gmod-schema Mailing List for Generic Model Organism Database Project

On Jun 30, 2006, at 6:23 AM, Hilmar Lapp wrote:
> Wasn't phylonode meant for this?
The phylogeny module, yep
>
> Also - concatenating this into species leads to hairy issues for
> searching if you do not have the species (and genus etc) linked
> through the taxonomic tree.
>
> Just random thoughts ...
>
> On Jun 30, 2006, at 9:12 AM, Jay Sundaram wrote:
>
>> I meant- we store the concatenated values in *organism.species*.
>>
>> Also, how can we represent the relationships among organisms in chado
>> (e.g. 'subspecies_of', 'strain_of')?
>> Is this currently possible?
>> Has anyone submitted a proposal for table: organism_relationship?
>> The table definition might be:
>>
>> CREATE TABLE organism_relationship (
>> organism_relationship_id NUMERIC(9,0) NOT NULL,
>> subject_id NUMERIC(9,0) NOT NULL,
>> object_id NUMERIC(9,0) NOT NULL,
>> type_id NUMERIC(9,0) NOT NULL,
>> );
>>
>>
>> With constraints:
>>
>> ALTER TABLE organism_relationship ADD CONSTRAINT
>> fk_organism_relationship01 FOREIGN KEY (subject_id) REFERENCES
>> organism(organism_id)
>> ALTER TABLE organism_relationship ADD CONSTRAINT
>> fk_organism_relationship02 FOREIGN KEY (subject_id) REFERENCES
>> organism(organism_id)
>> ALTER TABLE organism_relationship ADD CONSTRAINT
>> fk_organism_relationship03 FOREIGN KEY (subject_id) REFERENCES
>> cvterm(cvterm_id)
>> CREATE UNIQUE NONCLUSTERED INDEX uc1_organism_relationship ON
>> organism_relationship (subject_id, object_id, type_id)
>>
>>
>>
>>
>>
>> Jay Sundaram wrote:
>>
>>> Chris, Scott, Dave,
>>>
>>> What are your thoughts on introducing a new column:
>>> organism.strain and extending the uniqueness constraint to cover
>>> genus, species, strain.
>>> The addition would be backwards compatible and has the benefit of
>>> allowing us to store various strains in chado.
>>> Our current hack is to store the concatenated species and strain
>>> values in organism.strain.
>>>
>>> -Jay
>>>
>>>
>>> Using Tomcat but need to do more? Need to support web services,
>>> security?
>>> Get stuff done quickly with pre-integrated technology to make your
>>> job easier
>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache
>>> Geronimo
>>> http://sel.as-us.falkag.net/sel?
>>> cmd=lnk&kid=120709&bid=263057&dat=121642
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>
>>>
>>
>>
>> Using Tomcat but need to do more? Need to support web services,
>> security?
>> Get stuff done quickly with pre-integrated technology to make your
>> job easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache
>> Geronimo
>> http://sel.as-us.falkag.net/sel?
>> cmd=lnk&kid=120709&bid=263057&dat=121642
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
>
> Using Tomcat but need to do more? Need to support web services, 
> security?
> Get stuff done quickly with pre-integrated technology to make your 
> job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
> Geronimo
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

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Wasn't phylonode meant for this?
Also - concatenating this into species leads to hairy issues for 
searching if you do not have the species (and genus etc) linked 
through the taxonomic tree.
Just random thoughts ...
On Jun 30, 2006, at 9:12 AM, Jay Sundaram wrote:
> I meant- we store the concatenated values in *organism.species*.
>
> Also, how can we represent the relationships among organisms in chado
> (e.g. 'subspecies_of', 'strain_of')?
> Is this currently possible?
> Has anyone submitted a proposal for table: organism_relationship?
> The table definition might be:
>
> CREATE TABLE organism_relationship (
> organism_relationship_id NUMERIC(9,0) NOT NULL,
> subject_id NUMERIC(9,0) NOT NULL,
> object_id NUMERIC(9,0) NOT NULL,
> type_id NUMERIC(9,0) NOT NULL,
> );
>
>
> With constraints:
>
> ALTER TABLE organism_relationship ADD CONSTRAINT 
> fk_organism_relationship01 FOREIGN KEY (subject_id) REFERENCES 
> organism(organism_id)
> ALTER TABLE organism_relationship ADD CONSTRAINT 
> fk_organism_relationship02 FOREIGN KEY (subject_id) REFERENCES 
> organism(organism_id)
> ALTER TABLE organism_relationship ADD CONSTRAINT 
> fk_organism_relationship03 FOREIGN KEY (subject_id) REFERENCES 
> cvterm(cvterm_id)
> CREATE UNIQUE NONCLUSTERED INDEX uc1_organism_relationship ON 
> organism_relationship (subject_id, object_id, type_id)
>
>
>
>
>
> Jay Sundaram wrote:
>
>> Chris, Scott, Dave,
>>
>> What are your thoughts on introducing a new column: 
>> organism.strain and extending the uniqueness constraint to cover 
>> genus, species, strain.
>> The addition would be backwards compatible and has the benefit of 
>> allowing us to store various strains in chado.
>> Our current hack is to store the concatenated species and strain 
>> values in organism.strain.
>>
>> -Jay
>>
>>
>> Using Tomcat but need to do more? Need to support web services, 
>> security?
>> Get stuff done quickly with pre-integrated technology to make your 
>> job easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
>> Geronimo
>> http://sel.as-us.falkag.net/sel? 
>> cmd=lnk&kid=120709&bid=263057&dat=121642
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>>
>
>
> Using Tomcat but need to do more? Need to support web services, 
> security?
> Get stuff done quickly with pre-integrated technology to make your 
> job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
> Geronimo
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================

I meant- we store the concatenated values in *organism.species*.
Also, how can we represent the relationships among organisms in chado 
(e.g. 'subspecies_of', 'strain_of')?
Is this currently possible?
Has anyone submitted a proposal for table: organism_relationship?
The table definition might be:
CREATE TABLE organism_relationship (
 organism_relationship_id NUMERIC(9,0) NOT NULL,
 subject_id NUMERIC(9,0) NOT NULL,
 object_id NUMERIC(9,0) NOT NULL,
 type_id NUMERIC(9,0) NOT NULL,
);
With constraints:
ALTER TABLE organism_relationship ADD CONSTRAINT fk_organism_relationship01 FOREIGN KEY (subject_id) REFERENCES organism(organism_id)
ALTER TABLE organism_relationship ADD CONSTRAINT fk_organism_relationship02 FOREIGN KEY (subject_id) REFERENCES organism(organism_id)
ALTER TABLE organism_relationship ADD CONSTRAINT fk_organism_relationship03 FOREIGN KEY (subject_id) REFERENCES cvterm(cvterm_id)
CREATE UNIQUE NONCLUSTERED INDEX uc1_organism_relationship ON organism_relationship (subject_id, object_id, type_id)
Jay Sundaram wrote:
>Chris, Scott, Dave,
>
>What are your thoughts on introducing a new column: organism.strain and extending the uniqueness constraint to cover genus, species, strain. 
>The addition would be backwards compatible and has the benefit of allowing us to store various strains in chado. 
>Our current hack is to store the concatenated species and strain values in organism.strain.
>
>-Jay
>
>
>Using Tomcat but need to do more? Need to support web services, security?
>Get stuff done quickly with pre-integrated technology to make your job easier
>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>_______________________________________________
>Gmod-schema mailing list
>Gmo...@li...
>https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> 
>

In using Chado for production annotation we need to utilize the =
Companalysis module to store evidence such as blast data. A problem =
with our previous schema was that we had no way to differentiate between =
a search that hadn't been performed and one that was performed but =
returned no results. This is made much easier with the addition of the =
type_id column to analysisfeature. We store each feature that is part =
of an analysis and use type_id to indicate whether a feature is =
'input_of' or 'computed_by' the particular analysis (with those terms =
added in an ontology). This addition allows us to link a transcript, =
for example, through the analysisfeature table to see that some analysis =
had been performed. This was previously not possible (or easy) if the =
analysis returned no results.
It seems this would be a backwards-compatible addition. What does =
everyone think?
Joshua

Chris, Scott, Dave,
What are your thoughts on introducing a new column: organism.strain and extending the uniqueness constraint to cover genus, species, strain. 
The addition would be backwards compatible and has the benefit of allowing us to store various strains in chado. 
Our current hack is to store the concatenated species and strain values in organism.strain.
-Jay

Hi Rob,
The GFF bulk loader doesn't have update capabilities. The only way I
can think of to do this is to use Bio::SeqIO::chadoxml and then use XORT
to load, because I believe XORT will then do an update on existing
features.
The problem with this is that Bio::FeatureIO::gff, which knows how to
parse GFF3 files well produces Bio::SeqFeature::Annotated objects, but
Bio::SeqIO::chadoxml knows how to write Bio::Seq objects (specifically,
it expects to get Bio::Seq objects that look like they came from
GenBank).
What I would like to see done would be to modify Bio::SeqIO::chadoxml to
understand what to do with a Bio::SeqFeature, but even if that were in
place, it may be very difficult to do anyway, because the original load
using the GFF bulk loader may have generated uniquenames for the
features with no ID (or for features with an ID for which that
uniquename was already used in the database), and so, generating proper
chadoxml to do an update might be very tricky.
What I have done in the past is to figure out what features I want to
change in the database (that is, those for which I have updated GFF3),
and delete them by query. Chado has logic as part of the schema to do
very clean deletes of features: when you delete a feature, chado knows
to delete featureloc, feature_dbxrefs, etc that belong to the feature
being deleted, so it leaves the database in a pretty clean state. Then
I use the GFF3 bulk loader to reload.
Scott
On Wed, 2006年06月21日 at 17:51 -0600, Robert Buels wrote:=20
> Hi all,
>=20
> gmod_bulk_load_gff3.pl does a pretty nice job of loading gff3. Does it=20
> (or another script) have any provision for _updating_ the database, like=20
> adding only the rows that aren't already there, changing rows that have=20
> the same name but have changed locations, etc?
>=20
> Rob
>=20
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Hi Cyril,
I think that is a great idea; that is much better (at least from
inspection--I haven't actually tried it yet but I'm going to on my test
db, which is getting pretty big at ~6M rows in feature). Since it
doesn't change the api for feature_slice(int, int, int) putting it in
cvs shouldn't cause any problems, so go for it.
Thanks,
Scott
On Wed, 2006年06月21日 at 16:13 +0200, Cyril Pommier wrote:
> Hello Scott,
> I would like to propose you another optimisation of chado, and more=20
> precisely of featureloc_slice. I have tested it, and I think it is a=20
> real improvement.
> The better thing is that you don't have a cache effect, ie the first=20
> visit to a segment isn't significally slower than the second one.
>=20
> The idea is to include the information of the srcfeature directly inside=20
> the RTree index, rather than filtering the results returned by=20
> featureslice. The function featureloc_slice partially adresses this need=20
> by taking the srcfeature_id as parameter, but my proposal goes a step=20
> further (see the attached file for more details).
>=20
> Here is a good example of what you get when querying in chado (~3=20
> millions features):
>=20
> chadots2=3D> select count (*) from featureloc_slice_test(255041,10000,1=
10000);=20
> count=20
> -------
> 1072
> (1 row)=20
>=20
> Time: 21,906 ms
>=20
> chadots2=3D> select count (*) from featureloc_slice(255041,10000,110000=
);
> count=20
> -------
> 1072
> (1 row)
>=20
> Time: 5337,208 ms
>=20
> chadots2=3D> select count (*) from featureloc_slice(255041,10000,110000=
);
> count=20
> -------
> 1072
> (1 row)
>=20
> Time: 547,620 ms
>=20
>=20
> I have attached the source for this function.
>=20
> What do you think of this? As usual, feel free to forward this to the=20
> list if you want.
> If you are interressed, I could commit it to=20
> /chado/modules/sequence/range.plpgsql.
>=20
> Regards
>=20
> Cyril
>=20
> plain text document attachment (indexes.sql)
> --Evolution of the methods found in range.plpgsql
> --Goal : increase performances of segment fetching
> -- Implies to optimise featureloc_slice
>=20
> --Background : The existing featureloc_slice uses uses a spatial rtree in=
dex. The spatial objects used are a boxrange ((0,fmin), (fmax,500000000)) a=
nd a boxquery ((fmin,fmax),(fmin,fmax)) . The boxranges are indexed.=20
> -- To speed up things (for gbrowse) featureloc_slice has been=
 overiden to filter simultaneously on the boxrange and the srcfeature_id. T=
his gives good results.
> -- The goal here is to push this logic further and to include=
 the srcfeature_id filter directly into the boxrange object. We propose to =
consider the following boxs :=20
> -- boxrange : ((srcfeature_id,fmin),(srcfeature_id,fmax))
> -- boxquery : ((srcfeature_id,fmin),(srcfeature_id,fmax))
>=20
> --featureslice keep its signature, but its implementation is modified.
>=20
>=20
> -- create a point
> CREATE OR REPLACE FUNCTION create_point (int, int) RETURNS point AS
> 'SELECT point (1,ドル 2ドル)'
> LANGUAGE 'sql';
>=20
> CREATE OR REPLACE FUNCTION boxrange (int, int, int) RETURNS box AS
> 'SELECT box (create_point(1,ドル 2ドル), create_point(1,ドル3ドル))'
> LANGUAGE 'sql' IMMUTABLE;
>=20
> -- create a query box
> CREATE OR REPLACE FUNCTION boxquery (int, int, int) RETURNS box AS
> 'SELECT box (create_point(1,ドル 2ドル), create_point(1,ドル 3ドル))'
> LANGUAGE 'sql' IMMUTABLE;
>=20
> CREATE INDEX binloc_boxrange_src ON featureloc USING RTREE (boxrange(srcf=
eature_id,fmin, fmax));
>=20
> CREATE OR REPLACE FUNCTION featureloc_slice_test(int, int, int)
> RETURNS setof featureloc AS
> 'SELECT *=20
> FROM featureloc=20
> WHERE boxquery(1,ドル 2,ドル 3ドル) && boxrange(srcfeature_id,fmin,fmax)' =20
> LANGUAGE 'sql';
>=20
>=20
> --test queries
> select count (*) from featureloc where boxquery(255041,0,10000) && boxran=
ge(srcfeature_id,fmin,fmax);
>=20
> select count (*) from featureloc_slice_test(255041,0,10000)
>=20
> select count (*) from featureloc_slice(255041,0,10000)
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

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Hi all,
gmod_bulk_load_gff3.pl does a pretty nice job of loading gff3. Does it 
(or another script) have any provision for _updating_ the database, like 
adding only the rows that aren't already there, changing rows that have 
the same name but have changed locations, etc?
Rob
-- 
Robert Buels
SGN Bioinformatics Analyst
252A Emerson Hall, Cornell University
Ithaca, NY 14853
Tel: 503-889-8539
rm...@co...
http://www.sgn.cornell.edu

On Jun 21, 2006, at 4:43 PM, chris mungall wrote:
>> Right, this is what I had in mind of course. The namespace for this
>> triple should may be neither the anatomical ontology nor the
>> taxonomical ontology though, or at the very minimum it can't be
>> both (and then what is the default in implied semantics if they are
>> not explicit?).
>
> It makes no difference to the semantics of the statement of course
No it doesn't. Except if the relationship type existed in multiple 
namespaces but with different (or even conflicting) definitions. This 
would not be a desirable situation to begin with though I guess.
>
> Are you concerned because you may wish to, for instance, drop all
> cvterm_relationships that came from source X and reload them? This is
> really the main use of attaching a namespace to the triple - 
> provenance
Yes, indeed - basically identifiability and provenance. The namespace 
also, whether stated or not, implies an authority.
>
> OK, how about this: the default obo-namespace (cv_id) is always the
> cv_id of the subject_id
>
I'm all for making this explicit... :-)
	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================

On Jun 21, 2006, at 1:07 PM, Hilmar Lapp wrote:
>
> On Jun 21, 2006, at 3:08 PM, chris mungall wrote:
>
>>>
>>>> [...]
>>>>
>>>> Out of interest, do you need this for a particular ontology? None
>>>> of the existing obo ontologies use this feature so far.
>>>
>>> I used this quite a bit actually back at GNF for the Symgene/
>>> SymAtlas project. The XSPAN project seems to be doing this for
>>> mapping anatomy terms across species, and it may be relevant to us
>>> when we constrain anatomy terms by taxon that it applies to (using
>>> a taxon ontology).
>>
>> You shouldn't use the namespace mechanism to do this. This should be
>> done with links between terms using well-defined relations; eg
>>
>> placenta in_organism placental_mammal
>>
>
> Right, this is what I had in mind of course. The namespace for this 
> triple should may be neither the anatomical ontology nor the 
> taxonomical ontology though, or at the very minimum it can't be 
> both (and then what is the default in implied semantics if they are 
> not explicit?).
It makes no difference to the semantics of the statement of course
Are you concerned because you may wish to, for instance, drop all 
cvterm_relationships that came from source X and reload them? This is 
really the main use of attaching a namespace to the triple - provenance
OK, how about this: the default obo-namespace (cv_id) is always the 
cv_id of the subject_id
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>

On Jun 21, 2006, at 3:08 PM, chris mungall wrote:
>>
>>> [...]
>>>
>>> Out of interest, do you need this for a particular ontology? None
>>> of the existing obo ontologies use this feature so far.
>>
>> I used this quite a bit actually back at GNF for the Symgene/
>> SymAtlas project. The XSPAN project seems to be doing this for
>> mapping anatomy terms across species, and it may be relevant to us
>> when we constrain anatomy terms by taxon that it applies to (using
>> a taxon ontology).
>
> You shouldn't use the namespace mechanism to do this. This should be
> done with links between terms using well-defined relations; eg
>
> placenta in_organism placental_mammal
>
Right, this is what I had in mind of course. The namespace for this 
triple should may be neither the anatomical ontology nor the 
taxonomical ontology though, or at the very minimum it can't be both 
(and then what is the default in implied semantics if they are not 
explicit?).
	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================

On Jun 21, 2006, at 11:54 AM, Hilmar Lapp wrote:
>
> On Jun 21, 2006, at 12:26 PM, chris mungall wrote:
>
>>
>> On Jun 19, 2006, at 5:23 AM, Hilmar Lapp wrote:
>>
>>> Hi,
>>>
>>> is the ERD for the cv module at http://www.gmod.org/node/16 up-to-
>>> date? I believe so after looking at a schema checkout.
>>>
>>> I notice that first, relationships do not reference a cv (or
>>> namespace), although this would be very useful (especially if 
>>> subject
>>> and object aren't from the same ontology), and is indeed - unless 
>>> I'm
>>> mistaken - supported by the obo format (at least v1.2, no?).
>>
>>
>> it is indeed now supported. this should perhaps be added for 
>> compatibility with the latest version of the obo format. It should 
>> be nullable for backwards compatibility. If there's no objections 
>> after two weeks, you can add this.
>
> I'm not sure nullable is eventually what you want. If I recall the 
> obo spec correctly then not providing a namespace for the 
> relationship does not mean that there isn't one, basically you are 
> choosing the default namespace. Do you really want this kind of 
> implicit semantics in the schema as well rather than explicit?
>
> What I did in the past for BioSQL changes is to write/provide (SQL) 
> migration scripts. If you were to make it non-nullable, the 
> migration script here should be trivial, shouldn't it (e.g., use 
> the cv of the subject, possibly warn and log if subject and object 
> cv are not identical).
sure, there could be migration scripts and view layers. But it 
increases the complexity of the overall system. Apps need a well- 
defined protocol to determine which version of the schema they are 
speaking to.
Given that demand for this feature is fairly low, I'm inclined to 
leave it until the release after the forthcoming one.
>
> BTW existing applications should be unaffected either way except 
> those that use 'SELECT *' and those should burn anyway.
any loading code will be affected, unless we provided a DEFAULT clause
>
>> [...]
>>
>> Out of interest, do you need this for a particular ontology? None 
>> of the existing obo ontologies use this feature so far.
>
> I used this quite a bit actually back at GNF for the Symgene/ 
> SymAtlas project. The XSPAN project seems to be doing this for 
> mapping anatomy terms across species, and it may be relevant to us 
> when we constrain anatomy terms by taxon that it applies to (using 
> a taxon ontology).
You shouldn't use the namespace mechanism to do this. This should be 
done with links between terms using well-defined relations; eg
 placenta in_organism placental_mammal
Where the definition of in_organism follows the pattern in the other 
obo relations (in the above case it would mean that all placentas are 
in a placental mammal, but not all placental mammals have a placenta)
>
> Just bouncing some ideas around for how we might do this.
>
>>
>>> Interestingly, the path table for the transitive closure does
>>> reference a namespace. Oversight, or intention?
>>
>> It is a little inconsistent. If a new column is added to 
>> cvterm_relationship, the documentation for both these should be 
>> harmonized
>>
>>>
>>> Second, it doesn't seem to support treating triples as terms that 
>>> can
>>> partake in another triple as subject (or object). The desire to do
>>> this came up about 3 years ago from the Biojava front and is
>>> implemented in BioSQL, see
>>> http://www.open-bio.org/pipermail/biosql-l/2003-October/000455.html
>>
>> The way to do this would be via reification, as is the common 
>> pattern for RDF, which will buy us compatibility with W3C standards.
>>
>> Reification is a little ugly, but thankfully it should not be 
>> needed unless you are forcing Chado to do something quite 
>> esoteric. I think Matt's case in the link above is a little 
>> unusual. I am very keen on having rules for transitive closures 
>> specified using some logical formalism. However, _if_ these rules 
>> are to be stored directly in the schema then I would much prefer a 
>> distinct module for doing this, rather than overloading the term 
>> table, as Matt proposes to do. After all, these deductive rules 
>> would apply to other tables too.
>>
>>>
>>> I am thinking whether this wouldn't also be needed for EQ/E
>>> annotation if the quality (or attribute) is relational - couldn't 
>>> you
>>> express that by connecting the relationship between the entity and
>>> the quality terms with the second entity term?
>>
>> I'm not sure I understand this
>>
>> I think the proposed new pheno module should explicitly deal with 
>> relational qualities (eg "sensitive_to" from PATO, where this 
>> quality relates a bearer to perhaps a chemical).
>
> Probably, it's just not exactly clear to me yet how.
>
> My first, and probably not a good, idea was that you could relate 
> the entity term to the quality term via a relationship, and then 
> relate the relationship to another entity term if the relationship 
> was relational.
we should probably start a new thread on this
see the existing pheno module (though this will change)
no links between terms are required, the idea is to post-coordinate 
the phenotype description using separate terms
more on this later...
cheers
chris
>
> 	-hilmar
>
>>
>>>
>>> Any thoughts in this regard?
>>>
>>> 	-hilmar
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ontol-sw-dev mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>

On Jun 21, 2006, at 12:26 PM, chris mungall wrote:
>
> On Jun 19, 2006, at 5:23 AM, Hilmar Lapp wrote:
>
>> Hi,
>>
>> is the ERD for the cv module at http://www.gmod.org/node/16 up-to-
>> date? I believe so after looking at a schema checkout.
>>
>> I notice that first, relationships do not reference a cv (or
>> namespace), although this would be very useful (especially if subject
>> and object aren't from the same ontology), and is indeed - unless I'm
>> mistaken - supported by the obo format (at least v1.2, no?).
>
>
> it is indeed now supported. this should perhaps be added for 
> compatibility with the latest version of the obo format. It should 
> be nullable for backwards compatibility. If there's no objections 
> after two weeks, you can add this.
I'm not sure nullable is eventually what you want. If I recall the 
obo spec correctly then not providing a namespace for the 
relationship does not mean that there isn't one, basically you are 
choosing the default namespace. Do you really want this kind of 
implicit semantics in the schema as well rather than explicit?
What I did in the past for BioSQL changes is to write/provide (SQL) 
migration scripts. If you were to make it non-nullable, the migration 
script here should be trivial, shouldn't it (e.g., use the cv of the 
subject, possibly warn and log if subject and object cv are not 
identical).
BTW existing applications should be unaffected either way except 
those that use 'SELECT *' and those should burn anyway.
> [...]
>
> Out of interest, do you need this for a particular ontology? None 
> of the existing obo ontologies use this feature so far.
I used this quite a bit actually back at GNF for the Symgene/SymAtlas 
project. The XSPAN project seems to be doing this for mapping anatomy 
terms across species, and it may be relevant to us when we constrain 
anatomy terms by taxon that it applies to (using a taxon ontology).
Just bouncing some ideas around for how we might do this.
>
>> Interestingly, the path table for the transitive closure does
>> reference a namespace. Oversight, or intention?
>
> It is a little inconsistent. If a new column is added to 
> cvterm_relationship, the documentation for both these should be 
> harmonized
>
>>
>> Second, it doesn't seem to support treating triples as terms that can
>> partake in another triple as subject (or object). The desire to do
>> this came up about 3 years ago from the Biojava front and is
>> implemented in BioSQL, see
>> http://www.open-bio.org/pipermail/biosql-l/2003-October/000455.html
>
> The way to do this would be via reification, as is the common 
> pattern for RDF, which will buy us compatibility with W3C standards.
>
> Reification is a little ugly, but thankfully it should not be 
> needed unless you are forcing Chado to do something quite esoteric. 
> I think Matt's case in the link above is a little unusual. I am 
> very keen on having rules for transitive closures specified using 
> some logical formalism. However, _if_ these rules are to be stored 
> directly in the schema then I would much prefer a distinct module 
> for doing this, rather than overloading the term table, as Matt 
> proposes to do. After all, these deductive rules would apply to 
> other tables too.
>
>>
>> I am thinking whether this wouldn't also be needed for EQ/E
>> annotation if the quality (or attribute) is relational - couldn't you
>> express that by connecting the relationship between the entity and
>> the quality terms with the second entity term?
>
> I'm not sure I understand this
>
> I think the proposed new pheno module should explicitly deal with 
> relational qualities (eg "sensitive_to" from PATO, where this 
> quality relates a bearer to perhaps a chemical).
Probably, it's just not exactly clear to me yet how.
My first, and probably not a good, idea was that you could relate the 
entity term to the quality term via a relationship, and then relate 
the relationship to another entity term if the relationship was 
relational.
	-hilmar
>
>>
>> Any thoughts in this regard?
>>
>> 	-hilmar
>> -- 
>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Gmod-ontol-sw-dev mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev
>
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================

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On Jun 19, 2006, at 5:23 AM, Hilmar Lapp wrote:
> Hi,
>
> is the ERD for the cv module at http://www.gmod.org/node/16 up-to-
> date? I believe so after looking at a schema checkout.
>
> I notice that first, relationships do not reference a cv (or
> namespace), although this would be very useful (especially if subject
> and object aren't from the same ontology), and is indeed - unless I'm
> mistaken - supported by the obo format (at least v1.2, no?).
it is indeed now supported. this should perhaps be added for 
compatibility with the latest version of the obo format. It should be 
nullable for backwards compatibility. If there's no objections after 
two weeks, you can add this.
All GMOD applications and middleware should assume the existing 
schema however - an explicit switch should be used to use the newer 
schema.
Out of interest, do you need this for a particular ontology? None of 
the existing obo ontologies use this feature so far.
> Interestingly, the path table for the transitive closure does
> reference a namespace. Oversight, or intention?
It is a little inconsistent. If a new column is added to 
cvterm_relationship, the documentation for both these should be 
harmonized
>
> Second, it doesn't seem to support treating triples as terms that can
> partake in another triple as subject (or object). The desire to do
> this came up about 3 years ago from the Biojava front and is
> implemented in BioSQL, see
> http://www.open-bio.org/pipermail/biosql-l/2003-October/000455.html
The way to do this would be via reification, as is the common pattern 
for RDF, which will buy us compatibility with W3C standards.
Reification is a little ugly, but thankfully it should not be needed 
unless you are forcing Chado to do something quite esoteric. I think 
Matt's case in the link above is a little unusual. I am very keen on 
having rules for transitive closures specified using some logical 
formalism. However, _if_ these rules are to be stored directly in the 
schema then I would much prefer a distinct module for doing this, 
rather than overloading the term table, as Matt proposes to do. After 
all, these deductive rules would apply to other tables too.
>
> I am thinking whether this wouldn't also be needed for EQ/E
> annotation if the quality (or attribute) is relational - couldn't you
> express that by connecting the relationship between the entity and
> the quality terms with the second entity term?
I'm not sure I understand this
I think the proposed new pheno module should explicitly deal with 
relational qualities (eg "sensitive_to" from PATO, where this quality 
relates a bearer to perhaps a chemical).
>
> Any thoughts in this regard?
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
>
>
> _______________________________________________
> Gmod-ontol-sw-dev mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev

Hi everyone,
I hope to see many of you at the conference this year. Just wanted to 
remind everyone that the abstract deadline is tomorrow June 21st. 
Should be a good meeting I believe to present all the interesting 
things you're working on.
http://meetings.cshl.edu/meetings/infouk06.shtml
-S

Hollywood Intermediate Inc.
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H o l l y w o o d I n t e r m e d i a t e, Inc. (H-Y-W-I.PK - News), a provider of digital intermediate film mastering services, announced that High Definition preview masters as part of its normal digital intermediate service offerings and workflow.
"Typically, in current post-production workflow, HD dailies masters are edited into high quality preview masters including color timing, dirt removal, opticals and visual effects," said David Waters, H o l l y w o o d I n t e r m e d i a t e president. "Unfortunately, none of these processes translate to the theatrical release of the film as they must all be duplicated or repeated in either a higher resolution digital format, or photo chemical process."
H o l l y w o o d I n t e r m e d i a t e gives Motion Picture producers the ability to scan their selected original camera negative at 2k or 4k film resolution, conform a high resolution digital master for theatrical and broadcast release including dirt removal, opticals and visual effects, and output a High Definition preview master to be used for preview screenings and focus groups that can be deployed in any worldwide theater location.
"The challenge for completing the final editorial decisions on a motion picture are balanced between the ability to display the highest resolution picture for a test audience, and the costs and time in having to re-master your film based on a test audience response," said Jim Delany, H o l l y w o o d I n t e r m e d i a t e COO.
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You can't squeeze blood out of a turnip. Schools out for summer. The squeaky wheel gets the grease. Still waters run deep. Throw pearls before swine. You feel like a fish out of water. Stuck in a rut. Raking it in. The scum of the earth. Pull it up by the roots. Welcome to my garden. Walking on water. Up a tree. Putting the cart before the horse. Wait and see. Still waters run deep.

Hi,
is the ERD for the cv module at http://www.gmod.org/node/16 up-to- 
date? I believe so after looking at a schema checkout.
I notice that first, relationships do not reference a cv (or 
namespace), although this would be very useful (especially if subject 
and object aren't from the same ontology), and is indeed - unless I'm 
mistaken - supported by the obo format (at least v1.2, no?). 
Interestingly, the path table for the transitive closure does 
reference a namespace. Oversight, or intention?
Second, it doesn't seem to support treating triples as terms that can 
partake in another triple as subject (or object). The desire to do 
this came up about 3 years ago from the Biojava front and is 
implemented in BioSQL, see
http://www.open-bio.org/pipermail/biosql-l/2003-October/000455.html
I am thinking whether this wouldn't also be needed for EQ/E 
annotation if the quality (or attribute) is relational - couldn't you 
express that by connecting the relationship between the entity and 
the quality terms with the second entity term?
Any thoughts in this regard?
	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================

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Hello,
We would like to start loading microarray and interaction data into 
an instance of gmod/chado. I know that there has been mention of the 
first beta release of gmod, so I wanted to see whether there was a 
rough time frame for that release, just so we know if we need to 
upgrade from version 0.003 soon. Also, is anyone actively working on 
the rad module, or tables to store interaction data (I think we might 
just use feature_relationship for now)? Again, just want to know 
whether there will be any major changes to the areas of the schema we 
expect to be heavily using in the near future. It's totally fine 
either way, just checking!
Thanks,
Kara

Hello,
We are loading various types of functional genomics data (microarray, 
large-scale interactions, etc) into a chado/gmod instance, and find 
that our lives would be made much easier if we had a STUDYPROP table 
in the rad module (rather than having to go through STUDYDESIGN and 
STUDYDESIGNPROP to store various tag/values associated with studies/ 
datasets). Any objection to adding such a table?
Thanks,
Kara

Hello all. I'm curious as to what the current state of protein- 
protein interaction representation is in chado. I found an old 
thread with some mention of a possible Interaction Module, but I 
didn't see anything after that, or anything following up on it. 
What's the current thinking regarding this problem? Is there a test 
version of an Interaction Module floating around CVS somewhere?
Thanks for any information!
Todd

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Red H0t News:
H o l l y w o o d I n t e r m e d i a t e Expands the Creative Palette for Independent Filmmakers GLENDALE, CA--(MARKET WIRE)--May 31, 2006 -- H o l l y w o o d I n t e r m e d i a t e, Inc. A provider of digital intermediate film mastering services, announced today that its Matchframe Digital Intermediate division is currently providing full digital intermediate services for Super 16MM productions.
H o l l y w o o d I n t e r m e d i a t e, Inc. (H-Y-W-I.PK - News), a provider of digital intermediate film mastering services, announced that High Definition preview masters as part of its normal digital intermediate service offerings and workflow.
"Typically, in current post-production workflow, HD dailies masters are edited into high quality preview masters including color timing, dirt removal, opticals and visual effects," said David Waters, H o l l y w o o d I n t e r m e d i a t e president. "Unfortunately, none of these processes translate to the theatrical release of the film as they must all be duplicated or repeated in either a higher resolution digital format, or photo chemical process."
H o l l y w o o d I n t e r m e d i a t e gives Motion Picture producers the ability to scan their selected original camera negative at 2k or 4k film resolution, conform a high resolution digital master for theatrical and broadcast release including dirt removal, opticals and visual effects, and output a High Definition preview master to be used for preview screenings and focus groups that can be deployed in any worldwide theater location.
"The challenge for completing the final editorial decisions on a motion picture are balanced between the ability to display the highest resolution picture for a test audience, and the costs and time in having to re-master your film based on a test audience response," said Jim Delany, H o l l y w o o d I n t e r m e d i a t e COO.
"H o l l y w o o d I n t e r m e d i a t e offers a flexible alternative to traditional photochemical and video post-production processes for film mastering and preview screenings eliminating cost and time redundancies," said Waters. "We expect our HD preview screening master services to provide crucial workflow efficiencies helping H o l l y w o o d I n t e r m e d i a t e achieve market growth in the current digital intermediate and high definition marketplace."
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-----------------------
Stone cold sober. They're like two peas in a pod. A tree does not move unless there is wind. Stubborn as a mule. Sly as a fox. To gild refined gold, to paint the lily. Sow dry and set wet. A thing of beauty is a joy forever. Wait and see. A stick in the mud. You can lead a horse to water but you can't make him drink. They're like two peas in a pod. Shiver me timber. The scum of the earth. They're like two peas in a pod. Useless as tits on bull. Too little too late. When you get lemons, make lemonade.(When life gives you scraps make quilts.)
Your in hot water. Red as a beet. They're like two peas in a pod. Your barking up the wrong tree. Speak softly and carry a big stick. The scythe ran into a stone. When we love - we grow. When pigs fly. Watch and wait. You feel like a fish out of water. A thing of beauty is a joy forever. The way to a man's heart is through his stomach. So hungry I could eat a horse. Under the weather. Worked night and day. The way to a man's heart is through his stomach. Sour as a green apple. Up a tree. Rain, rain go away; come again some other day. A tree does not move unless there is wind. Plain as water. The shoes on the other foot now.