Changes between Version 29 and Version 30 of PombasePlanningMeetingMinutes20130703


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Timestamp:
Jul 5, 2013, 11:14:36 AM (7 years ago)
Author:
gomidori
Comment:

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  • PombasePlanningMeetingMinutes20130703

    v29 v30  
    3333  * sub-AI: FAQ item to document what GFF3 is (curators and Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1408)
    3434
    35   * sub-AI: Short term solution = Change form from ‘submit data’ to something that lets people point us to the data + describes the data types at the source (genome version…). Make this in more of an ‘advert’ style format. Rename the link. (Midori) (addendum: link rename DONE on dev -mah, 20130704 https://www.ebi.ac.uk/panda/jira/browse/PB-1407)
     35  * sub-AI: Short term solution = Change form from ‘submit data’ to something that lets people point us to the data + describes the data types at the source (genome version…). Make this in more of an ‘advert’ style format. Rename the link. (Midori) (addendum: link rename DONE on dev -mah, 20130704; rest is in https://www.ebi.ac.uk/panda/jira/browse/PB-1407)
    3636
    3737 * AI: Need to document how users can visualize their data privately (Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1409)
     
    119119=== Versioning ===
    120120
    121 Paul: compara version does not exist.
    122 Dan: we also need to capture the GO file.
    123 Val: won’t be necessary, done with datestamp.
    124 Midori: Should update GAF from GO subversion repository, which has date-stamps and svn revision numbers. We could use either, but date might be friendlier to users. (There's usually more than one GO svn commit per Chado version, but that shouldn't pose a problem for us as long as we track which date or revision we're using.)
    125 Val: what is INSDC version?
    126 Dan: it is an assembly database. “GCA_0000..2” There is also another assembly version.
    127 Val: aren’t there are more than two?
    128 Dan: number 1 has no mitochondrial genes. Number 2 has mitochondrial genes. Paul: the current assembly files from 2007. Val to find out anything prior to this. Val can then give these numbers that predates the current versioning system. Val also wants to know what gene build refers to, Dan to send it to her. Make JIRA tracker item. We start from v34. Can people access historical pages? We went live ‘officially’ with 29. No sequence changes since 2007.
     121Paul: compara version does not exist.  [[BR]]
     122Dan: we also need to capture the GO file.  [[BR]]
     123Val: won’t be necessary, done with datestamp.  [[BR]]
     124Midori: Should update GAF from GO subversion repository, which has date-stamps and svn revision numbers. We could use either, but date might be friendlier to users. (There's usually more than one GO svn commit per Chado version, but that shouldn't pose a problem for us as long as we track which date or revision we're using.) [[BR]]
     125Val: what is INSDC version?  [[BR]]
     126Dan: it is an assembly database. “GCA_0000..2” There is also another assembly version.  [[BR]]
     127Val: aren’t there are more than two?  [[BR]]
     128Dan: number 1 has no mitochondrial genes. Number 2 has mitochondrial genes.  [[BR]]
     129Paul: the current assembly files from 2007. [[BR]]
     130Val to find out anything prior to this. Val can then give these numbers that predates the current versioning system. Val also wants to know what gene build refers to, Dan to send it to her. [[BR]]
     131Make JIRA tracker item. We start from v34. Can people access historical pages? We went live ‘officially’ with 29. No sequence changes since 2007.
    129132
    130133AI: Generate a web page at update time populated with the following info: https://www.ebi.ac.uk/panda/jira/browse/PB-1420
     
    196199 * AI: Document how to submit data to ftp directory (what file format for what data-types. Using accession numbers or uploading data files, genome assembly date, PMID) (Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1411)
    197200  * sub-AI: FAQ item to document what GFF3 is (curators and Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1408)
    198   * sub-AI: Short term solution = Change form from ‘submit data’ to something that lets people point us to the data + describes the data types at the source (genome version…). Make this in more of an ‘advert’ style format. Rename the link. (Midori) (addendum: link rename DONE on dev -mah, 20130704 https://www.ebi.ac.uk/panda/jira/browse/PB-1407)
     201  * sub-AI: Short term solution = Change form from ‘submit data’ to something that lets people point us to the data + describes the data types at the source (genome version…). Make this in more of an ‘advert’ style format. Rename the link. (Midori) (addendum: link rename DONE on dev -mah, 20130704; rest is in https://www.ebi.ac.uk/panda/jira/browse/PB-1407)
    199202
    200203 * AI: Need to document how users can visualize their data privately (Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1409)
     
    206209 * AI: relationships for graph generation
    207210 * All actions rolled into https://www.ebi.ac.uk/panda/jira/browse/PB-1311
    208  * AI: Mark to check with Eugene that syncs happen on the days that they should happen. https://www.ebi.ac.uk/panda/jira/browse/PB-1414[[BR]]
     211 * AI: Mark to check with Eugene that syncs happen on the days that they should happen. https://www.ebi.ac.uk/panda/jira/browse/PB-1414
    209212 * AI: Change text on front page from about pombase https://www.ebi.ac.uk/panda/jira/browse/PB-1415 (Mark)
    210213 * AI community curation launch (menu links) https://www.ebi.ac.uk/panda/jira/browse/PB-1382 and https://www.ebi.ac.uk/panda/jira/browse/PB-1389
    211  * AI: Make FAQ item re what information the GFF3 files contain. www.sequenceontology.org/gff3 (https://www.ebi.ac.uk/panda/jira/browse/PB-1408) [[BR]]
    212  * AI: Make FAQ item for how to use the restful interface to bulk download data beta.rest.ensemblgenomes.org  (Dan or Mark https://www.ebi.ac.uk/panda/jira/browse/PB-1408) [[BR]]
    213  * AI: Val to make Jira ticket to remind Mark to use “this file” (the one generated by ensemble?) https://www.ebi.ac.uk/panda/jira/browse/PB-1418 [[BR]]
    214  * AI: make custom sequence download FAQ of how to do this in biomart (Antonia and will pass to Midori). DONE  https://www.ebi.ac.uk/panda/jira/browse/PB-1418 [[BR]]
     214 * AI: Make FAQ item re what information the GFF3 files contain. www.sequenceontology.org/gff3 (https://www.ebi.ac.uk/panda/jira/browse/PB-1408)
     215 * AI: Make FAQ item for how to use the restful interface to bulk download data beta.rest.ensemblgenomes.org  (Dan or Mark https://www.ebi.ac.uk/panda/jira/browse/PB-1408)
     216 * AI: Val to make Jira ticket to remind Mark to use “this file” (the one generated by ensemble?) https://www.ebi.ac.uk/panda/jira/browse/PB-1418
     217 * AI: make custom sequence download FAQ of how to do this in biomart (Antonia and will pass to Midori). DONE  https://www.ebi.ac.uk/panda/jira/browse/PB-1418
    215218 * AI: Mark needs to know when new SO qualifiers (like TR box) are added (open jira item for Kim to generate a list) (https://www.ebi.ac.uk/panda/jira/browse/PB-1343).. also not TR box is a gene feature not a transcript feature
    216219 * AI: Remove ':pep' from identifiers in cDNA FASTA file (Kim)  https://sourceforge.net/p/pombase/chado/200/