#230 write ontology panel gets too big

closed-out-of-date
OBO-Edit (271)
1
2011-08-30
2008-05-15
No

Hi,

I am doing some work just now that requires me to use the write ontology panel with the advanced options visible and the filter terms and filter links panels activated with a filter added in each. With all these things going on at once the panel becomes so big that It no longer fits on my laptop screen, so I can't save the ontology out correctly. Would it be possible to have these various controls on tabs so the don't all have to be on the screen at once?

Thanks,

Jen

Discussion

  • Jennifer Deegan

    Jennifer Deegan - 2008-05-15

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    user_id=735846
    Originator: YES

    Hi,

    I have looked at the code for this as I know how to implement the solution quite quickly and simply. There is a very similar piece of tabbed gui with appearing/disappearing quality in the obomerge gui and we could just reuse the code. However the code that is currently there is really quite complicated and would take me a while to correctly unravel. If anybody more experienced at unraveling would like to do a double act with me on fixing this then that might get things done a lot quicker.

    We could do this over webex the same way that we often edit the ontologies when two people need to be present to get something done quickly.

    Thanks,

    Jen

     
  • Jennifer Deegan

    Jennifer Deegan - 2008-05-16
    • priority: 5 --> 1
     
  • Jennifer Deegan

    Jennifer Deegan - 2008-05-16

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    Originator: YES

    Hi,

    On further investigation via the large screen, I think that in fact this filter does not do what I need it to do anyway, so I will put this bug report on a low priority.

    Thanks,

    Jen

     
  • Nomi Harris

    Nomi Harris - 2008-07-15

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    user_id=424895
    Originator: NO

    Can you tell us more about this filtering not doing what you need? Is it not working right, or were you just trying to do something that it's not equipped to handle?

     
  • Nomi Harris

    Nomi Harris - 2008-07-15
    • summary: write ontology panel --> write ontology panel gets too big
     
  • Jennifer Deegan

    Jennifer Deegan - 2008-07-15

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    user_id=735846
    Originator: YES

    Hi Nomi,

    I'm pretty certain that I was trying to do a filter that OBO-Edit does not support. I was trying to set it up to save out only terms that have a given relationship type. For example if I loaded the GO ontologies (http://www.geneontology.org/ontology/gene_ontology_edit.obo) and then tried to save out only the stanzas for terms that have a part_of relationship in them. I do not want to save out the ancestors of terms that have a part_of relationship, just the terms themselves.

    So I would not want to save out this term:

    [Term]
    id: GO:0000001
    name: mitochondrion inheritance
    namespace: biological_process
    def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]
    synonym: "mitochondrial inheritance" EXACT []
    is_a: GO:0048308 ! organelle inheritance
    is_a: GO:0048311 ! mitochondrion distribution

    (There is not part_of relationship here.)

    But I would want to save out this term:

    [Term]
    id: GO:0000060
    name: protein import into nucleus, translocation
    namespace: biological_process
    def: "The vectorial transfer of a protein from the cytoplasm into the nucleus, through the nuclear pore and across the nuclear envelope." [GOC:jl, GOC:vw, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]
    synonym: "protein translocation during protein import into nucleus" EXACT []
    synonym: "protein translocation during protein transport from cytoplasm to nucleus" EXACT []
    synonym: "protein translocation during protein-nucleus import" EXACT []
    synonym: "protein transport from cytoplasm to nucleus, translocation" EXACT []
    synonym: "protein-nucleus import, translocation" EXACT []
    is_a: GO:0006886 ! intracellular protein transport
    relationship: part_of GO:0006606 ! protein import into nucleus

    (This one has a part_of relationship.)

    This is not an urgent problem at all for me as I have now written a perl script that does the job for me. Thanks for looking into it though.

    Jen

     
  • Jennifer Deegan

    Jennifer Deegan - 2008-08-06

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    user_id=735846
    Originator: YES

    I have found a workaround for the panel size problem so this can be low priority.

    Jen

     
  • Jennifer Deegan

    Jennifer Deegan - 2008-10-15

    It would be nice to have this in OBO-Edit 3 if that was possible.

    Thanks,

    Jen

     
  • Midori Harris

    Midori Harris - 2011-01-27

    moving to feature requests; still not high priority

     
  • Midori Harris

    Midori Harris - 2011-01-27
    • labels: 726998 --> OBO-Edit
     
  • Midori Harris

    Midori Harris - 2011-08-30
    • status: open --> closed-out-of-date
     

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