Populating cvtermpath with owltools

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Populating cvtermpath with owltools

Kim Rutherford
Hi all.

A while ago, there was a thread about populating cvtermpath.  In the
thread Chris M wrote:

> However, I'd say the best approach is to wrap owltools[*]. The simplest
> way to do this would be to run it on the command line, taking 1 or
> more obo (or owl) files on the command line, and asking for a 4-column
> TSV dump that can be loaded into cvtermpath. I've added this to the
> command line options:

>  owltools gene_ontology_write.obo --save-closure-for-chado go.inf


I was wondering if anyone had tried this?

Thanks.

Kim.

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Re: Populating cvtermpath with owltools

Siddhartha Basu
Hi Kim,
Actually, i am planning to try this in next week. Here is my plan
briefly,

* It will a command line perl application which will be part of
  Modware-Loader(https://github.com/dictyBase/Modware-Loader)
  distribution. It's still a work in
  progress and might take a while to put in CPAN, but works fine from a github install.
  Here are few additonal docs to show how we use it ...
  http://dictybase.github.io/blog/2013/03/06/exporting-discoideum-annotations/
  http://dictybase.github.io/install-modware-loader/index.html
 
* My idea is to bundle the owltools jar with this distrubution and then
  read it from a pipe and load in chado.
  This might not be the most elegant solution, however, at this
  point owltools seems to be the officially maintained tool to
  get a correct transitive closure of an ontology in obo format.
  There might be other but i am not aware currently. If there is
  something in pure perl equivalent to owltools, i am open to ideas.

* There was another idea floating around for a while is to generate
  these closure periodically and host it on the web so that we could bypass
  the installtion of owltools. Would be nice to have this.

Anyway, Kim if you are interested, may be we could work out a
collaborative solution, please let me know.

thanks,
-siddhartha








On Mon, 26 Aug 2013, Kim Rutherford wrote:

> Hi all.
>
> A while ago, there was a thread about populating cvtermpath.  In the
> thread Chris M wrote:
>
> > However, I'd say the best approach is to wrap owltools[*]. The simplest
> > way to do this would be to run it on the command line, taking 1 or
> > more obo (or owl) files on the command line, and asking for a 4-column
> > TSV dump that can be loaded into cvtermpath. I've added this to the
> > command line options:
>
> >  owltools gene_ontology_write.obo --save-closure-for-chado go.inf
>
>
> I was wondering if anyone had tried this?
>
> Thanks.
>
> Kim.
>
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Re: Populating cvtermpath with owltools

Kim Rutherford
On Monday 26 August 2013 at 10:11:48, Siddhartha Basu wrote:

> Actually, i am planning to try this in next week.

That's great to hear.


> Here is my plan briefly,
>
> * It will a command line perl application which will be part of
>   Modware-Loader(https://github.com/dictyBase/Modware-Loader)
>   distribution.

That sounds good.


> * My idea is to bundle the owltools jar with this distrubution and
>   then read it from a pipe and load in chado.

Can I suggest you have an option to run the owltools command to get the
output?  We have owltools installed locally (and in the PATH) and we
keep it up to date.


>   This might not be the most elegant solution, however, at this point
>   owltools seems to be the officially maintained tool to get a
>   correct transitive closure of an ontology in obo format.

I agree, it's the best option.  Owltools is supported and being
developed.  It wouldn't make sense to re-implement the tricky stuff
(like reasoning) in Perl when there a good package available.


> * There was another idea floating around for a while is to generate
>   these closure periodically and host it on the web so that we could
>   bypass the installtion of owltools. Would be nice to have this.

That would be nice, but owltools is so quick generating the closure
that I'd prefer to use it rather than download a file.  If I run
owltools (or a wrapper) locally I'll know that I definitely using the
same version of the ontology.

I'm keen to help with testing if you implement something.  Please let
me know what I can do.

Kim.

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Re: Populating cvtermpath with owltools

Siddhartha Basu
Hi Kim,
Sorry for the late response.
Your suggestion seems fine, will let the command consume owltools ouput
through pipe or redirection, should make it more standalone and
deployment friendly. I should be able to put out a initial working version by next
Wed. Hope that sounds reasonable.

Thanks for your help.

-siddhartha


On Tue, 27 Aug 2013, Kim Rutherford wrote:

> On Monday 26 August 2013 at 10:11:48, Siddhartha Basu wrote:
>
> > Actually, i am planning to try this in next week.
>
> That's great to hear.
>
>
> > Here is my plan briefly,
> >
> > * It will a command line perl application which will be part of
> >   Modware-Loader(https://github.com/dictyBase/Modware-Loader)
> >   distribution.
>
> That sounds good.
>
>
> > * My idea is to bundle the owltools jar with this distrubution and
> >   then read it from a pipe and load in chado.
>
> Can I suggest you have an option to run the owltools command to get the
> output?  We have owltools installed locally (and in the PATH) and we
> keep it up to date.
>
>
> >   This might not be the most elegant solution, however, at this point
> >   owltools seems to be the officially maintained tool to get a
> >   correct transitive closure of an ontology in obo format.
>
> I agree, it's the best option.  Owltools is supported and being
> developed.  It wouldn't make sense to re-implement the tricky stuff
> (like reasoning) in Perl when there a good package available.
>
>
> > * There was another idea floating around for a while is to generate
> >   these closure periodically and host it on the web so that we could
> >   bypass the installtion of owltools. Would be nice to have this.
>
> That would be nice, but owltools is so quick generating the closure
> that I'd prefer to use it rather than download a file.  If I run
> owltools (or a wrapper) locally I'll know that I definitely using the
> same version of the ontology.
>
> I'm keen to help with testing if you implement something.  Please let
> me know what I can do.
>
> Kim.

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Re: Populating cvtermpath with owltools

Chris Mungall
Thanks Sidd and Kim, the plan is sound, it will be great to have this as part of the GMOD suite


On Thu, Aug 29, 2013 at 11:59 AM, Siddhartha Basu <[hidden email]> wrote:
Hi Kim,
Sorry for the late response.
Your suggestion seems fine, will let the command consume owltools ouput
through pipe or redirection, should make it more standalone and
deployment friendly. I should be able to put out a initial working version by next
Wed. Hope that sounds reasonable.

Thanks for your help.

-siddhartha


On Tue, 27 Aug 2013, Kim Rutherford wrote:

> On Monday 26 August 2013 at 10:11:48, Siddhartha Basu wrote:
>
> > Actually, i am planning to try this in next week.
>
> That's great to hear.
>
>
> > Here is my plan briefly,
> >
> > * It will a command line perl application which will be part of
> >   Modware-Loader(https://github.com/dictyBase/Modware-Loader)
> >   distribution.
>
> That sounds good.
>
>
> > * My idea is to bundle the owltools jar with this distrubution and
> >   then read it from a pipe and load in chado.
>
> Can I suggest you have an option to run the owltools command to get the
> output?  We have owltools installed locally (and in the PATH) and we
> keep it up to date.
>
>
> >   This might not be the most elegant solution, however, at this point
> >   owltools seems to be the officially maintained tool to get a
> >   correct transitive closure of an ontology in obo format.
>
> I agree, it's the best option.  Owltools is supported and being
> developed.  It wouldn't make sense to re-implement the tricky stuff
> (like reasoning) in Perl when there a good package available.
>
>
> > * There was another idea floating around for a while is to generate
> >   these closure periodically and host it on the web so that we could
> >   bypass the installtion of owltools. Would be nice to have this.
>
> That would be nice, but owltools is so quick generating the closure
> that I'd prefer to use it rather than download a file.  If I run
> owltools (or a wrapper) locally I'll know that I definitely using the
> same version of the ontology.
>
> I'm keen to help with testing if you implement something.  Please let
> me know what I can do.
>
> Kim.

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Re: Populating cvtermpath with owltools

Siddhartha Basu
Not a problem, anyway i could contribute.

-siddhartha

On Thu, 29 Aug 2013, Chris Mungall wrote:

>    Thanks Sidd and Kim, the plan is sound, it will be great to have this as
>    part of the GMOD suite
>
>    On Thu, Aug 29, 2013 at 11:59 AM, Siddhartha Basu <[hidden email]>
>    wrote:
>
>      Hi Kim,
>      Sorry for the late response.
>      Your suggestion seems fine, will let the command consume owltools ouput
>      through pipe or redirection, should make it more standalone and
>      deployment friendly. I should be able to put out a initial working
>      version by next
>      Wed. Hope that sounds reasonable.
>
>      Thanks for your help.
>
>      -siddhartha
>
>      On Tue, 27 Aug 2013, Kim Rutherford wrote:
>
>      > On Monday 26 August 2013 at 10:11:48, Siddhartha Basu wrote:
>      >
>      > > Actually, i am planning to try this in next week.
>      >
>      > That's great to hear.
>      >
>      >
>      > > Here is my plan briefly,
>      > >
>      > > * It will a command line perl application which will be part of
>      > >   Modware-Loader(https://github.com/dictyBase/Modware-Loader)
>      > >   distribution.
>      >
>      > That sounds good.
>      >
>      >
>      > > * My idea is to bundle the owltools jar with this distrubution and
>      > >   then read it from a pipe and load in chado.
>      >
>      > Can I suggest you have an option to run the owltools command to get
>      the
>      > output?  We have owltools installed locally (and in the PATH) and we
>      > keep it up to date.
>      >
>      >
>      > >   This might not be the most elegant solution, however, at this
>      point
>      > >   owltools seems to be the officially maintained tool to get a
>      > >   correct transitive closure of an ontology in obo format.
>      >
>      > I agree, it's the best option.  Owltools is supported and being
>      > developed.  It wouldn't make sense to re-implement the tricky stuff
>      > (like reasoning) in Perl when there a good package available.
>      >
>      >
>      > > * There was another idea floating around for a while is to generate
>      > >   these closure periodically and host it on the web so that we could
>      > >   bypass the installtion of owltools. Would be nice to have this.
>      >
>      > That would be nice, but owltools is so quick generating the closure
>      > that I'd prefer to use it rather than download a file.  If I run
>      > owltools (or a wrapper) locally I'll know that I definitely using the
>      > same version of the ontology.
>      >
>      > I'm keen to help with testing if you implement something.  Please let
>      > me know what I can do.
>      >
>      > Kim.
>
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Re: Populating cvtermpath with owltools

Siddhartha Basu
In reply to this post by Siddhartha Basu
Hi Kim,
I have released the cvtermpath loader. Please give it a shot.
Download the latest release from release page....
https://github.com/dictyBase/Modware-Loader/releases/tag/v1.6.0
or follow the installation section in the front page
https://github.com/dictyBase/Modware-Loader

Hope that help,
thanks,
-siddhartha

On Mon, 09 Sep 2013, Siddhartha Basu wrote:

> Hi Kim,
> I think you are trying the obo-loader for chado, not the cvtermpath
> loader module i am talking about.
> Anyway, you have to load cvprop ontology before you could load any other
> ontology using that script. It uses cvprop table to store basic metadata
> about every ontology particularly to check what version of ontology you
> are trying to load. To load cvprop ontology please use adhocobo2chado
> script.
>
> Hope this helps,
> thanks,
> -siddhartha
>
> On Sat, 07 Sep 2013, Kim Rutherford wrote:
>
> > On Friday 6 September 2013 at 10:07:38, Siddhartha Basu wrote:
> >
> > > Hi Kim,
> > > Quick update, would be a little late in getting that code out. Didn't
> > > get a chance to start before today, hope to get it out by next tuesday.
> > > Sorry for any inconvenience.
> >
> > Hi.
> >
> > I now get this message:
> >
> >   [09-07-2013 08:32:16] FATAL > obo2chado.pm:56 - cvprop ontology is not loaded!!! cannot continue
> >   cvprop ontology is not loaded!!! cannot continue at /usr/local/share/perl/5.14.2/Modware/Load/Command/obo2chado.pm line 56
> >
> > My Chado doesn't have a cvprop ontology.  Is it new?  We're using an
> > old GMOD release from 2 years ago.  Could that be the problem?
> >
> > Thanks for your help.
> >
> > Kim.

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