Re: [OBO-Edit Working Group] filtered save

[Chris M. <cj...@be...>]

On Jun 5, 2009, at 12:18 PM, David Osumi-Sutherland wrote:

> Hi Jen,
>
> As Midori says, you should be using a term filter, not a link filter.
> I think your filter is looking for relations (TypeDefs) with an is_a
> child called "fruit development" (although to choose [name] don't you
> have to choose [type] rather than [self] in the first box?.)  The fact
> that this saved anything might suggest a bug.   However, I haven't
> used this filter to do anything involving relations between
> relations.  Thinking about what those would mean makes my head spin.
> Perhaps we should strip that functionality out of OE2 for now, as I
> can see that having it there can be confusing and I can't really see a
> need for it.  Maybe Chris can suggest some possible uses?

something to do with regulates

the potential for confusion could be reduced by restricting the values  
to be relations, such that it's impossible to enter 'fruit  
development' as a relation constraint

>
> = Poss soln to your problem =
>
> This term filter:
>
> Select terms that [have] a [name] that [equals] the value <fruit
> development> in [children] that can be reached via [is_a]
>
> will save one term stanza:
> reproductive structure development
>
> if you want the child term itself, you need to add a second leg with
> 'OR' that just searches for that term.
> If you want all is_a paths to root choose [descendant] in place of
> [children]. to save all subtypes of fruit development choose
> [ancestor] etc.
>
> I have successfully used the link filter in combination with the link-
> pile reasoner, to strip out redundant is_a links on save.
> Similarly, if you could use a link filter with a term filter to
> restrict the types of relationship saved, e.g. to is_a.
>
> Hope this helps,
>
> David
>
>
> On 5 Jun 2009, at 5/Jun/2009 11:35:38, Jennifer Deegan (nee Clark)
> wrote:
>
>> Hi Midori,
>>
>> Interesting! That is not what is happening with me. When I do the
>> filtered save I get the normal file including all of the links that
>> fit the search criteria that I put in. I wonder what I am doing
>> differently? Does your dialog box look much like mine in the
>> attached picture? I'm not using the exact example I quoted because I
>> am using a tiny test ontology for simplicity. I have just checked it
>> into cvs as \go\software\test_resources\OBO-Edit\FilteredSave
>> \FileWithIntersections
>>
>> Jen
>>
>> Midori Harris wrote:
>>> Wow. I see what it's doing, and I have no idea if that's how it's
>>> supposed to work.
>>> When I try the filtered save you describe, it does filter links --
>>> but writes out all the term stanzas, minus links! In other words,
>>> it only strips out the actual link tags, not terms involved in non-
>>> matching links. So it's not the same as if I didn't do a filtered
>>> save, because most of the links haven't been included. I haven't
>>> tried reloading the saved file, but I bet it would look scarily odd
>>> in OE.
>>> I think if you want a file that contains only the terms of
>>> interest, you have to use term filtering. The [is intersection]
>>> option is available in the term search, and it works for me in a
>>> filtered save.
>>> m
>>> On Fri, 5 Jun 2009, Jennifer Deegan (nee Clark) wrote:
>>>> Hi,
>>>>
>>>> Has anybody successfully used the 'Filter Links' check box option
>>>> in the
>>>> save dialog in OBO-Edit? I have just been reading through the help
>>>> guide
>>>> to find out how to use it and it seems that if I say for example:
>>>>
>>>> [Child][have][name][equals]"fruit development"
>>>>
>>>> then I should get a file that contains:
>>>>
>>>> "fruit development" -is_a-> "reproductive structure development"
>>>>
>>>> but in fact what I get is the entire file saved out as if I hadn't
>>>> set
>>>> up any filter at all.
>>>>
>>>> If I set up a link filter to save out only intersection
>>>> relationships:
>>>>
>>>> [self][have][is intersection]
>>>>
>>>> I still get the entire file saved out, rather than just the
>>>> intersection
>>>> links.
>>>>
>>>> I have also figured out that the 'Always save properties' checkbox
>>>> works, but that there is no 'Never save properties' option.
>>>>
>>>> Thanks,
>>>>
>>>> Jen
>>>>
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>> <
>> pic
>> .JPG
>>>
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>
> David Osumi-Sutherland
> FlyBase,
> Department of Genetics,
> University of Cambridge,
> Downing Street,
> Cambridge, UK
> +44 (0)1223 333 963
>
>
> ------------------------------------------------------------------------------
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the  
> latest
> innovations from Sun and the OpenSource community. Download a copy and
> enjoy capabilities such as Networking, Storage and Virtualization.
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