Ontologies v.s. feature synonyms

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Ontologies v.s. feature synonyms

Karl O. Pinc
Hi,

I'm looking for guidance regarding
when to use the SYNONYM and FEATURE_SYNONYM
tables v.s. when to make a CV and related
CVTERM rows and use the cvterm_id in
FEATURE_CVTERM rows.

It seems that synonyms allow for obsolescence
but this would also be true of cv terms
since a new version of the cv can be created.

Thanks.

Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: Ontologies v.s. feature synonyms

Scott Cain
Hi Karl,

I'm not sure I understand what you don't understand: synonym and feature_synonym is for alternate names for features.  While I suppose you could stuff that into feature_cvterm (by creating a synonym cv), it doesn't seem anywhere near as natural (not that something seeming nature has kept us from doing something a different way in the project :-)

What am I not getting?

Scott



On Fri, May 30, 2014 at 10:45 AM, Karl O. Pinc <[hidden email]> wrote:
Hi,

I'm looking for guidance regarding
when to use the SYNONYM and FEATURE_SYNONYM
tables v.s. when to make a CV and related
CVTERM rows and use the cvterm_id in
FEATURE_CVTERM rows.

It seems that synonyms allow for obsolescence
but this would also be true of cv terms
since a new version of the cv can be created.

Thanks.

Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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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 v.s. feature synonyms

Karl O. Pinc
Hi Scott,

Well, right now I'm thinking about chromosomes,
working purely at the structural level,
and what the chromosomes are called.
I guess the question is "when is a name a
name and when is a name something more official
that belongs in an ontology?"

It's not a question with a real answer,
but it seems more efficient from the
db side to use ontologies to name things.
At some point this is bound to break down
and I'd like help exploring the problem.

On 05/30/2014 09:54:07 AM, Scott Cain wrote:

> Hi Karl,
>
> I'm not sure I understand what you don't understand: synonym and
> feature_synonym is for alternate names for features.  While I suppose
> you
> could stuff that into feature_cvterm (by creating a synonym cv), it
> doesn't
> seem anywhere near as natural (not that something seeming nature has
> kept
> us from doing something a different way in the project :-)
>
> What am I not getting?
>
> Scott
>
>
>
> On Fri, May 30, 2014 at 10:45 AM, Karl O. Pinc <[hidden email]> wrote:
>
> > Hi,
> >
> > I'm looking for guidance regarding
> > when to use the SYNONYM and FEATURE_SYNONYM
> > tables v.s. when to make a CV and related
> > CVTERM rows and use the cvterm_id in
> > FEATURE_CVTERM rows.
> >
> > It seems that synonyms allow for obsolescence
> > but this would also be true of cv terms
> > since a new version of the cv can be created.
> >
> > Thanks.
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >                  -- Robert A. Heinlein
> >
> >
> >
> ------------------------------------------------------------------------------
> > Time is money. Stop wasting it! Get your web API in 5 minutes.
> > www.restlet.com/download
> > http://p.sf.net/sfu/restlet
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at
> scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>




Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: Ontologies v.s. feature synonyms

Stephen Ficklin-2
I think perhaps a simple way to think about it is that names (synonyms)  
are intended for identification of individuals (i.e. individual
features, stocks, terms in a vocabulary, etc).  Whereas controlled
vocabulary terms don't identify individuals but annotate those
individual with descriptions of their behavior, relationships,
properties etc.

If your terms are descriptive about individuals then the CV tables make
sense.  If your terms are used to identify individuals via alternate
names then the synonym tables are better.


On 5/30/2014 11:34 AM, Karl O. Pinc wrote:

> Hi Scott,
>
> Well, right now I'm thinking about chromosomes,
> working purely at the structural level,
> and what the chromosomes are called.
> I guess the question is "when is a name a
> name and when is a name something more official
> that belongs in an ontology?"
>
> It's not a question with a real answer,
> but it seems more efficient from the
> db side to use ontologies to name things.
> At some point this is bound to break down
> and I'd like help exploring the problem.
>
> On 05/30/2014 09:54:07 AM, Scott Cain wrote:
>> Hi Karl,
>>
>> I'm not sure I understand what you don't understand: synonym and
>> feature_synonym is for alternate names for features.  While I suppose
>> you
>> could stuff that into feature_cvterm (by creating a synonym cv), it
>> doesn't
>> seem anywhere near as natural (not that something seeming nature has
>> kept
>> us from doing something a different way in the project :-)
>>
>> What am I not getting?
>>
>> Scott
>>
>>
>>
>> On Fri, May 30, 2014 at 10:45 AM, Karl O. Pinc <[hidden email]> wrote:
>>
>>> Hi,
>>>
>>> I'm looking for guidance regarding
>>> when to use the SYNONYM and FEATURE_SYNONYM
>>> tables v.s. when to make a CV and related
>>> CVTERM rows and use the cvterm_id in
>>> FEATURE_CVTERM rows.
>>>
>>> It seems that synonyms allow for obsolescence
>>> but this would also be true of cv terms
>>> since a new version of the cv can be created.
>>>
>>> Thanks.
>>>
>>> Karl <[hidden email]>
>>> Free Software:  "You don't pay back, you pay forward."
>>>                   -- Robert A. Heinlein
>>>
>>>
>>>
>> ------------------------------------------------------------------------------
>>> Time is money. Stop wasting it! Get your web API in 5 minutes.
>>> www.restlet.com/download
>>> http://p.sf.net/sfu/restlet
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at
>> scottcain dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                   -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> Time is money. Stop wasting it! Get your web API in 5 minutes.
> www.restlet.com/download
> http://p.sf.net/sfu/restlet
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


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Re: Ontologies v.s. feature synonyms

Karl O. Pinc
Thanks.  This is helpful.

On 05/30/2014 10:53:51 AM, Stephen Ficklin wrote:

> I think perhaps a simple way to think about it is that names
> (synonyms)  
> are intended for identification of individuals (i.e. individual
> features, stocks, terms in a vocabulary, etc).  Whereas controlled
> vocabulary terms don't identify individuals but annotate those
> individual with descriptions of their behavior, relationships,
> properties etc.
>
> If your terms are descriptive about individuals then the CV tables
> make
> sense.  If your terms are used to identify individuals via alternate
> names then the synonym tables are better.
>
>
> On 5/30/2014 11:34 AM, Karl O. Pinc wrote:
> > Hi Scott,
> >
> > Well, right now I'm thinking about chromosomes,
> > working purely at the structural level,
> > and what the chromosomes are called.
> > I guess the question is "when is a name a
> > name and when is a name something more official
> > that belongs in an ontology?"
> >
> > It's not a question with a real answer,
> > but it seems more efficient from the
> > db side to use ontologies to name things.
> > At some point this is bound to break down
> > and I'd like help exploring the problem.
> >
> > On 05/30/2014 09:54:07 AM, Scott Cain wrote:
> >> Hi Karl,
> >>
> >> I'm not sure I understand what you don't understand: synonym and
> >> feature_synonym is for alternate names for features.  While I
> suppose
> >> you
> >> could stuff that into feature_cvterm (by creating a synonym cv),
> it
> >> doesn't
> >> seem anywhere near as natural (not that something seeming nature
> has
> >> kept
> >> us from doing something a different way in the project :-)
> >>
> >> What am I not getting?
> >>
> >> Scott
> >>
> >>
> >>
> >> On Fri, May 30, 2014 at 10:45 AM, Karl O. Pinc <[hidden email]>
> wrote:
> >>
> >>> Hi,
> >>>
> >>> I'm looking for guidance regarding
> >>> when to use the SYNONYM and FEATURE_SYNONYM
> >>> tables v.s. when to make a CV and related
> >>> CVTERM rows and use the cvterm_id in
> >>> FEATURE_CVTERM rows.
> >>>
> >>> It seems that synonyms allow for obsolescence
> >>> but this would also be true of cv terms
> >>> since a new version of the cv can be created.
> >>>
> >>> Thanks.
> >>>
> >>> Karl <[hidden email]>
> >>> Free Software:  "You don't pay back, you pay forward."
> >>>                   -- Robert A. Heinlein
> >>>
> >>>
> >>>
> >>
> ------------------------------------------------------------------------------
> >>> Time is money. Stop wasting it! Get your web API in 5 minutes.
> >>> www.restlet.com/download
> >>> http://p.sf.net/sfu/restlet
> >>> _______________________________________________
> >>> Gmod-schema mailing list
> >>> [hidden email]
> >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>>
> >>
> >>
> >> --
> >>
> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at
> >> scottcain dot
> >> net
> >> GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087
> >> Ontario Institute for Cancer Research
> >>
> >
> >
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >                   -- Robert A. Heinlein
> >
> >
> ------------------------------------------------------------------------------
> > Time is money. Stop wasting it! Get your web API in 5 minutes.
> > www.restlet.com/download
> > http://p.sf.net/sfu/restlet
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>




Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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