From: Chris M. <cj...@fr...> - 2005-07-26 21:21:36
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I'm missing something. Why can't Etienne just place the SO type for TE gene in the type column of the GFF file and load this into the database? Is there some piece of code that validates the file against SOFA, and if so, why can't it just be overridden to validate against SO? This presumably is what we'll do, post-alpha release, surely, if we want to continue to use GFF3 as a roundtripping format for chado? On Tue, 26 Jul 2005, Scott Cain wrote: > Simply put, the problem is that transposable_element_gene used to be in > SOFA but it isn't anymore. I think it was removed by accident, but that > doesn't help the code that depends on SOFA being correct. > > On Tue, 2005-07-26 at 14:15 -0700, Chris Mungall wrote: > > That sounds like it'll be a lot more complicated than just proceeding w= ith > > the proper solution, which is surely to have the SO term rather than th= e > > SOFA term as the type. I don't see what the problem is here. But I'm no= t > > familiar with the chado gff code so I'll shut up now... > > > > On Tue, 26 Jul 2005, Scott Cain wrote: > > > > > Ah, I see. > > > > > > Well, one could add to each of the changed lines: > > > Ontology_term=3DSO:0000111, which would add an entry in feature_cvter= m for > > > each of the features to make it clear that they are TEgenes. They co= uld > > > then be excluded or queried for using that. > > > > > > On Tue, 2005-07-26 at 13:56 -0700, Chris Mungall wrote: > > > > That's what I thought, and I'm disagreeing with the proposed soluti= on. a > > > > bit of mungeing is fine, but turning TE genes into generic genes is= not > > > > acceptable if a biologist is going to be querying this database (un= less > > > > there is some hack that can address this at the display level). Wha= t I > > > > was proposing was some kind of solution that will be compatible wit= h > > > > whatever the post-alpha release is. > > > > > > > > On Tue, 26 Jul 2005, Scott Cain wrote: > > > > > > > > > Hi Chris, > > > > > > > > > > You certainly do sound like a broken record. (Hmm, will our chil= dren > > > > > understand that idiom when they grow up...) :-) > > > > > > > > > > If you recall, I indicated that the loading of both SO and SOFA w= ill 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 p= roblem > > > > > at about the same time the Karen had her baby, so I don't think i= t was > > > > > ever addressed. The short term solution to get the SGD data to l= oad 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 decid= e that SO > > > > > > should be loaded, and SOFA is just a subset of SO? > > > > > > > > > > > > I would strongly recommend against changing TE genes to genes. > > > > > > > > > > > > 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 than > > > > > > to lose important granularity in the feature type? > > > > > > > > > > > > On Tue, 26 Jul 2005, Scott Cain wrote: > > > > > > > > > > > > > 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 cre= ated terms > > > > > > > > 3 | Statistical Terms | Locally cre= ated terms > > > > > > > > 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'chromos= ome'; > > > > > > > > cvterm_id | cv_id | name | definit= ion | > > > > > > > > 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 seq= uence > > > > > > > > ontologies, the error no cv terms for chromosome went away= , but > > > > > > > > actually i have the same error with transposable_element_ge= ne ( no > > > > > > > > cvterm for transposable_element_gene at > > > > > > > > /usr/bin/gmod_bulk_load_gff3.pl line 679 ...). This is the= query you > > > > > > > > asked on transposable_element_gene: > > > > > > > > dev_chado_02=3D# select * from cvterm where name=3D'transpo= sable_element_gene'; > > > > > > > > cvterm_id | cv_id | name | > > > > > > > > definition | dbxr= ef_id | > > > > > > > > is_obsolete | is_relationshiptype > > > > > > > > -----------+-------+---------------------------+-----------= --------------------- > > > > > > > > -----------------------------------------------------------= --------------------- > > > > > > > > ------------------------------+-----------+-------------+--= ------------------- > > > > > > > > 784 | 7 | transposable_element_gene | A gene enc= oded within > > > > > > > > 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 mailing > > > > > > > > > list to the cc list. When you reply, please trim Lincoln= 's and the > > > > > > > > > gbrowse mailing list off the cc list (but please leave th= e schema > > > > > > > > > mailing list on). > > > > > > > > > > > > > > > > > > Please execute this queries in the dev_chado_01 psql shel= l and send 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_bu= lk_load_gff, > > > > > > > > > > This is what i receive: > > > > > > > > > > [root@jamga gmod-0.003]# gmod_bulk_load_gff3.pl --organ= ism yeast > > > > > > > > > > --gfffile saccharomyces_cerevisiae.gff > > > > > > > > > > Preparing data for inserting into the dev_chado_01 data= base > > > > > > > > > > (This may take a while ...) > > > > > > > > > > no cvterm for chromosome at /usr/bin/gmod_bulk_load_gff= 3.pl line 679, > > > > > > > > > > <GEN0> line 20. > > > > > > > > > > > > > > > > > > > > Do you know how i can fixe it? > > > > > > > > > > thank you > > > > > > > > > > noumen > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > > > > > > > SF.Net email is sponsored by: Discover Easy Linux Migra= tion Strategies > > > > > > > > > > from IBM. Find simple to follow Roadmaps, straightforwa= rd articles, > > > > > > > > > > informative Webcasts and more! Get everything you need = to get up to > > > > > > > > > > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=164= 92&op=C3=8Ck > > > > > > > > > > _______________________________________________ > > > > > > > > > > Gmod-gbrowse mailing list > > > > > > > > > > Gmo...@li... > > > > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrow= se > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > ---------------------------------------------------------= --------------- > > > > > > > > > Scott Cain, Ph. D. = ca...@cs... > > > > > > > > > GMOD Coordinator (http://www.gmod.org/) = 216-392-3087 > > > > > > > > > Cold Spring Harbor Laboratory > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > -------------------------------------------------------------= ----------- > > > > > > > Scott Cain, Ph. D. ca= in...@cs... > > > > > > > GMOD Coordinator (http://www.gmod.org/) 2= 16-392-3087 > > > > > > > Cold Spring Harbor Laboratory > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > > > > SF.Net email is sponsored by: Discover Easy Linux Migration S= trategies > > > > > > > from IBM. Find simple to follow Roadmaps, straightforward art= icles, > > > > > > > informative Webcasts and more! Get everything you need to get= up to > > > > > > > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op= =3Dclick > > > > > > > _______________________________________________ > > > > > > > Gmod-schema mailing list > > > > > > > Gmo...@li... > > > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > -----------------------------------------------------------------= ------- > > > > > Scott Cain, Ph. D. cain@c= shl.edu > > > > > GMOD Coordinator (http://www.gmod.org/) 216-3= 92-3087 > > > > > Cold Spring Harbor Laboratory > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > SF.Net email is sponsored by: Discover Easy Linux Migration Strateg= ies > > > > from IBM. Find simple to follow Roadmaps, straightforward articles, > > > > informative Webcasts and more! Get everything you need to get up to > > > > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&opk > > > > _______________________________________________ > > > > Gmod-schema mailing list > > > > Gmo...@li... > > > > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > > > > > -- > > > ---------------------------------------------------------------------= --- > > > Scott Cain, Ph. D. cain@cshl.= edu > > > GMOD Coordinator (http://www.gmod.org/) 216-392-3= 087 > > > Cold Spring Harbor Laboratory > > > > > > > > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. ca...@cs... > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > Cold Spring Harbor Laboratory > > |