Changes between Version 7 and Version 8 of PombasePlanningMeetingMinutes20130703


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Timestamp:
Jul 4, 2013, 12:28:00 AM (8 years ago)
Author:
antonialock
Comment:

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  • PombasePlanningMeetingMinutes20130703

    v7 v8  
    2929Question: Paul/Val: Should we allow users to visualize RNA seq files or perhaps we should ‘force’ users to submit their RNA seq to elsewhere to get an accession number?
    3030
    31  * ‘‘‘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) (curators?)
    32   * sub-’’‘‘AI:’’’’’’’ FAQ item to document what GFF3 is (curators)
    33   * 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)
    34  * ‘‘‘AI:’’’’’’’ Need to document how users can visualize their data privately (who?)
    35  * ‘‘‘AI:’’’’’’’ Search SRA for pombe (related to mapping of short reads?) (jira ticket created) (DAN)
    36 
    37  * future ‘‘‘AI:’’’’’’’ Need to document how users can visualize their data privately (who?)
    38  * future ‘‘‘AI:’’’’’’’ Make a validation system that lets people submit data in a format already made usable to us (Paul?)
     31 * ‘‘‘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) (curators?)
     32  * sub-‘‘AI:’’’’’’’ FAQ item to document what GFF3 is (curators)
     33  * 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)
     34 * ‘‘‘AI:’’’’’’’ Need to document how users can visualize their data privately (who?)
     35 * ‘‘‘AI:’’’’’’’ Search SRA for pombe (related to mapping of short reads?) (jira ticket created) (DAN)
     36
     37 * future ‘‘‘AI:’’’’’’’ Need to document how users can visualize their data privately (who?)
     38 * future ‘‘‘AI:’’’’’’’ Make a validation system that lets people submit data in a format already made usable to us (Paul?)
    3939
    4040 == Feedback pombe 2013 ==
     
    5656I suspect Format #8 might be of particular interest.”
    5757
    58 ‘‘‘AI:’’’’’’’ Chado future long term flag, reinstate pre-cached ‘others’ column that links to page where all genes are shown. (who, Jira?)
    59 ‘‘‘AI:’’’’’’’ Change gene page order to GO MF BP CC phenotype
    60 ‘‘‘AI:’’’’’’’ Antonia to get going with the list of gene captions
    61 ‘‘‘AI:’’’’’’’ Kim to write a loader for the flatfile of gene captions
     58‘‘‘AI:’’’’’’’ Chado future long term flag, reinstate pre-cached ‘others’ column that links to page where all genes are shown. (who, Jira?)
     59‘‘‘AI:’’’’’’’ Change gene page order to GO MF BP CC phenotype
     60‘‘‘AI:’’’’’’’ Antonia to get going with the list of gene captions
     61‘‘‘AI:’’’’’’’ Kim to write a loader for the flatfile of gene captions
    6262AI future: sort out display for gene captions on gene pages (Mark)
    63 ‘‘‘AI:’’’’’’’ restriction enzyme mapping onto track (who?). Use the REBASE? If not possible find what sites there are and calculate ourselves?
    64 AI future: Paul to see to that these get included as a track.
     63‘‘‘AI:’’’’’’’ restriction enzyme mapping onto track (who?). Use the REBASE? If not possible find what sites there are and calculate ourselves?
     64‘‘‘AI:’’’’’’’ future: Paul to see to that these get included as a track.
    6565
    6666== Frequent errors displayed on gene pages ==
     
    7070
    7171Dan; Eugene can can sort this after next ensembl release. Currently it is on the same server as 1000 genomes. There is another server that can be used.
    72 
    73 ‘‘‘‘AI:’’’’’’’ Fix the errors (Dan?)
     72‘‘‘AI:’’’’’’’ Fix the errors (Dan?)
    7473
    7574== Graphs are misleading without all relationships ==
     
    7978Midori points out that the release generates ‘everything’ and ‘simplified’ versions. OLS is the simplest or a simple version. Mark says that OLS is not the one we load but he is not sure what version we use.
    8079
    81  * ‘‘‘AI:’’’’’’’ relationships for graph generation
    82   * ‘‘‘AI:’’’’’’’ Mark to tell Midori which version we load.
    83   * ‘‘‘AI:’’’’’’’ Midori to tell Mark which one we should use.
    84   * ‘‘‘AI:’’’’’’’ curators to document what relations we want to show
    85   * ‘‘‘AI:’’’’’’’ Mark looks into making the graphs show them
     80 * ‘‘‘AI:’’’’’’’ relationships for graph generation
     81  * ‘‘‘AI:’’’’’’’ Mark to tell Midori which version we load.
     82  * ‘‘‘AI:’’’’’’’ Midori to tell Mark which one we should use.
     83  * ‘‘‘AI:’’’’’’’ curators to document what relations we want to show
     84  * ‘‘‘AI:’’’’’’’ Mark looks into making the graphs show them
    8685
    8786 === Keeping front page news current ===
     
    8988 Dev to live should sync daily at 10.00. Midori points out that that did not happen this morning.
    9089
    91 ‘‘‘AI:’’’’’’’ Mark to check with Eugene that syncs happen on the days that they should happen.
    92 ‘‘‘AI:’’’’’’’ Change text on front page from about pombase (Midori)
     90‘‘‘AI:’’’’’’’ Mark to check with Eugene that syncs happen on the days that they should happen.
     91‘‘‘AI:’’’’’’’ Change text on front page from about pombase (Midori)
    9392   * community curation launch  (menu links)
    9493
     
    9897Val wanted to know if we can get stats for how many times particular files are downloaded. Paul says that the information is stored so it can be done at some point. He wants to leave it until longer after geneDB decommissioning.
    9998
    100 AI future: Generate stats for how many times particular files are downloaded from ftp site. Wait until longer after GeneDB decommissioning.
     99‘‘‘AI:’’’’’’’ future: Generate stats for how many times particular files are downloaded from ftp site. Wait until longer after GeneDB decommissioning.
    101100
    102101Val also wanted to know why the ontology wasn’t synced with the annotations that went live. Mark said that the term name was missing because it wasn’t loaded into the ensemble genome db. He reckons he might have loaded from an older file by mistake as he normally runs all updates at the same time.
     
    104103Ensembl supports the GFF3, not GTF, file format and we should document to our  users what this format contains. From this Friday onwards GFF3 files will be generated as part of the ensemble release. Pombase can use those. However we can also tell our geeky users they can use the rest resource to bulk download data.
    105104
    106 ‘‘‘AI:’’’’’’’ Make FAQ item re what information the GFF3 files contain. www.sequenceontology.org/gff3 (curators)
    107 ‘‘‘AI:’’’’’’’ Make FAQ item for how to use the rest resource to bulk download data beta.rest.ensemblgenomes.org  (who?)
    108 ‘‘‘AI:’’’’’’’ Val to make Jira ticket to remind Mark to use “this file” (the one generated by ensemble?)
    109 ‘‘‘AI:’’’’’’’ make custom sequence download FAQ of how to do this in biomart (Antonia and will pass to Midori).
     105‘‘‘AI:’’’’’’’ Make FAQ item re what information the GFF3 files contain. www.sequenceontology.org/gff3 (curators)
     106‘‘‘AI:’’’’’’’ Make FAQ item for how to use the rest resource to bulk download data beta.rest.ensemblgenomes.org  (who?)
     107‘‘‘AI:’’’’’’’ Val to make Jira ticket to remind Mark to use “this file” (the one generated by ensemble?)
     108‘‘‘AI:’’’’’’’ make custom sequence download FAQ of how to do this in biomart (Antonia and will pass to Midori).
    110109
    111110 == Chado ==
    112  * ‘‘‘AI:’’’’’’’ Mark needs to know when new SO qualifiers (like TR box) are added (open jira item for Kim to generate a list) (was this done?)
    113  * ‘‘‘AI:’’’’’’’ Remove ':pep' from identifiers in cDNA FASTA file (Kim)  subtask of Val’s FTP site stuff.
    114  * ‘‘‘AI:’’’’’’’? Discussed moving to similar schema as for transcripts, so proteins are named systematic_ID.1 .2 matching alternative transcripts and only differentiated by "type" Any changes related to this are postponed until after 2013 which gives us time to think if this is what we really want to do (Kim sounded not keen)
     111 * ‘‘‘AI:’’’’’’’ Mark needs to know when new SO qualifiers (like TR box) are added (open jira item for Kim to generate a list) (was this done?)
     112 * ‘‘‘AI:’’’’’’’ Remove ':pep' from identifiers in cDNA FASTA file (Kim)  subtask of Val’s FTP site stuff.
     113 * ‘‘‘AI:’’’’’’’? Discussed moving to similar schema as for transcripts, so proteins are named systematic_ID.1 .2 matching alternative transcripts and only differentiated by "type" Any changes related to this are postponed until after 2013 which gives us time to think if this is what we really want to do (Kim sounded not keen)
    115114
    116115
     
    126125Dan; 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.
    127126
    128 ‘‘‘AI:’’’’’’’ Val to find assembly files pre-dating 2007, not sure what else from here?
     127‘‘‘AI:’’’’’’’ Val to find assembly files pre-dating 2007, not sure what else from here?
    129128
    130129 
     
    135134Should we put this as an action item to follow up next time?
    136135
    137 ‘‘‘AI:’’’’’’’ Kim to check if these are reciprocally represented in chado?
     136‘‘‘AI:’’’’’’’ Kim to check if these are reciprocally represented in chado?
    138137
    139138=== Canto ===
    140139
    141140Do people delete invitation-to-curate emails because they look automatically generated? Also email might be long, Antonia had a comment on this.
    142 ‘‘‘AI:’’’’’’’ check with Kim if we can make them look like they come from a person rather than semi-automated?
     141‘‘‘AI:’’’’’’’ check with Kim if we can make them look like they come from a person rather than semi-automated?
    143142
    144143=== Other general issues ===
     
    149148    * note promoter should be part of gene, not transcript
    150149
    151 Q- AI?
     150Q- ‘‘‘AI:’’’’’’’?
    152151
    153152
     
    158157Antonia to follow up with Sara Moles lab to see how well co-curation works. is starting with Sara mole's lab next month, other London labs and Warwick for starters
    159158
    160 AI future: Antonia to follow up on co-curation
     159‘‘‘AI:’’’’’’’ future: Antonia to follow up on co-curation
    161160
    162161