Ontologies and Chado

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Ontologies and Chado

Scott Cain
Hi all,

As a few of us are working on new release of Chado, I've discovered the wonder of BFO (Big F'ing Ontology, right?)

So here's my very vague question: what do I need to know?  It seems that OBO_REL no longer exists, which is going to be a hassle for many Chado-related tools, which considered it fairly fundamental (with its is_a and part_of and a consistent cv.name of 'relationship').  I'm guessing BFO should completely replace OBO_REL, and RO is not really going to be needed in general instances of Chado (though obviously some users may want it, it isn't fundamental in the same way). 

Anything else?  Also, what is the obo purl for BFO? I tried to guess it a few times and failed.

Thanks,
Scott


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Ontario Institute for Cancer Research

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Re: Ontologies and Chado

Chris Mungall


On 23 Jul 2015, at 8:56, Scott Cain wrote:

> Hi all,
>
> As a few of us are working on new release of Chado, I've discovered
> the
> wonder of BFO (Big F'ing Ontology, right?)
>
> So here's my very vague question: what do I need to know?  It seems
> that
> OBO_REL no longer exists, which is going to be a hassle for many
> Chado-related tools, which considered it fairly fundamental (with its
> is_a
> and part_of and a consistent cv.name of 'relationship').  I'm guessing
> BFO
> should completely replace OBO_REL, and RO is not really going to be
> needed
> in general instances of Chado (though obviously some users may want
> it, it
> isn't fundamental in the same way).

Hi Scott,

I recommend that Chado uses RO, you can get the .obo from here:
http://purl.obolibrary.org/obo/ro.obo

Note this includes some classes from BFO, it should be possible to
produce a more minimal relation only edition/subset.

There are two pain points for you:

  1. Chado needs an edge label for "is_a"
  2. There is code that makes an assumption that there will be a
relation with OBO-Format ID "OBO_REL:part_of"

We can make a special edition just for Chado. For 1, we would add a
special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really
make any sense in terms of the mapping to OWL, where SubClass is a
builtin construct. But we can ignore this, as this edition is just for
Chado.

For 2, it's up to you. You can try and coordinate the move for Chado to
use BFO:0000050 (which is in RO). Or we can have the Chado edition have
the old OBO_REL:part_of as well, with some documentation that the goal
is to eventually move away from this, and an equivalent properties axiom
(not something we'd normally do, but this is a specific edition designed
to solve a particular problem)

I filed a ticket for this:
https://github.com/oborel/obo-relations/issues/68

>
> Anything else?  Also, what is the obo purl for BFO? I tried to guess
> it a
> few times and failed.
>
> Thanks,
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at
> scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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Re: [bfo-devel] Re: Ontologies and Chado

Asiyah Yu Lin
Somebody needs to work on the OBO version for BFO2, or BFO2 with basic relations, such as part_of.
I encountered with another group asking OBO files for BFO.

Best,
Asiyah

On Thu, Jul 23, 2015 at 12:43 PM, Chris Mungall <[hidden email]> wrote:


On 23 Jul 2015, at 8:56, Scott Cain wrote:

Hi all,

As a few of us are working on new release of Chado, I've discovered the
wonder of BFO (Big F'ing Ontology, right?)

So here's my very vague question: what do I need to know?  It seems that
OBO_REL no longer exists, which is going to be a hassle for many
Chado-related tools, which considered it fairly fundamental (with its is_a
and part_of and a consistent cv.name of 'relationship').  I'm guessing BFO
should completely replace OBO_REL, and RO is not really going to be needed
in general instances of Chado (though obviously some users may want it, it
isn't fundamental in the same way).

Hi Scott,

I recommend that Chado uses RO, you can get the .obo from here: http://purl.obolibrary.org/obo/ro.obo

Note this includes some classes from BFO, it should be possible to produce a more minimal relation only edition/subset.

There are two pain points for you:

 1. Chado needs an edge label for "is_a"
 2. There is code that makes an assumption that there will be a relation with OBO-Format ID "OBO_REL:part_of"

We can make a special edition just for Chado. For 1, we would add a special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really make any sense in terms of the mapping to OWL, where SubClass is a builtin construct. But we can ignore this, as this edition is just for Chado.

For 2, it's up to you. You can try and coordinate the move for Chado to use BFO:0000050 (which is in RO). Or we can have the Chado edition have the old OBO_REL:part_of as well, with some documentation that the goal is to eventually move away from this, and an equivalent properties axiom (not something we'd normally do, but this is a specific edition designed to solve a particular problem)

I filed a ticket for this:
https://github.com/oborel/obo-relations/issues/68


Anything else?  Also, what is the obo purl for BFO? I tried to guess it a
few times and failed.

Thanks,
Scott


--
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net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
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Re: Ontologies and Chado

Scott Cain
In reply to this post by Chris Mungall
Hi Chris,

I'm fine with creating a "Chado edition" of RO; the other thing we would certainly need is a 'derives_from', but it looks like that is present in RO, though I'm noticing that the names of all of the features in RO lack underscores--is that how they'd get stored in Chado as well?  Or is that part of what would be in the Chado edition?

Of course, it must also be loadable in Chado, and RO currently fails to load using xsltproc/DBIx::DBStag in Chado, but that may be due to the missing is_a or something else, I haven't looked closely at what the problem is.  If another method is preferable, that needs to be worked in to the build procedure.

Thanks,
Scott

(cross posted from the github issue, and bfo-devel removed, since it will bounce.)

On Thu, Jul 23, 2015 at 12:43 PM, Chris Mungall <[hidden email]> wrote:


On 23 Jul 2015, at 8:56, Scott Cain wrote:

Hi all,

As a few of us are working on new release of Chado, I've discovered the
wonder of BFO (Big F'ing Ontology, right?)

So here's my very vague question: what do I need to know?  It seems that
OBO_REL no longer exists, which is going to be a hassle for many
Chado-related tools, which considered it fairly fundamental (with its is_a
and part_of and a consistent cv.name of 'relationship').  I'm guessing BFO
should completely replace OBO_REL, and RO is not really going to be needed
in general instances of Chado (though obviously some users may want it, it
isn't fundamental in the same way).

Hi Scott,

I recommend that Chado uses RO, you can get the .obo from here: http://purl.obolibrary.org/obo/ro.obo

Note this includes some classes from BFO, it should be possible to produce a more minimal relation only edition/subset.

There are two pain points for you:

 1. Chado needs an edge label for "is_a"
 2. There is code that makes an assumption that there will be a relation with OBO-Format ID "OBO_REL:part_of"

We can make a special edition just for Chado. For 1, we would add a special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really make any sense in terms of the mapping to OWL, where SubClass is a builtin construct. But we can ignore this, as this edition is just for Chado.

For 2, it's up to you. You can try and coordinate the move for Chado to use BFO:0000050 (which is in RO). Or we can have the Chado edition have the old OBO_REL:part_of as well, with some documentation that the goal is to eventually move away from this, and an equivalent properties axiom (not something we'd normally do, but this is a specific edition designed to solve a particular problem)

I filed a ticket for this:
https://github.com/oborel/obo-relations/issues/68


Anything else?  Also, what is the obo purl for BFO? I tried to guess it a
few times and failed.

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Ontologies and Chado

Chris Mungall
All the relation IDs in RO are standard OBO-style RO:nnnnnn, this would be stored in dbxref table in the usual way. The labels are human readable (and chado shouldn't care about the labels)

Haven't checked the stag issue not sure when I would get a chance to

On Thu, Jul 23, 2015 at 10:12 AM, Scott Cain <[hidden email]> wrote:
Hi Chris,

I'm fine with creating a "Chado edition" of RO; the other thing we would certainly need is a 'derives_from', but it looks like that is present in RO, though I'm noticing that the names of all of the features in RO lack underscores--is that how they'd get stored in Chado as well?  Or is that part of what would be in the Chado edition?

Of course, it must also be loadable in Chado, and RO currently fails to load using xsltproc/DBIx::DBStag in Chado, but that may be due to the missing is_a or something else, I haven't looked closely at what the problem is.  If another method is preferable, that needs to be worked in to the build procedure.

Thanks,
Scott

(cross posted from the github issue, and bfo-devel removed, since it will bounce.)

On Thu, Jul 23, 2015 at 12:43 PM, Chris Mungall <[hidden email]> wrote:


On 23 Jul 2015, at 8:56, Scott Cain wrote:

Hi all,

As a few of us are working on new release of Chado, I've discovered the
wonder of BFO (Big F'ing Ontology, right?)

So here's my very vague question: what do I need to know?  It seems that
OBO_REL no longer exists, which is going to be a hassle for many
Chado-related tools, which considered it fairly fundamental (with its is_a
and part_of and a consistent cv.name of 'relationship').  I'm guessing BFO
should completely replace OBO_REL, and RO is not really going to be needed
in general instances of Chado (though obviously some users may want it, it
isn't fundamental in the same way).

Hi Scott,

I recommend that Chado uses RO, you can get the .obo from here: http://purl.obolibrary.org/obo/ro.obo

Note this includes some classes from BFO, it should be possible to produce a more minimal relation only edition/subset.

There are two pain points for you:

 1. Chado needs an edge label for "is_a"
 2. There is code that makes an assumption that there will be a relation with OBO-Format ID "OBO_REL:part_of"

We can make a special edition just for Chado. For 1, we would add a special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really make any sense in terms of the mapping to OWL, where SubClass is a builtin construct. But we can ignore this, as this edition is just for Chado.

For 2, it's up to you. You can try and coordinate the move for Chado to use BFO:0000050 (which is in RO). Or we can have the Chado edition have the old OBO_REL:part_of as well, with some documentation that the goal is to eventually move away from this, and an equivalent properties axiom (not something we'd normally do, but this is a specific edition designed to solve a particular problem)

I filed a ticket for this:
https://github.com/oborel/obo-relations/issues/68


Anything else?  Also, what is the obo purl for BFO? I tried to guess it a
few times and failed.

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Ontologies and Chado

Scott Cain
"shouldn't care about the labels"--nice sentiment, that. :-)

I'll worry about stag after I have a RO I can use.

On Thu, Jul 23, 2015 at 2:05 PM, Chris Mungall <[hidden email]> wrote:
All the relation IDs in RO are standard OBO-style RO:nnnnnn, this would be stored in dbxref table in the usual way. The labels are human readable (and chado shouldn't care about the labels)

Haven't checked the stag issue not sure when I would get a chance to

On Thu, Jul 23, 2015 at 10:12 AM, Scott Cain <[hidden email]> wrote:
Hi Chris,

I'm fine with creating a "Chado edition" of RO; the other thing we would certainly need is a 'derives_from', but it looks like that is present in RO, though I'm noticing that the names of all of the features in RO lack underscores--is that how they'd get stored in Chado as well?  Or is that part of what would be in the Chado edition?

Of course, it must also be loadable in Chado, and RO currently fails to load using xsltproc/DBIx::DBStag in Chado, but that may be due to the missing is_a or something else, I haven't looked closely at what the problem is.  If another method is preferable, that needs to be worked in to the build procedure.

Thanks,
Scott

(cross posted from the github issue, and bfo-devel removed, since it will bounce.)

On Thu, Jul 23, 2015 at 12:43 PM, Chris Mungall <[hidden email]> wrote:


On 23 Jul 2015, at 8:56, Scott Cain wrote:

Hi all,

As a few of us are working on new release of Chado, I've discovered the
wonder of BFO (Big F'ing Ontology, right?)

So here's my very vague question: what do I need to know?  It seems that
OBO_REL no longer exists, which is going to be a hassle for many
Chado-related tools, which considered it fairly fundamental (with its is_a
and part_of and a consistent cv.name of 'relationship').  I'm guessing BFO
should completely replace OBO_REL, and RO is not really going to be needed
in general instances of Chado (though obviously some users may want it, it
isn't fundamental in the same way).

Hi Scott,

I recommend that Chado uses RO, you can get the .obo from here: http://purl.obolibrary.org/obo/ro.obo

Note this includes some classes from BFO, it should be possible to produce a more minimal relation only edition/subset.

There are two pain points for you:

 1. Chado needs an edge label for "is_a"
 2. There is code that makes an assumption that there will be a relation with OBO-Format ID "OBO_REL:part_of"

We can make a special edition just for Chado. For 1, we would add a special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really make any sense in terms of the mapping to OWL, where SubClass is a builtin construct. But we can ignore this, as this edition is just for Chado.

For 2, it's up to you. You can try and coordinate the move for Chado to use BFO:0000050 (which is in RO). Or we can have the Chado edition have the old OBO_REL:part_of as well, with some documentation that the goal is to eventually move away from this, and an equivalent properties axiom (not something we'd normally do, but this is a specific edition designed to solve a particular problem)

I filed a ticket for this:
https://github.com/oborel/obo-relations/issues/68


Anything else?  Also, what is the obo purl for BFO? I tried to guess it a
few times and failed.

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Ontologies and Chado

Siddhartha Basu
In reply to this post by Chris Mungall
On Thu, 23 Jul 2015, Chris Mungall wrote:

>    All the relation IDs in RO are standard OBO-style RO:nnnnnn, this would be
>    stored in dbxref table in the usual way. The labels are human readable
>    (and chado shouldn't care about the labels)
So my application code that search by name have to be changed after
switching to new RO(name with space and no more underscores). Does it
also means that search by name is not recommended.

-siddhartha

>
>    Haven't checked the stag issue not sure when I would get a chance to
>    On Thu, Jul 23, 2015 at 10:12 AM, Scott Cain <[hidden email]> wrote:
>
>      Hi Chris,
>      I'm fine with creating a "Chado edition" of RO; the other thing we would
>      certainly need is a 'derives_from', but it looks like that is present in
>      RO, though I'm noticing that the names of all of the features in RO lack
>      underscores--is that how they'd get stored in Chado as well?A  Or is
>      that part of what would be in the Chado edition?
>      Of course, it must also be loadable in Chado, and RO currently fails to
>      load using xsltproc/DBIx::DBStag in Chado, but that may be due to the
>      missing is_a or something else, I haven't looked closely at what the
>      problem is.A  If another method is preferable, that needs to be worked
>      in to the build procedure.
>      Thanks,
>      Scott
>      (cross posted from the github issue, and bfo-devel removed, since it
>      will bounce.)
>      On Thu, Jul 23, 2015 at 12:43 PM, Chris Mungall <[hidden email]>
>      wrote:
>
>        On 23 Jul 2015, at 8:56, Scott Cain wrote:
>
>          Hi all,
>
>          As a few of us are working on new release of Chado, I've discovered
>          the
>          wonder of BFO (Big F'ing Ontology, right?)
>
>          So here's my very vague question: what do I need to know?A  It seems
>          that
>          OBO_REL no longer exists, which is going to be a hassle for many
>          Chado-related tools, which considered it fairly fundamental (with
>          its is_a
>          and part_of and a consistent cv.name of 'relationship').A  I'm
>          guessing BFO
>          should completely replace OBO_REL, and RO is not really going to be
>          needed
>          in general instances of Chado (though obviously some users may want
>          it, it
>          isn't fundamental in the same way).
>
>        Hi Scott,
>
>        I recommend that Chado uses RO, you can get the .obo from here:
>        http://purl.obolibrary.org/obo/ro.obo
>
>        Note this includes some classes from BFO, it should be possible to
>        produce a more minimal relation only edition/subset.
>
>        There are two pain points for you:
>
>        A 1. Chado needs an edge label for "is_a"
>        A 2. There is code that makes an assumption that there will be a
>        relation with OBO-Format ID "OBO_REL:part_of"
>
>        We can make a special edition just for Chado. For 1, we would add a
>        special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really
>        make any sense in terms of the mapping to OWL, where SubClass is a
>        builtin construct. But we can ignore this, as this edition is just for
>        Chado.
>
>        For 2, it's up to you. You can try and coordinate the move for Chado
>        to use BFO:0000050 (which is in RO). Or we can have the Chado edition
>        have the old OBO_REL:part_of as well, with some documentation that the
>        goal is to eventually move away from this, and an equivalent
>        properties axiom (not something we'd normally do, but this is a
>        specific edition designed to solve a particular problem)
>
>        I filed a ticket for this:
>        https://github.com/oborel/obo-relations/issues/68
>
>          Anything else?A  Also, what is the obo purl for BFO? I tried to
>          guess it a
>          few times and failed.
>
>          Thanks,
>          Scott
>
>          --
>          ------------------------------------------------------------------------
>          Scott Cain, Ph. D.A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A
>          A scott at scottcain dot
>          net
>          GMOD Coordinator (http://gmod.org/)A  A  A  A  A  A  A  A  A  A
>          A 216-392-3087
>          Ontario Institute for Cancer Research
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>          _______________________________________________
>          Gmod-schema mailing list
>          [hidden email]
>          https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>      --
>      ------------------------------------------------------------------------
>      Scott Cain, Ph. D.A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A A
>      scott at scottcain dot net
>      GMOD Coordinator (http://gmod.org/)A  A  A  A  A  A  A  A  A  A A
>      216-392-3087
>      Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------

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