Re: [Gmod-schema] Re: [Gmod-gbrowse] problems while executing the script gmod_bulk_load_gff (no cv term for chromosome)

[Scott C. <ca...@cs...>]

Hi Chris,

You certainly do sound like a broken record.  (Hmm, will our children
understand that idiom when they grow up...)  :-)

If you recall, I indicated that the loading of both SO and SOFA will end
with the last alpha I released a few weeks ago.  I don't remember what
the deal is with TE gene; I believe Stan and I talked about the problem
at about the same time the Karen had her baby, so I don't think it was
ever addressed.  The short term solution to get the SGD data to load is
to munge it so that it conforms to the GFF3 spec.

Scott

On Tue, 2005-07-26 at 13:04 -0700, Chris Mungall wrote:
> Sorry if I'm sounding like a broken record, but didn't we decide that S=
O
> should be loaded, and SOFA is just a subset of SO?
>=20
> I would strongly recommend against changing TE genes to genes.
>=20
> What is the problem with using SO instead of SOFA? Does the GFF loader
> assume that things are mapped to SOFA? Is it not better to fix this tha=
n
> to lose important granularity in the feature type?
>=20
> On Tue, 26 Jul 2005, Scott Cain wrote:
>=20
> > Right--transposable_element_gene is no longer in SOFA.  I've alerted =
SGD
> > about this problem, but there is nothing I can do directly.  I would
> > suggest finding all occurrences of transposable_element_gene and
> > changing them to 'gene'.
> >
> > On Tue, 2005-07-26 at 13:41 -0600, Etienne Noumen wrote:
> > > Hi,
> > > This is what i got:
> > > dev_chado_02=3D# select * from cv;
> > >  cv_id |                 name                 |
> > > definitio n
> > > -------+--------------------------------------+--------------------=
-------------
> > > --------------------------
> > >      1 | null                                 |
> > >      2 | local                                | Locally created ter=
ms
> > >      3 | Statistical Terms                    | Locally created ter=
ms
> > > for statis tics
> > >      4 | developmental stages                 |
> > >      5 | autocreated                          | Terms that are
> > > automatically ins erted by loading software
> > >      6 | Relationship Ontology                |
> > >      7 | Sequence Ontology                    |
> > >      8 | Sequence Ontology Feature Annotation |
> > > (8 rows)
> > >
> > > dev_chado_02=3D# select * from cvterm where name=3D'chromosome';
> > >  cvterm_id | cv_id |    name    |                   definition  |
> > > dbxref_id | is_obsolete | is_relationshiptype
> > > -----------+-------+------------+----------------------------------=
-------------
> > > -+-----------+-------------+---------------------
> > >       1177 |     8 | chromosome | Structural unit composed of long =
DNA
> > > molecule.  |      1356 |           0 |                   0
> > >        282 |     7 | chromosome | Structural unit composed of long =
DNA
> > > molecule.  |       305 |           0 |                   0
> > > (2 rows)
> > > After executing manually the gmod_load_onyologies.pl on sequence
> > > ontologies, the error no cv terms for chromosome  went away, but
> > > actually i have the same error with transposable_element_gene ( no
> > > cvterm for transposable_element_gene at
> > > /usr/bin/gmod_bulk_load_gff3.pl line 679  ...). This is the query y=
ou
> > > asked on transposable_element_gene:
> > > dev_chado_02=3D# select * from cvterm where name=3D'transposable_el=
ement_gene';
> > >  cvterm_id | cv_id |           name            |
> > >             definition                               | dbxref_id |
> > > is_obsolete | is_relationshiptype
> > > -----------+-------+---------------------------+-------------------=
-------------
> > > -------------------------------------------------------------------=
-------------
> > > ------------------------------+-----------+-------------+----------=
-----------
> > >        784 |     7 | transposable_element_gene | A gene encoded wit=
hin
> > > a transpo sable element. For example gag, int, env and pol are the
> > > transpable element gene s of the TY element in yeast. |       900 |
> > >        0 |                   0
> > >
> > > Thank you
> > > noumen
> > >
> > > And whn execution gmod_bulk_load_gff3.pl, it stops
> > > Thanx for reply.
> > > On 7/26/05, Scott Cain <ca...@cs...> wrote:
> > > > Hi Etienne,
> > > >
> > > > Since this is more of a chado question, I added the gmod-schema m=
ailing
> > > > list to the cc list.  When you reply, please trim Lincoln's and t=
he
> > > > gbrowse mailing list off the cc list (but please leave the schema
> > > > mailing list on).
> > > >
> > > > Please execute this queries in the dev_chado_01 psql shell and se=
nd the
> > > > results:
> > > >
> > > > # select * from cv;
> > > > # select * from cvterm where name=3D'chromosome';
> > > >
> > > > Thanks,
> > > > Scott
> > > >
> > > >
> > > > On Mon, 2005-07-25 at 11:41 -0600, Etienne Noumen wrote:
> > > > > I have some problem while executing  the script gmod_bulk_load_=
gff,
> > > > > This is what i receive:
> > > > > [root@jamga gmod-0.003]# gmod_bulk_load_gff3.pl --organism yeas=
t
> > > > > --gfffile saccharomyces_cerevisiae.gff
> > > > > Preparing data for inserting into the dev_chado_01 database
> > > > > (This may take a while ...)
> > > > > no cvterm for chromosome at /usr/bin/gmod_bulk_load_gff3.pl lin=
e 679,
> > > > > <GEN0> line 20.
> > > > >
> > > > > Do you know how i can fixe it?
> > > > > thank you
> > > > > noumen
> > > > >
> > > > >
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> > > > >
> > > > --
> > > > -----------------------------------------------------------------=
-------
> > > > Scott Cain, Ph. D.                                         cain@c=
shl.edu
> > > > GMOD Coordinator (http://www.gmod.org/)                     216-3=
92-3087
> > > > Cold Spring Harbor Laboratory
> > > >
> > > >
> > >
> > --
> > ---------------------------------------------------------------------=
---
> > Scott Cain, Ph. D.                                         cain@cshl.=
edu
> > GMOD Coordinator (http://www.gmod.org/)                     216-392-3=
087
> > Cold Spring Harbor Laboratory
> >
> >
> >
> > -------------------------------------------------------
> > SF.Net email is sponsored by: Discover Easy Linux Migration Strategie=
s
> > from IBM. Find simple to follow Roadmaps, straightforward articles,
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> >
>=20
>=20
>=20
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory