
     152  * question, do Ensembl support GFF (which plavour?) or GTF and where is the file described - GFF3 and GTF FTP dumps provided by EnsemblGenomes.org as of EG19
    153153  * Is GTF/GFF production now part of update pipelinge (file is  now from April so does not match last release date, is it still generated from "Restful" Interface) - GFF will be on FTP site from EG19 onwards
    154   * Is restful interface ready to document in our FAS (i.e general release?) - Documentation is at beta.rest.ensemblgenomes.org
     154  * Is restful interface ready to document in our FAS (i.e general release?) - Documentation is at beta.rest.ensemblgenomes.org. Beta label likely to be removed by Ensembl in autumn but no known issues and would strongly encourage use.
    155155  * FROM MAY Minor issue with the last update, some gene lists were missing for specific ontology terms. This was due to the annotation extension term names not being updated with the ontology. Mark has changed this so that everything (ontology terms and extensions0 are updated, so this should not happen in future ...this happened again for the last update (see ticket)
    156156
     
    191191
    192192 What needs to happen next?
     193
    193194 
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