proposed cvprop table

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proposed cvprop table

Scott Cain
Hello,

Below is the sql for a proposed cvprop table, for storing things like
remarks and versions for a cv.  It's a pretty straight forward prop
table, so I don't expect much in the way of objection, but if you do
object, now is the time to mention it.

Scott

-- ================================================
-- TABLE: cvprop
-- ================================================
create table cvprop (
    cvprop_id serial not null,
    primary key (cvprop_id),
    cv_id int not null,
    foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
    type_id int not null,
    foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
    value text not null default '',
    rank int not null default 0,
    constraint cvprop_c1 unique (cv_id,type_id,rank)
);

COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
attached to a cv using this table.  A notable example would be the cv
version';

COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
is a cvterm. The meaning of the property is defined in that cvterm.';
COMMENT ON COLUMN cvprop.value IS 'The value of the property,
represented as text. Numeric values are converted to their text
representation.';

COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
cv can have multiple values for any particular property type -
these are ordered in a list using rank, counting from zero. For
properties that are single-valued rather than multi-valued, the
default 0 value should be used.';


--
------------------------------------------------------------------------
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: proposed cvprop table

Daniel Quest
So the ontology that has the concepts like ontology_version ect will
itself need to be loaded before any other ontology can be loaded?  Or
is this table only used after an ontology is loaded?  --- as the final
element of processing.  Where do these properties come from?  Is there
a concept of version control on ontologies currently?

-Daniel

On Tue, Nov 9, 2010 at 3:59 PM, Scott Cain <[hidden email]> wrote:

> Hello,
>
> Below is the sql for a proposed cvprop table, for storing things like
> remarks and versions for a cv.  It's a pretty straight forward prop
> table, so I don't expect much in the way of objection, but if you do
> object, now is the time to mention it.
>
> Scott
>
> -- ================================================
> -- TABLE: cvprop
> -- ================================================
> create table cvprop (
>    cvprop_id serial not null,
>    primary key (cvprop_id),
>    cv_id int not null,
>    foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>    type_id int not null,
>    foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>    value text not null default '',
>    rank int not null default 0,
>    constraint cvprop_c1 unique (cv_id,type_id,rank)
> );
>
> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
> attached to a cv using this table.  A notable example would be the cv
> version';
>
> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
> is a cvterm. The meaning of the property is defined in that cvterm.';
> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
> represented as text. Numeric values are converted to their text
> representation.';
>
> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
> cv can have multiple values for any particular property type -
> these are ordered in a list using rank, counting from zero. For
> properties that are single-valued rather than multi-valued, the
> default 0 value should be used.';
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

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Re: proposed cvprop table

Scott Cain
Hi Daniel,

Good questions.  Clearly, any ontology loader would have to be
prepared for the situation where these terms are not present in the
cvterm table, since a cv that has these terms will have to be loaded
without them.  That said, I would envision a controlled vocabulary
with these terms to be among the first things to be loaded, perhaps
before the option is even given to the user to load ontologies (either
that, or it could be the first item on the list of ontologies to load,
which would be easier for me to implement).

For where the properties come from, the only place I could imagine
getting them from are the obo files themselves.  Typically, the top of
an obo file looks like this:

format-version: 1.2
date: 06:10:2010 17:55
auto-generated-by: OBO-Edit 2.1-beta3
subsetdef: biosapiens "biosapiens protein feature ontology"
subsetdef: SOFA "SO feature annotation"
synonymtypedef: aa1 "amino acid 1 letter code"
synonymtypedef: aa3 "amino acid 3 letter code"
synonymtypedef: AAMOD "amino acid modification"
synonymtypedef: BS "biosapiens"
synonymtypedef: dbsnp "dbsnp variant terms"
synonymtypedef: ebi_variants "ensembl variant terms"
synonymtypedef: RNAMOD "RNA modification" EXACT
default-namespace: sequence
remark: autogenerated-by\:   DAG-Edit version 1.417\nsaved-by\:
eilbeck\ndate\:         Tue May 11 15\:18\:44 PDT 2004\nversion\:
$Revision\: 1.45 $

and all of those things could be extracted and stored as properties of
the cv.  Missing from this header is a data-version tag, which Chris
Mungall tells me is used for reporting release versions of obo files
(though I haven't seen it in real life yet).  My hope is that by
creating this infrastructure, with Chado/GMOD as a fairly large
consumer of ontologies, it will encourage producers of ontologies to
start including useful information about their releases in this
section of their obo files.

Scott


On Wed, Nov 10, 2010 at 1:54 PM, Daniel Quest <[hidden email]> wrote:

> So the ontology that has the concepts like ontology_version ect will
> itself need to be loaded before any other ontology can be loaded?  Or
> is this table only used after an ontology is loaded?  --- as the final
> element of processing.  Where do these properties come from?  Is there
> a concept of version control on ontologies currently?
>
> -Daniel
>
> On Tue, Nov 9, 2010 at 3:59 PM, Scott Cain <[hidden email]> wrote:
>> Hello,
>>
>> Below is the sql for a proposed cvprop table, for storing things like
>> remarks and versions for a cv.  It's a pretty straight forward prop
>> table, so I don't expect much in the way of objection, but if you do
>> object, now is the time to mention it.
>>
>> Scott
>>
>> -- ================================================
>> -- TABLE: cvprop
>> -- ================================================
>> create table cvprop (
>>    cvprop_id serial not null,
>>    primary key (cvprop_id),
>>    cv_id int not null,
>>    foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>    type_id int not null,
>>    foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>    value text not null default '',
>>    rank int not null default 0,
>>    constraint cvprop_c1 unique (cv_id,type_id,rank)
>> );
>>
>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>> attached to a cv using this table.  A notable example would be the cv
>> version';
>>
>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>> is a cvterm. The meaning of the property is defined in that cvterm.';
>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>> represented as text. Numeric values are converted to their text
>> representation.';
>>
>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>> cv can have multiple values for any particular property type -
>> these are ordered in a list using rank, counting from zero. For
>> properties that are single-valued rather than multi-valued, the
>> default 0 value should be used.';
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------------------------
>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>> David G. Thomson, author of the best-selling book "Blueprint to a
>> Billion" shares his insights and actions to help propel your
>> business during the next growth cycle. Listen Now!
>> http://p.sf.net/sfu/SAP-dev2dev
>> _______________________________________________
>> 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

------------------------------------------------------------------------------
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David G. Thomson, author of the best-selling book "Blueprint to a
Billion" shares his insights and actions to help propel your
business during the next growth cycle. Listen Now!
http://p.sf.net/sfu/SAP-dev2dev
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Re: proposed cvprop table

Hilmar Lapp-3
In reply to this post by Scott Cain
Looks great to me, except that value should be nullable.

        -hilmar

On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:

> Hello,
>
> Below is the sql for a proposed cvprop table, for storing things like
> remarks and versions for a cv.  It's a pretty straight forward prop
> table, so I don't expect much in the way of objection, but if you do
> object, now is the time to mention it.
>
> Scott
>
> -- ================================================
> -- TABLE: cvprop
> -- ================================================
> create table cvprop (
>    cvprop_id serial not null,
>    primary key (cvprop_id),
>    cv_id int not null,
>    foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>    type_id int not null,
>    foreign key (type_id) references cvterm (cvterm_id) INITIALLY  
> DEFERRED,
>    value text not null default '',
>    rank int not null default 0,
>    constraint cvprop_c1 unique (cv_id,type_id,rank)
> );
>
> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
> attached to a cv using this table.  A notable example would be the cv
> version';
>
> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
> is a cvterm. The meaning of the property is defined in that cvterm.';
> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
> represented as text. Numeric values are converted to their text
> representation.';
>
> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
> cv can have multiple values for any particular property type -
> these are ordered in a list using rank, counting from zero. For
> properties that are single-valued rather than multi-valued, the
> default 0 value should be used.';
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





------------------------------------------------------------------------------
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Billion" shares his insights and actions to help propel your
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Re: proposed cvprop table

Scott Cain
Hi Hilmar,

I don't have a problem with a nullable value; do you have a specific
case in mind, or just planning ahead?

Scott


On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:

> Looks great to me, except that value should be nullable.
>
>        -hilmar
>
> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>
>> Hello,
>>
>> Below is the sql for a proposed cvprop table, for storing things like
>> remarks and versions for a cv.  It's a pretty straight forward prop
>> table, so I don't expect much in the way of objection, but if you do
>> object, now is the time to mention it.
>>
>> Scott
>>
>> -- ================================================
>> -- TABLE: cvprop
>> -- ================================================
>> create table cvprop (
>>   cvprop_id serial not null,
>>   primary key (cvprop_id),
>>   cv_id int not null,
>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>   type_id int not null,
>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>   value text not null default '',
>>   rank int not null default 0,
>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>> );
>>
>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>> attached to a cv using this table.  A notable example would be the cv
>> version';
>>
>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>> is a cvterm. The meaning of the property is defined in that cvterm.';
>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>> represented as text. Numeric values are converted to their text
>> representation.';
>>
>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>> cv can have multiple values for any particular property type -
>> these are ordered in a list using rank, counting from zero. For
>> properties that are single-valued rather than multi-valued, the
>> default 0 value should be used.';
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
>> ------------------------------------------------------------------------------
>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>> David G. Thomson, author of the best-selling book "Blueprint to a
>> Billion" shares his insights and actions to help propel your
>> business during the next growth cycle. Listen Now!
>> http://p.sf.net/sfu/SAP-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>



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

------------------------------------------------------------------------------
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book "Blueprint to a
Billion" shares his insights and actions to help propel your
business during the next growth cycle. Listen Now!
http://p.sf.net/sfu/SAP-dev2dev
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Re: proposed cvprop table

Daniel Quest
Hi Scott,

Thinking more globally, I make ontologies in OWL format directly.
These ontologies do not require these fields... so I guess, if you
load an OWL ontology directly then it may have different CVprops from
a OBO ontology?  Is that what you are thinking?

-Daniel

On Wed, Nov 10, 2010 at 2:37 PM, Scott Cain <[hidden email]> wrote:

> Hi Hilmar,
>
> I don't have a problem with a nullable value; do you have a specific
> case in mind, or just planning ahead?
>
> Scott
>
>
> On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:
>> Looks great to me, except that value should be nullable.
>>
>>        -hilmar
>>
>> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>>
>>> Hello,
>>>
>>> Below is the sql for a proposed cvprop table, for storing things like
>>> remarks and versions for a cv.  It's a pretty straight forward prop
>>> table, so I don't expect much in the way of objection, but if you do
>>> object, now is the time to mention it.
>>>
>>> Scott
>>>
>>> -- ================================================
>>> -- TABLE: cvprop
>>> -- ================================================
>>> create table cvprop (
>>>   cvprop_id serial not null,
>>>   primary key (cvprop_id),
>>>   cv_id int not null,
>>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>>   type_id int not null,
>>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>>   value text not null default '',
>>>   rank int not null default 0,
>>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>>> );
>>>
>>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>>> attached to a cv using this table.  A notable example would be the cv
>>> version';
>>>
>>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>>> is a cvterm. The meaning of the property is defined in that cvterm.';
>>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>>> represented as text. Numeric values are converted to their text
>>> representation.';
>>>
>>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>>> cv can have multiple values for any particular property type -
>>> these are ordered in a list using rank, counting from zero. For
>>> properties that are single-valued rather than multi-valued, the
>>> default 0 value should be used.';
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>> Billion" shares his insights and actions to help propel your
>>> business during the next growth cycle. Listen Now!
>>> http://p.sf.net/sfu/SAP-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>> --
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

------------------------------------------------------------------------------
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book "Blueprint to a
Billion" shares his insights and actions to help propel your
business during the next growth cycle. Listen Now!
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Re: proposed cvprop table

Scott Cain
Hi Daniel,

What drove my interest in doing this is capturing version information
about the ontology.  If it's available, I want it.  Since the only
ontology loader I have handy is for obo files, I just opened a few obo
files to see what sort of metadata I could get.  The other piece of
metadata that would be nice to capture is members of slims so that
they could be reconstructed on the fly if needed (for example, by an
editing tool that wants to use a slim version of an ontology that is
loaded in Chado).

Presumably, for a loader of OWL files, I would want it to map any
available metadata to available terms, and of course, if there is
other metadata not represented by the current cv_properties cv, terms
could be created for them as well.

Scott


On Wed, Nov 10, 2010 at 3:31 PM, Daniel Quest <[hidden email]> wrote:

> Hi Scott,
>
> Thinking more globally, I make ontologies in OWL format directly.
> These ontologies do not require these fields... so I guess, if you
> load an OWL ontology directly then it may have different CVprops from
> a OBO ontology?  Is that what you are thinking?
>
> -Daniel
>
> On Wed, Nov 10, 2010 at 2:37 PM, Scott Cain <[hidden email]> wrote:
>> Hi Hilmar,
>>
>> I don't have a problem with a nullable value; do you have a specific
>> case in mind, or just planning ahead?
>>
>> Scott
>>
>>
>> On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:
>>> Looks great to me, except that value should be nullable.
>>>
>>>        -hilmar
>>>
>>> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>>>
>>>> Hello,
>>>>
>>>> Below is the sql for a proposed cvprop table, for storing things like
>>>> remarks and versions for a cv.  It's a pretty straight forward prop
>>>> table, so I don't expect much in the way of objection, but if you do
>>>> object, now is the time to mention it.
>>>>
>>>> Scott
>>>>
>>>> -- ================================================
>>>> -- TABLE: cvprop
>>>> -- ================================================
>>>> create table cvprop (
>>>>   cvprop_id serial not null,
>>>>   primary key (cvprop_id),
>>>>   cv_id int not null,
>>>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>>>   type_id int not null,
>>>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>>>   value text not null default '',
>>>>   rank int not null default 0,
>>>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>>>> );
>>>>
>>>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>>>> attached to a cv using this table.  A notable example would be the cv
>>>> version';
>>>>
>>>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>>>> is a cvterm. The meaning of the property is defined in that cvterm.';
>>>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>>>> represented as text. Numeric values are converted to their text
>>>> representation.';
>>>>
>>>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>>>> cv can have multiple values for any particular property type -
>>>> these are ordered in a list using rank, counting from zero. For
>>>> properties that are single-valued rather than multi-valued, the
>>>> default 0 value should be used.';
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>> Billion" shares his insights and actions to help propel your
>>>> business during the next growth cycle. Listen Now!
>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>> --
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------------------------
>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>> David G. Thomson, author of the best-selling book "Blueprint to a
>> Billion" shares his insights and actions to help propel your
>> business during the next growth cycle. Listen Now!
>> http://p.sf.net/sfu/SAP-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
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>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
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>



--
------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: proposed cvprop table

Hilmar Lapp-3
In reply to this post by Scott Cain

On Nov 10, 2010, at 2:37 PM, Scott Cain wrote:

> I don't have a problem with a nullable value; do you have a specific
> case in mind, or just planning ahead?

Some metadata annotations may only consist of the ontology term itself  
and not have any additional value. Also, this would then be consistent  
with all the other *prop tables.

        -hilmar
--
===========================================================
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===========================================================





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Re: proposed cvprop table

Robert Buels
In reply to this post by Scott Cain
Actually, I'm going to go a step further and advocate a 'version' column
being added to the cv table itself.

Ontologies change, it's one of their main characteristics.  I cannot
think of a situation in which an ontology *shouldn't* have a version
number.  If an ontology is not versioned, I am inclined to think that is
Wrong.

Thoughts?

Rob

Scott Cain wrote:

> Hi Daniel,
>
> What drove my interest in doing this is capturing version information
> about the ontology.  If it's available, I want it.  Since the only
> ontology loader I have handy is for obo files, I just opened a few obo
> files to see what sort of metadata I could get.  The other piece of
> metadata that would be nice to capture is members of slims so that
> they could be reconstructed on the fly if needed (for example, by an
> editing tool that wants to use a slim version of an ontology that is
> loaded in Chado).
>
> Presumably, for a loader of OWL files, I would want it to map any
> available metadata to available terms, and of course, if there is
> other metadata not represented by the current cv_properties cv, terms
> could be created for them as well.
>
> Scott
>
>
> On Wed, Nov 10, 2010 at 3:31 PM, Daniel Quest <[hidden email]> wrote:
>> Hi Scott,
>>
>> Thinking more globally, I make ontologies in OWL format directly.
>> These ontologies do not require these fields... so I guess, if you
>> load an OWL ontology directly then it may have different CVprops from
>> a OBO ontology?  Is that what you are thinking?
>>
>> -Daniel
>>
>> On Wed, Nov 10, 2010 at 2:37 PM, Scott Cain <[hidden email]> wrote:
>>> Hi Hilmar,
>>>
>>> I don't have a problem with a nullable value; do you have a specific
>>> case in mind, or just planning ahead?
>>>
>>> Scott
>>>
>>>
>>> On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:
>>>> Looks great to me, except that value should be nullable.
>>>>
>>>>        -hilmar
>>>>
>>>> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> Below is the sql for a proposed cvprop table, for storing things like
>>>>> remarks and versions for a cv.  It's a pretty straight forward prop
>>>>> table, so I don't expect much in the way of objection, but if you do
>>>>> object, now is the time to mention it.
>>>>>
>>>>> Scott
>>>>>
>>>>> -- ================================================
>>>>> -- TABLE: cvprop
>>>>> -- ================================================
>>>>> create table cvprop (
>>>>>   cvprop_id serial not null,
>>>>>   primary key (cvprop_id),
>>>>>   cv_id int not null,
>>>>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>>>>   type_id int not null,
>>>>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>>>>   value text not null default '',
>>>>>   rank int not null default 0,
>>>>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>>>>> );
>>>>>
>>>>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>>>>> attached to a cv using this table.  A notable example would be the cv
>>>>> version';
>>>>>
>>>>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>>>>> is a cvterm. The meaning of the property is defined in that cvterm.';
>>>>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>>>>> represented as text. Numeric values are converted to their text
>>>>> representation.';
>>>>>
>>>>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>>>>> cv can have multiple values for any particular property type -
>>>>> these are ordered in a list using rank, counting from zero. For
>>>>> properties that are single-valued rather than multi-valued, the
>>>>> default 0 value should be used.';
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>>> dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>>> Billion" shares his insights and actions to help propel your
>>>>> business during the next growth cycle. Listen Now!
>>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>>> _______________________________________________
>>>>> Gmod-schema mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>> --
>>>> ===========================================================
>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>> Billion" shares his insights and actions to help propel your
>>> business during the next growth cycle. Listen Now!
>>> http://p.sf.net/sfu/SAP-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>> ------------------------------------------------------------------------------
>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>> David G. Thomson, author of the best-selling book "Blueprint to a
>> Billion" shares his insights and actions to help propel your
>> business during the next growth cycle. Listen Now!
>> http://p.sf.net/sfu/SAP-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>
wwwwwww

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Re: proposed cvprop table

Jonathan "Duke" Leto
Howdy,

Yes, I agree that a 'version' column is needed on the CV table. This
will even allow the
possibility in the future for storing multiple versions of a CV and
choosing between them.

Ontologies without version numbers are broken.

Duke

On Tue, Nov 16, 2010 at 10:15 AM, Robert Buels <[hidden email]> wrote:

> Actually, I'm going to go a step further and advocate a 'version' column
> being added to the cv table itself.
>
> Ontologies change, it's one of their main characteristics.  I cannot
> think of a situation in which an ontology *shouldn't* have a version
> number.  If an ontology is not versioned, I am inclined to think that is
> Wrong.
>
> Thoughts?
>
> Rob
>
> Scott Cain wrote:
>> Hi Daniel,
>>
>> What drove my interest in doing this is capturing version information
>> about the ontology.  If it's available, I want it.  Since the only
>> ontology loader I have handy is for obo files, I just opened a few obo
>> files to see what sort of metadata I could get.  The other piece of
>> metadata that would be nice to capture is members of slims so that
>> they could be reconstructed on the fly if needed (for example, by an
>> editing tool that wants to use a slim version of an ontology that is
>> loaded in Chado).
>>
>> Presumably, for a loader of OWL files, I would want it to map any
>> available metadata to available terms, and of course, if there is
>> other metadata not represented by the current cv_properties cv, terms
>> could be created for them as well.
>>
>> Scott
>>
>>
>> On Wed, Nov 10, 2010 at 3:31 PM, Daniel Quest <[hidden email]> wrote:
>>> Hi Scott,
>>>
>>> Thinking more globally, I make ontologies in OWL format directly.
>>> These ontologies do not require these fields... so I guess, if you
>>> load an OWL ontology directly then it may have different CVprops from
>>> a OBO ontology?  Is that what you are thinking?
>>>
>>> -Daniel
>>>
>>> On Wed, Nov 10, 2010 at 2:37 PM, Scott Cain <[hidden email]> wrote:
>>>> Hi Hilmar,
>>>>
>>>> I don't have a problem with a nullable value; do you have a specific
>>>> case in mind, or just planning ahead?
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:
>>>>> Looks great to me, except that value should be nullable.
>>>>>
>>>>>        -hilmar
>>>>>
>>>>> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> Below is the sql for a proposed cvprop table, for storing things like
>>>>>> remarks and versions for a cv.  It's a pretty straight forward prop
>>>>>> table, so I don't expect much in the way of objection, but if you do
>>>>>> object, now is the time to mention it.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>> -- ================================================
>>>>>> -- TABLE: cvprop
>>>>>> -- ================================================
>>>>>> create table cvprop (
>>>>>>   cvprop_id serial not null,
>>>>>>   primary key (cvprop_id),
>>>>>>   cv_id int not null,
>>>>>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>>>>>   type_id int not null,
>>>>>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>>>>>   value text not null default '',
>>>>>>   rank int not null default 0,
>>>>>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>>>>>> );
>>>>>>
>>>>>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>>>>>> attached to a cv using this table.  A notable example would be the cv
>>>>>> version';
>>>>>>
>>>>>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>>>>>> is a cvterm. The meaning of the property is defined in that cvterm.';
>>>>>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>>>>>> represented as text. Numeric values are converted to their text
>>>>>> representation.';
>>>>>>
>>>>>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>>>>>> cv can have multiple values for any particular property type -
>>>>>> these are ordered in a list using rank, counting from zero. For
>>>>>> properties that are single-valued rather than multi-valued, the
>>>>>> default 0 value should be used.';
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>>>> dot net
>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>> Ontario Institute for Cancer Research
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>>>> Billion" shares his insights and actions to help propel your
>>>>>> business during the next growth cycle. Listen Now!
>>>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>> --
>>>>> ===========================================================
>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>> ------------------------------------------------------------------------------
>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>> Billion" shares his insights and actions to help propel your
>>>> business during the next growth cycle. Listen Now!
>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>> ------------------------------------------------------------------------------
>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>> Billion" shares his insights and actions to help propel your
>>> business during the next growth cycle. Listen Now!
>>> http://p.sf.net/sfu/SAP-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>>
> wwwwwww
>
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Re: proposed cvprop table

Robert Buels
In reply to this post by Robert Buels
Erm, to be clear, I also support the cvprop table.

Rob



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Re: proposed cvprop table

Josh Goodman
In reply to this post by Jonathan "Duke" Leto
+1 to cv.version.

While this is obviously the more disruptive option I agree with the reasons below for adding it.  I
do still want to see a cvprop table.

Cheers,
Josh

On 11/16/2010 01:31 PM, Jonathan Leto wrote:

> Howdy,
>
> Yes, I agree that a 'version' column is needed on the CV table. This
> will even allow the
> possibility in the future for storing multiple versions of a CV and
> choosing between them.
>
> Ontologies without version numbers are broken.
>
> Duke
>
> On Tue, Nov 16, 2010 at 10:15 AM, Robert Buels <[hidden email]> wrote:
>> Actually, I'm going to go a step further and advocate a 'version' column
>> being added to the cv table itself.
>>
>> Ontologies change, it's one of their main characteristics.  I cannot
>> think of a situation in which an ontology *shouldn't* have a version
>> number.  If an ontology is not versioned, I am inclined to think that is
>> Wrong.
>>
>> Thoughts?
>>
>> Rob
>>
>> Scott Cain wrote:
>>> Hi Daniel,
>>>
>>> What drove my interest in doing this is capturing version information
>>> about the ontology.  If it's available, I want it.  Since the only
>>> ontology loader I have handy is for obo files, I just opened a few obo
>>> files to see what sort of metadata I could get.  The other piece of
>>> metadata that would be nice to capture is members of slims so that
>>> they could be reconstructed on the fly if needed (for example, by an
>>> editing tool that wants to use a slim version of an ontology that is
>>> loaded in Chado).
>>>
>>> Presumably, for a loader of OWL files, I would want it to map any
>>> available metadata to available terms, and of course, if there is
>>> other metadata not represented by the current cv_properties cv, terms
>>> could be created for them as well.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Nov 10, 2010 at 3:31 PM, Daniel Quest <[hidden email]> wrote:
>>>> Hi Scott,
>>>>
>>>> Thinking more globally, I make ontologies in OWL format directly.
>>>> These ontologies do not require these fields... so I guess, if you
>>>> load an OWL ontology directly then it may have different CVprops from
>>>> a OBO ontology?  Is that what you are thinking?
>>>>
>>>> -Daniel
>>>>
>>>> On Wed, Nov 10, 2010 at 2:37 PM, Scott Cain <[hidden email]> wrote:
>>>>> Hi Hilmar,
>>>>>
>>>>> I don't have a problem with a nullable value; do you have a specific
>>>>> case in mind, or just planning ahead?
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:
>>>>>> Looks great to me, except that value should be nullable.
>>>>>>
>>>>>>        -hilmar
>>>>>>
>>>>>> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> Below is the sql for a proposed cvprop table, for storing things like
>>>>>>> remarks and versions for a cv.  It's a pretty straight forward prop
>>>>>>> table, so I don't expect much in the way of objection, but if you do
>>>>>>> object, now is the time to mention it.
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>> -- ================================================
>>>>>>> -- TABLE: cvprop
>>>>>>> -- ================================================
>>>>>>> create table cvprop (
>>>>>>>   cvprop_id serial not null,
>>>>>>>   primary key (cvprop_id),
>>>>>>>   cv_id int not null,
>>>>>>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>>>>>>   type_id int not null,
>>>>>>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>>>>>>   value text not null default '',
>>>>>>>   rank int not null default 0,
>>>>>>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>>>>>>> );
>>>>>>>
>>>>>>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>>>>>>> attached to a cv using this table.  A notable example would be the cv
>>>>>>> version';
>>>>>>>
>>>>>>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>>>>>>> is a cvterm. The meaning of the property is defined in that cvterm.';
>>>>>>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>>>>>>> represented as text. Numeric values are converted to their text
>>>>>>> representation.';
>>>>>>>
>>>>>>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>>>>>>> cv can have multiple values for any particular property type -
>>>>>>> these are ordered in a list using rank, counting from zero. For
>>>>>>> properties that are single-valued rather than multi-valued, the
>>>>>>> default 0 value should be used.';
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>>>>> dot net
>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>>> Ontario Institute for Cancer Research
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>>>>> Billion" shares his insights and actions to help propel your
>>>>>>> business during the next growth cycle. Listen Now!
>>>>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>>>>> _______________________________________________
>>>>>>> Gmod-schema mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>> --
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>>> Billion" shares his insights and actions to help propel your
>>>>> business during the next growth cycle. Listen Now!
>>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>>> _______________________________________________
>>>>> Gmod-schema mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>
>>>> ------------------------------------------------------------------------------
>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>> Billion" shares his insights and actions to help propel your
>>>> business during the next growth cycle. Listen Now!
>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>>
>>>
>> wwwwwww
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and  rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today
>> http://p.sf.net/sfu/msIE9-sfdev2dev
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>>
>
>
>

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Re: proposed cvprop table

David Emmert
In reply to this post by Scott Cain
>> +1 to cv.version.
>>
>> While this is obviously the more disruptive option I agree with the reasons below for adding it.  I
>> do still want to see a cvprop table.

I'm kind of amazed we didn't spot this flaw sooner, but I agree with both additions.  
Will cv.version be not-null?  If so, I suggest adding a default -- maybe "0.0"?

Best,

-Dave

>From [hidden email]  Tue Nov 16 15:24:16 2010
>> To: [hidden email]
>> Subject: Re: [Gmod-schema] proposed cvprop table
>>
>> +1 to cv.version.
>>
>> While this is obviously the more disruptive option I agree with the reasons below for adding it.  I
>> do still want to see a cvprop table.
>>
>> Cheers,
>> Josh
>>
>> On 11/16/2010 01:31 PM, Jonathan Leto wrote:
>> > Howdy,
>> >
>> > Yes, I agree that a 'version' column is needed on the CV table. This
>> > will even allow the
>> > possibility in the future for storing multiple versions of a CV and
>> > choosing between them.
>> >
>> > Ontologies without version numbers are broken.
>> >
>> > Duke
>> >
>> > On Tue, Nov 16, 2010 at 10:15 AM, Robert Buels <[hidden email]> wrote:
>> >> Actually, I'm going to go a step further and advocate a 'version' column
>> >> being added to the cv table itself.
>> >>
>> >> Ontologies change, it's one of their main characteristics.  I cannot
>> >> think of a situation in which an ontology *shouldn't* have a version
>> >> number.  If an ontology is not versioned, I am inclined to think that is
>> >> Wrong.
>> >>
>> >> Thoughts?
>> >>
>> >> Rob
>> >>
>> >> Scott Cain wrote:
>> >>> Hi Daniel,
>> >>>
>> >>> What drove my interest in doing this is capturing version information
>> >>> about the ontology.  If it's available, I want it.  Since the only
>> >>> ontology loader I have handy is for obo files, I just opened a few obo
>> >>> files to see what sort of metadata I could get.  The other piece of
>> >>> metadata that would be nice to capture is members of slims so that
>> >>> they could be reconstructed on the fly if needed (for example, by an
>> >>> editing tool that wants to use a slim version of an ontology that is
>> >>> loaded in Chado).
>> >>>
>> >>> Presumably, for a loader of OWL files, I would want it to map any
>> >>> available metadata to available terms, and of course, if there is
>> >>> other metadata not represented by the current cv_properties cv, terms
>> >>> could be created for them as well.
>> >>>
>> >>> Scott
>> >>>
>> >>>
>> >>> On Wed, Nov 10, 2010 at 3:31 PM, Daniel Quest <[hidden email]> wrote:
>> >>>> Hi Scott,
>> >>>>
>> >>>> Thinking more globally, I make ontologies in OWL format directly.
>> >>>> These ontologies do not require these fields... so I guess, if you
>> >>>> load an OWL ontology directly then it may have different CVprops from
>> >>>> a OBO ontology?  Is that what you are thinking?
>> >>>>
>> >>>> -Daniel
>> >>>>
>> >>>> On Wed, Nov 10, 2010 at 2:37 PM, Scott Cain <[hidden email]> wrote:
>> >>>>> Hi Hilmar,
>> >>>>>
>> >>>>> I don't have a problem with a nullable value; do you have a specific
>> >>>>> case in mind, or just planning ahead?
>> >>>>>
>> >>>>> Scott
>> >>>>>
>> >>>>>
>> >>>>> On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:
>> >>>>>> Looks great to me, except that value should be nullable.
>> >>>>>>
>> >>>>>>        -hilmar
>> >>>>>>
>> >>>>>> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>> >>>>>>
>> >>>>>>> Hello,
>> >>>>>>>
>> >>>>>>> Below is the sql for a proposed cvprop table, for storing things like
>> >>>>>>> remarks and versions for a cv.  It's a pretty straight forward prop
>> >>>>>>> table, so I don't expect much in the way of objection, but if you do
>> >>>>>>> object, now is the time to mention it.
>> >>>>>>>
>> >>>>>>> Scott
>> >>>>>>>
>> >>>>>>> -- ================================================
>> >>>>>>> -- TABLE: cvprop
>> >>>>>>> -- ================================================
>> >>>>>>> create table cvprop (
>> >>>>>>>   cvprop_id serial not null,
>> >>>>>>>   primary key (cvprop_id),
>> >>>>>>>   cv_id int not null,
>> >>>>>>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>> >>>>>>>   type_id int not null,
>> >>>>>>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>> >>>>>>>   value text not null default '',
>> >>>>>>>   rank int not null default 0,
>> >>>>>>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>> >>>>>>> );
>> >>>>>>>
>> >>>>>>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>> >>>>>>> attached to a cv using this table.  A notable example would be the cv
>> >>>>>>> version';
>> >>>>>>>
>> >>>>>>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>> >>>>>>> is a cvterm. The meaning of the property is defined in that cvterm.';
>> >>>>>>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>> >>>>>>> represented as text. Numeric values are converted to their text
>> >>>>>>> representation.';
>> >>>>>>>
>> >>>>>>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>> >>>>>>> cv can have multiple values for any particular property type -
>> >>>>>>> these are ordered in a list using rank, counting from zero. For
>> >>>>>>> properties that are single-valued rather than multi-valued, the
>> >>>>>>> default 0 value should be used.';
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> --
>> >>>>>>> ------------------------------------------------------------------------
>> >>>>>>> Scott Cain, Ph. D.                                   scott at scottcain
>> >>>>>>> dot net
>> >>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >>>>>>> Ontario Institute for Cancer Research
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> ------------------------------------------------------------------------------
>> >>>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>> >>>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>> >>>>>>> Billion" shares his insights and actions to help propel your
>> >>>>>>> business during the next growth cycle. Listen Now!
>> >>>>>>> http://p.sf.net/sfu/SAP-dev2dev
>> >>>>>>> _______________________________________________
>> >>>>>>> Gmod-schema mailing list
>> >>>>>>> [hidden email]
>> >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>>> --
>> >>>>>> ===========================================================
>> >>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>> >>>>>> ===========================================================
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>>> ------------------------------------------------------------------------
>> >>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> >>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >>>>> Ontario Institute for Cancer Research
>> >>>>>
>> >>>>> ------------------------------------------------------------------------------
>> >>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>> >>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>> >>>>> Billion" shares his insights and actions to help propel your
>> >>>>> business during the next growth cycle. Listen Now!
>> >>>>> http://p.sf.net/sfu/SAP-dev2dev
>> >>>>> _______________________________________________
>> >>>>> Gmod-schema mailing list
>> >>>>> [hidden email]
>> >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>>
>> >>>> ------------------------------------------------------------------------------
>> >>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>> >>>> David G. Thomson, author of the best-selling book "Blueprint to a
>> >>>> Billion" shares his insights and actions to help propel your
>> >>>> business during the next growth cycle. Listen Now!
>> >>>> http://p.sf.net/sfu/SAP-dev2dev
>> >>>> _______________________________________________
>> >>>> Gmod-schema mailing list
>> >>>> [hidden email]
>> >>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>>
>> >>>
>> >>>
>> >>>
>> >> wwwwwww
>> >>
>> >> ------------------------------------------------------------------------------
>> >> Beautiful is writing same markup. Internet Explorer 9 supports
>> >> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>> >> Spend less time writing and  rewriting code and more time creating great
>> >> experiences on the web. Be a part of the beta today
>> >> http://p.sf.net/sfu/msIE9-sfdev2dev
>> >> _______________________________________________
>> >> Gmod-schema mailing list
>> >> [hidden email]
>> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>
>> >
>> >
>> >
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and  rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today
>> http://p.sf.net/sfu/msIE9-sfdev2dev
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>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>

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Re: proposed cvprop table

Scott Cain
Hi All,

I missed the tail end of the this conversation when I was traveling.
I agree that a version column in the cv term is not an unreasonable
addition.

What happens in the case where a obo file is loaded from a version
control system (which happens fairly often).  Where does the version
information come from (of course, this applies equally to a
"data-version" property in the cvprop table as well; I don't know the
solution for either case).  I don't really expect the authors of an
ontology to update the version in the file when a change is made to
file between releases.  Basically, what I'm getting at is that in many
cases, I don't think you'll be able to trust the version information,
regardless of where it is stored.  I suppose a nice thing for a loader
to do would be to also store the datetime that it was loaded, so that
if the version information is not reliable (if the file was loaded
from cvs), you could at least reason on whether the ontology is "old."

So, given this, I'm not sure that a version column in the cv table is
that necessary an improvement, given a cvprop table.

Thoughts?
Scott


On Tue, Nov 16, 2010 at 4:26 PM, David Emmert <[hidden email]> wrote:

>>> +1 to cv.version.
>>>
>>> While this is obviously the more disruptive option I agree with the reasons below for adding it.  I
>>> do still want to see a cvprop table.
>
> I'm kind of amazed we didn't spot this flaw sooner, but I agree with both additions.
> Will cv.version be not-null?  If so, I suggest adding a default -- maybe "0.0"?
>
> Best,
>
> -Dave
>
> >From [hidden email]  Tue Nov 16 15:24:16 2010
>>> To: [hidden email]
>>> Subject: Re: [Gmod-schema] proposed cvprop table
>>>
>>> +1 to cv.version.
>>>
>>> While this is obviously the more disruptive option I agree with the reasons below for adding it.  I
>>> do still want to see a cvprop table.
>>>
>>> Cheers,
>>> Josh
>>>
>>> On 11/16/2010 01:31 PM, Jonathan Leto wrote:
>>> > Howdy,
>>> >
>>> > Yes, I agree that a 'version' column is needed on the CV table. This
>>> > will even allow the
>>> > possibility in the future for storing multiple versions of a CV and
>>> > choosing between them.
>>> >
>>> > Ontologies without version numbers are broken.
>>> >
>>> > Duke
>>> >
>>> > On Tue, Nov 16, 2010 at 10:15 AM, Robert Buels <[hidden email]> wrote:
>>> >> Actually, I'm going to go a step further and advocate a 'version' column
>>> >> being added to the cv table itself.
>>> >>
>>> >> Ontologies change, it's one of their main characteristics.  I cannot
>>> >> think of a situation in which an ontology *shouldn't* have a version
>>> >> number.  If an ontology is not versioned, I am inclined to think that is
>>> >> Wrong.
>>> >>
>>> >> Thoughts?
>>> >>
>>> >> Rob
>>> >>
>>> >> Scott Cain wrote:
>>> >>> Hi Daniel,
>>> >>>
>>> >>> What drove my interest in doing this is capturing version information
>>> >>> about the ontology.  If it's available, I want it.  Since the only
>>> >>> ontology loader I have handy is for obo files, I just opened a few obo
>>> >>> files to see what sort of metadata I could get.  The other piece of
>>> >>> metadata that would be nice to capture is members of slims so that
>>> >>> they could be reconstructed on the fly if needed (for example, by an
>>> >>> editing tool that wants to use a slim version of an ontology that is
>>> >>> loaded in Chado).
>>> >>>
>>> >>> Presumably, for a loader of OWL files, I would want it to map any
>>> >>> available metadata to available terms, and of course, if there is
>>> >>> other metadata not represented by the current cv_properties cv, terms
>>> >>> could be created for them as well.
>>> >>>
>>> >>> Scott
>>> >>>
>>> >>>
>>> >>> On Wed, Nov 10, 2010 at 3:31 PM, Daniel Quest <[hidden email]> wrote:
>>> >>>> Hi Scott,
>>> >>>>
>>> >>>> Thinking more globally, I make ontologies in OWL format directly.
>>> >>>> These ontologies do not require these fields... so I guess, if you
>>> >>>> load an OWL ontology directly then it may have different CVprops from
>>> >>>> a OBO ontology?  Is that what you are thinking?
>>> >>>>
>>> >>>> -Daniel
>>> >>>>
>>> >>>> On Wed, Nov 10, 2010 at 2:37 PM, Scott Cain <[hidden email]> wrote:
>>> >>>>> Hi Hilmar,
>>> >>>>>
>>> >>>>> I don't have a problem with a nullable value; do you have a specific
>>> >>>>> case in mind, or just planning ahead?
>>> >>>>>
>>> >>>>> Scott
>>> >>>>>
>>> >>>>>
>>> >>>>> On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:
>>> >>>>>> Looks great to me, except that value should be nullable.
>>> >>>>>>
>>> >>>>>>        -hilmar
>>> >>>>>>
>>> >>>>>> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>>> >>>>>>
>>> >>>>>>> Hello,
>>> >>>>>>>
>>> >>>>>>> Below is the sql for a proposed cvprop table, for storing things like
>>> >>>>>>> remarks and versions for a cv.  It's a pretty straight forward prop
>>> >>>>>>> table, so I don't expect much in the way of objection, but if you do
>>> >>>>>>> object, now is the time to mention it.
>>> >>>>>>>
>>> >>>>>>> Scott
>>> >>>>>>>
>>> >>>>>>> -- ================================================
>>> >>>>>>> -- TABLE: cvprop
>>> >>>>>>> -- ================================================
>>> >>>>>>> create table cvprop (
>>> >>>>>>>   cvprop_id serial not null,
>>> >>>>>>>   primary key (cvprop_id),
>>> >>>>>>>   cv_id int not null,
>>> >>>>>>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>> >>>>>>>   type_id int not null,
>>> >>>>>>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>> >>>>>>>   value text not null default '',
>>> >>>>>>>   rank int not null default 0,
>>> >>>>>>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>>> >>>>>>> );
>>> >>>>>>>
>>> >>>>>>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>>> >>>>>>> attached to a cv using this table.  A notable example would be the cv
>>> >>>>>>> version';
>>> >>>>>>>
>>> >>>>>>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>>> >>>>>>> is a cvterm. The meaning of the property is defined in that cvterm.';
>>> >>>>>>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>>> >>>>>>> represented as text. Numeric values are converted to their text
>>> >>>>>>> representation.';
>>> >>>>>>>
>>> >>>>>>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>>> >>>>>>> cv can have multiple values for any particular property type -
>>> >>>>>>> these are ordered in a list using rank, counting from zero. For
>>> >>>>>>> properties that are single-valued rather than multi-valued, the
>>> >>>>>>> default 0 value should be used.';
>>> >>>>>>>
>>> >>>>>>>
>>> >>>>>>> --
>>> >>>>>>> ------------------------------------------------------------------------
>>> >>>>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> >>>>>>> dot net
>>> >>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> >>>>>>> Ontario Institute for Cancer Research
>>> >>>>>>>
>>> >>>>>>>
>>> >>>>>>> ------------------------------------------------------------------------------
>>> >>>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>> >>>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>> >>>>>>> Billion" shares his insights and actions to help propel your
>>> >>>>>>> business during the next growth cycle. Listen Now!
>>> >>>>>>> http://p.sf.net/sfu/SAP-dev2dev
>>> >>>>>>> _______________________________________________
>>> >>>>>>> Gmod-schema mailing list
>>> >>>>>>> [hidden email]
>>> >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >>>>>> --
>>> >>>>>> ===========================================================
>>> >>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>> >>>>>> ===========================================================
>>> >>>>>>
>>> >>>>>>
>>> >>>>>>
>>> >>>>>>
>>> >>>>>>
>>> >>>>>
>>> >>>>>
>>> >>>>> --
>>> >>>>> ------------------------------------------------------------------------
>>> >>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> >>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> >>>>> Ontario Institute for Cancer Research
>>> >>>>>
>>> >>>>> ------------------------------------------------------------------------------
>>> >>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>> >>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>> >>>>> Billion" shares his insights and actions to help propel your
>>> >>>>> business during the next growth cycle. Listen Now!
>>> >>>>> http://p.sf.net/sfu/SAP-dev2dev
>>> >>>>> _______________________________________________
>>> >>>>> Gmod-schema mailing list
>>> >>>>> [hidden email]
>>> >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >>>>>
>>> >>>> ------------------------------------------------------------------------------
>>> >>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>> >>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>> >>>> Billion" shares his insights and actions to help propel your
>>> >>>> business during the next growth cycle. Listen Now!
>>> >>>> http://p.sf.net/sfu/SAP-dev2dev
>>> >>>> _______________________________________________
>>> >>>> Gmod-schema mailing list
>>> >>>> [hidden email]
>>> >>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >>>>
>>> >>>
>>> >>>
>>> >>>
>>> >> wwwwwww
>>> >>
>>> >> ------------------------------------------------------------------------------
>>> >> Beautiful is writing same markup. Internet Explorer 9 supports
>>> >> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>>> >> Spend less time writing and  rewriting code and more time creating great
>>> >> experiences on the web. Be a part of the beta today
>>> >> http://p.sf.net/sfu/msIE9-sfdev2dev
>>> >> _______________________________________________
>>> >> Gmod-schema mailing list
>>> >> [hidden email]
>>> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >>
>>> >
>>> >
>>> >
>>>
>>> ------------------------------------------------------------------------------
>>> Beautiful is writing same markup. Internet Explorer 9 supports
>>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>>> Spend less time writing and  rewriting code and more time creating great
>>> experiences on the web. Be a part of the beta today
>>> http://p.sf.net/sfu/msIE9-sfdev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev
> _______________________________________________
> 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

------------------------------------------------------------------------------
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Re: proposed cvprop table

Chris Mungall

If someone provides a "data-version" tag then they are making a promise to you that this uniquely identifiers the version, so you should trust it as much as you trust everything else in the ontology.

Most ontologies don't have a data-version tag for the reasons you mention below. The solution is to split between an editors version and a release version (this is how GO manages the data-version tag). The release version is made automatically from the editors version at whatever frequency the ontology producers feel comfortable with, and the data-version tag is inserted at this time. This is analogous to managing source code in a source repository, and daily builds.

On Nov 30, 2010, at 12:55 PM, Scott Cain wrote:

> Hi All,
>
> I missed the tail end of the this conversation when I was traveling.
> I agree that a version column in the cv term is not an unreasonable
> addition.
>
> What happens in the case where a obo file is loaded from a version
> control system (which happens fairly often).  Where does the version
> information come from (of course, this applies equally to a
> "data-version" property in the cvprop table as well; I don't know the
> solution for either case).  I don't really expect the authors of an
> ontology to update the version in the file when a change is made to
> file between releases.  Basically, what I'm getting at is that in many
> cases, I don't think you'll be able to trust the version information,
> regardless of where it is stored.  I suppose a nice thing for a loader
> to do would be to also store the datetime that it was loaded, so that
> if the version information is not reliable (if the file was loaded
> from cvs), you could at least reason on whether the ontology is "old."
>
> So, given this, I'm not sure that a version column in the cv table is
> that necessary an improvement, given a cvprop table.
>
> Thoughts?
> Scott
>
>
> On Tue, Nov 16, 2010 at 4:26 PM, David Emmert <[hidden email]> wrote:
>>>> +1 to cv.version.
>>>>
>>>> While this is obviously the more disruptive option I agree with the reasons below for adding it.  I
>>>> do still want to see a cvprop table.
>>
>> I'm kind of amazed we didn't spot this flaw sooner, but I agree with both additions.
>> Will cv.version be not-null?  If so, I suggest adding a default -- maybe "0.0"?
>>
>> Best,
>>
>> -Dave
>>
>>> From [hidden email]  Tue Nov 16 15:24:16 2010
>>>> To: [hidden email]
>>>> Subject: Re: [Gmod-schema] proposed cvprop table
>>>>
>>>> +1 to cv.version.
>>>>
>>>> While this is obviously the more disruptive option I agree with the reasons below for adding it.  I
>>>> do still want to see a cvprop table.
>>>>
>>>> Cheers,
>>>> Josh
>>>>
>>>> On 11/16/2010 01:31 PM, Jonathan Leto wrote:
>>>>> Howdy,
>>>>>
>>>>> Yes, I agree that a 'version' column is needed on the CV table. This
>>>>> will even allow the
>>>>> possibility in the future for storing multiple versions of a CV and
>>>>> choosing between them.
>>>>>
>>>>> Ontologies without version numbers are broken.
>>>>>
>>>>> Duke
>>>>>
>>>>> On Tue, Nov 16, 2010 at 10:15 AM, Robert Buels <[hidden email]> wrote:
>>>>>> Actually, I'm going to go a step further and advocate a 'version' column
>>>>>> being added to the cv table itself.
>>>>>>
>>>>>> Ontologies change, it's one of their main characteristics.  I cannot
>>>>>> think of a situation in which an ontology *shouldn't* have a version
>>>>>> number.  If an ontology is not versioned, I am inclined to think that is
>>>>>> Wrong.
>>>>>>
>>>>>> Thoughts?
>>>>>>
>>>>>> Rob
>>>>>>
>>>>>> Scott Cain wrote:
>>>>>>> Hi Daniel,
>>>>>>>
>>>>>>> What drove my interest in doing this is capturing version information
>>>>>>> about the ontology.  If it's available, I want it.  Since the only
>>>>>>> ontology loader I have handy is for obo files, I just opened a few obo
>>>>>>> files to see what sort of metadata I could get.  The other piece of
>>>>>>> metadata that would be nice to capture is members of slims so that
>>>>>>> they could be reconstructed on the fly if needed (for example, by an
>>>>>>> editing tool that wants to use a slim version of an ontology that is
>>>>>>> loaded in Chado).
>>>>>>>
>>>>>>> Presumably, for a loader of OWL files, I would want it to map any
>>>>>>> available metadata to available terms, and of course, if there is
>>>>>>> other metadata not represented by the current cv_properties cv, terms
>>>>>>> could be created for them as well.
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Nov 10, 2010 at 3:31 PM, Daniel Quest <[hidden email]> wrote:
>>>>>>>> Hi Scott,
>>>>>>>>
>>>>>>>> Thinking more globally, I make ontologies in OWL format directly.
>>>>>>>> These ontologies do not require these fields... so I guess, if you
>>>>>>>> load an OWL ontology directly then it may have different CVprops from
>>>>>>>> a OBO ontology?  Is that what you are thinking?
>>>>>>>>
>>>>>>>> -Daniel
>>>>>>>>
>>>>>>>> On Wed, Nov 10, 2010 at 2:37 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>> Hi Hilmar,
>>>>>>>>>
>>>>>>>>> I don't have a problem with a nullable value; do you have a specific
>>>>>>>>> case in mind, or just planning ahead?
>>>>>>>>>
>>>>>>>>> Scott
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Nov 10, 2010 at 2:24 PM, Hilmar Lapp <[hidden email]> wrote:
>>>>>>>>>> Looks great to me, except that value should be nullable.
>>>>>>>>>>
>>>>>>>>>>        -hilmar
>>>>>>>>>>
>>>>>>>>>> On Nov 9, 2010, at 3:59 PM, Scott Cain wrote:
>>>>>>>>>>
>>>>>>>>>>> Hello,
>>>>>>>>>>>
>>>>>>>>>>> Below is the sql for a proposed cvprop table, for storing things like
>>>>>>>>>>> remarks and versions for a cv.  It's a pretty straight forward prop
>>>>>>>>>>> table, so I don't expect much in the way of objection, but if you do
>>>>>>>>>>> object, now is the time to mention it.
>>>>>>>>>>>
>>>>>>>>>>> Scott
>>>>>>>>>>>
>>>>>>>>>>> -- ================================================
>>>>>>>>>>> -- TABLE: cvprop
>>>>>>>>>>> -- ================================================
>>>>>>>>>>> create table cvprop (
>>>>>>>>>>>   cvprop_id serial not null,
>>>>>>>>>>>   primary key (cvprop_id),
>>>>>>>>>>>   cv_id int not null,
>>>>>>>>>>>   foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
>>>>>>>>>>>   type_id int not null,
>>>>>>>>>>>   foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
>>>>>>>>>>>   value text not null default '',
>>>>>>>>>>>   rank int not null default 0,
>>>>>>>>>>>   constraint cvprop_c1 unique (cv_id,type_id,rank)
>>>>>>>>>>> );
>>>>>>>>>>>
>>>>>>>>>>> COMMENT ON TABLE cvprop IS 'Additional extensible properties can be
>>>>>>>>>>> attached to a cv using this table.  A notable example would be the cv
>>>>>>>>>>> version';
>>>>>>>>>>>
>>>>>>>>>>> COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot
>>>>>>>>>>> is a cvterm. The meaning of the property is defined in that cvterm.';
>>>>>>>>>>> COMMENT ON COLUMN cvprop.value IS 'The value of the property,
>>>>>>>>>>> represented as text. Numeric values are converted to their text
>>>>>>>>>>> representation.';
>>>>>>>>>>>
>>>>>>>>>>> COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
>>>>>>>>>>> cv can have multiple values for any particular property type -
>>>>>>>>>>> these are ordered in a list using rank, counting from zero. For
>>>>>>>>>>> properties that are single-valued rather than multi-valued, the
>>>>>>>>>>> default 0 value should be used.';
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>>>>>>>>> dot net
>>>>>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>>>>>>> Ontario Institute for Cancer Research
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>>>>>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>>>>>>>>> Billion" shares his insights and actions to help propel your
>>>>>>>>>>> business during the next growth cycle. Listen Now!
>>>>>>>>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Gmod-schema mailing list
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>> --
>>>>>>>>>> ===========================================================
>>>>>>>>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
>>>>>>>>>> ===========================================================
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>>>>> Ontario Institute for Cancer Research
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>>>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>>>>>>> Billion" shares his insights and actions to help propel your
>>>>>>>>> business during the next growth cycle. Listen Now!
>>>>>>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>>>>>>> _______________________________________________
>>>>>>>>> Gmod-schema mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>>>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>>>>>> Billion" shares his insights and actions to help propel your
>>>>>>>> business during the next growth cycle. Listen Now!
>>>>>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-schema mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> wwwwwww
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Beautiful is writing same markup. Internet Explorer 9 supports
>>>>>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>>>>>> Spend less time writing and  rewriting code and more time creating great
>>>>>> experiences on the web. Be a part of the beta today
>>>>>> http://p.sf.net/sfu/msIE9-sfdev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Beautiful is writing same markup. Internet Explorer 9 supports
>>>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>>>> Spend less time writing and  rewriting code and more time creating great
>>>> experiences on the web. Be a part of the beta today
>>>> http://p.sf.net/sfu/msIE9-sfdev2dev
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and  rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today
>> http://p.sf.net/sfu/msIE9-sfdev2dev
>> _______________________________________________
>> 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
>
> ------------------------------------------------------------------------------
> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> Tap into the largest installed PC base & get more eyes on your game by
> optimizing for Intel(R) Graphics Technology. Get started today with the
> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> http://p.sf.net/sfu/intelisp-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
http://p.sf.net/sfu/intelisp-dev2dev
_______________________________________________
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