gmane.science.biology.gmod.schema

Re: Postgres 9.2

Siddhartha Basu — 2013-06-11T20:38:04

Hi Ganesh,
I have loaded the default chado schema(both official release/svn
checkout) in 9.2, haven't faced any problem yet.

thanks,
-siddhartha

On Tue, 11 Jun 2013, Srinivasamoorthy, Ganesh - INTL wrote:


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Postgres 9.2

Srinivasamoorthy, Ganesh - INTL — 2013-06-11T15:33:34

I am planning to install Chado on Postgres 9.2 server.
Any comments ? has any later version than what is mentioned on the Chado page (8.1) given any problems ?


Ganesh
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Re: Problem loading NCBI taxonomy

Nicolas Joannin — 2013-06-06T02:56:48

Hello Naama,

Thanks for the quick reply :)
I have tried a subset of the taxonomy and that works, as long as there is
only one branch (as we discussed in another thread).
I guess your thought about the taxonomy not having a root node makes
sense...
Let me know when you have a fix and I'll test it!

Cheers,
Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Thu, Jun 6, 2013 at 11:39 AM, Naama Menda <naama.menda< at >cornell.edu>wrote:

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Re: Problem loading NCBI taxonomy

Naama Menda — 2013-06-06T02:39:09

yes, it takes forever because NCBI taxonomy is big. If you run it on a
machine with more CPU it will be faster, but will still take some time to
run.
I've never tried to load the entire taxonomy, since we don't really need to
store the entire thing.
that is the case, I'll have to add a 'dummy' root.
I've also seen NCBI dumps that have some glitch in one of the nodes, but I
don't think that's the case here (and I have to say that the NCBI helpdesk
is very responsive, and they've always fixed those issues quickly when I
contacted them!).

Have you tried loading a subset of the taxonomy? Did that finish?

Thanks for helping debugging this!
-Naama




Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
nm249< at >cornell.edu


On Wed, Jun 5, 2013 at 9:34 PM, Nicolas Joannin
<nicolas.joannin< at >gmail.com>wrote:

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Re: Problem loading NCBI taxonomy

Nicolas Joannin — 2013-06-06T01:34:36

Hi Naama,

The script has finally finished running on my laptop: it took forever :)
Unfortunately, it failed :(
See the last few lines of the script below.

I do not need to load all of the NCBI Taxonomy, so there is no need to
debug this for my sake.
I hadn't anticipated that it would be so long, and therefore thought it
would be fun to try...

If you do debug it, I can test it on my desktop machine at work, just let
me know!

Best regards,
Nicolas

Output (end thereof):
New organism 1380665 (species=Blackburnia costata)
New organism 1380666 (species=Arenaria montana)
Arenaria montana LEVEL=( species) Synonym is Arenaria montana L.
New organism 1380667 (species=Influenza A virus (A/reassortant/NYMC
X-197(Brisbane/11/2010 x Puerto Rico/8/1934)(H3N2)))
New organism 1380668 (species=Blumea cf. canalensis Bernardi 9667)
New organism 1380669 (species=Nematanthus brasiliensis)
New organism 1380670 (species=Nostoc sp. HKAR-2)
the root_id is
An error occured! Rolling back!
 Context::Preserve::preserve_context(): No organism id found for root node!
 at load_ncbi_taxonomy.pl line 558

 Resetting database sequences...






Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Mon, Jun 3, 2013 at 2:34 PM, Nicolas Joannin
<nicolas.joannin< at >gmail.com>wrote:

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Re: stag-storenode.pl overwrites existing cvterms in vocabularies different from the one being loaded

Scott Cain — 2013-06-05T15:59:39

Chris,

I second the thanks--it saved me time searching for a bug that doesn't
exist :-)

Scott



On Wed, Jun 5, 2013 at 10:47 AM, Mara Kim <hacker.root< at >gmail.com> wrote:

Re: stag-storenode.pl overwrites existing cvterms in vocabularies different from the one being loaded

Mara Kim — 2013-06-05T14:47:32

Good catch, Chris.  That did in fact solve the problem.  Thanks a million!


On Fri, May 31, 2013 at 7:31 PM, Chris Mungall <cjmungall< at >lbl.gov> wrote:

Re: Small modification to DBIx::DBStag

Scott Cain — 2013-06-04T17:00:55

Yep, I was thinking the same thing--I was just talking with Rob Buels about
it in fact.  I suspect that will happen with the next release of Chado.

Scott



On Tue, Jun 4, 2013 at 12:55 PM, Siddhartha Basu <biosidd< at >gmail.com> wrote:

Re: Small modification to DBIx::DBStag

Siddhartha Basu — 2013-06-04T16:55:35

Hi Scott,

On Tue, 04 Jun 2013, Scott Cain wrote:

I should have checked the CPAN before i posted, sorry for any
confusion.

Just wondering, whether its time to consider another ontology loader for
replacement, for instance, the one maintained/written by Naama Menda.
I haven't used it seriously though(still in Oracle), just throwing out
and idea.

thanks,
-siddhartha








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Re: Small modification to DBIx::DBStag

Scott Cain — 2013-06-04T14:59:35

Hi Chris and Siddhartha,

I'm pretty sure I'm already a co-maintainer (in fact, if you look at
search.cpan.org you'll see me as the owner, since I built the last
release).  What I didn't have was commit privs on Chris's github repo.

Also, as it turns out, the problem is deeper than just a "simple fix" to
DBIx::DBStag: DBIx::DBSchema needs fixed too, and I'm not even sure of the
best way to do it.  I've contacted the author for suggestions and help.

Thanks,
Scott



On Tue, Jun 4, 2013 at 10:49 AM, Siddhartha Basu <biosidd< at >gmail.com> wrote:

Re: Chado genomic rearangement

Siddhartha Basu — 2013-06-04T14:54:15

Hi Clement,
Did you get any response ?
And if you have tried any implementation , would be interested to know.
One more thing, could you show any example/snippet of your dataset that
you want to load, might try to have an implementation.

thanks,
-siddhartha

On Wed, 15 May 2013, clement fanteria wrote:





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Re: Small modification to DBIx::DBStag

Siddhartha Basu — 2013-06-04T14:49:00

Hi Chris,
You could try the co-maintainership system in PAUSE.

thanks,
-siddhartha

On Mon, 03 Jun 2013, Chris Mungall wrote:





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Re: Error running load_ncbi_taxonomy.pl with inputfile

Nicolas Joannin — 2013-06-04T01:30:30

Hi Naama,

Thanks again for your help!
Indeed, that was the problem. I had several unrelated branches of the tree
that I wanted to load, so there were several roots.
Will load them all individually...

Best regards,
Nicolas





Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Tue, Jun 4, 2013 at 2:35 AM, Naama Menda <naama.menda< at >cornell.edu> wrote:

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Re: Small modification to DBIx::DBStag

Chris Mungall — 2013-06-03T21:50:47

Hi Scott

That sounds fine to me I made you a collaborator on

https://github.com/cmungall/DBIx-DBStag

(or you can fork and push changes to me if you prefer)

I should probably give you PAUSE rights too. I'm not quite sure how that's done.

On Jun 3, 2013, at 2:19 PM, Scott Cain wrote:


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Small modification to DBIx::DBStag

Scott Cain — 2013-06-03T21:19:50

Hi Chris,

I know you'd probably like for DBIx::DBStag to die a quiet death, but until
it does, I'd like to implement a small change to it and stag-storenode.pl.
The problem is when Chado is installed in a non-public schema (like as is
the default thing to do when using Tripal).  DBIx::DBSchema assumes that
the default schema is public, and forces qualifying tables with the schema
when constructing queries (though it may be possible to set the default
schema to an empty string, which would be ideal).

My plan is to work on getting around this "design flaw" by adding options
to stag-storenode.pl and the constructor of DBIx::DBStag, unless you have
suggestions for a better approach.

Thanks,
Scott

Re: Problems mith make onthology

Scott Cain — 2013-06-03T19:36:42

Hi Marcel,

I just tried to reproduce this and failed (that is, I was able to
successfully load PO after squashing a bug that causes a problem between
Tripal and dBIx::DBSchema--unrelated to your problem though).

I wonder if either the download of PO was truncated or its conversion to
oboxml was truncated, resulting in a corrupted file.  Take a look at the
two po_anatomy files in tmp/po (.obo and .oboxml).  At the end of the obo
file, I have:

[Typedef]
id: participates_in
name: participates_in
holds_over_chain: part_of participates_in

and at the end of the oboxml file I have:

  <cvterm_relationship>
    <type_id>part_of</type_id>
    <subject_id>PO:0030087</subject_id>
    <object_id>PO:0030018</object_id>
  </cvterm_relationship>
  <!--is_a relationship types between typedefs-->
  <!--cvterm metadata-->
  <!--instance-level relations-->
</chado>

(hmm, hopefully, the xml snippet I just pasted will render in your mail
client; it ends with a closing "chado" tag; if not, let me know and I'll
find somewhere else for it.)

If both of those look ok, I'm not sure what the problem is.  The first
obvious thing to try is to remove the tmp/po directory and try the load
again.  Also, if it doesn't work, can you tell me what is on and around
line 3736 of DBStag.pm (the line where the error occurs)?

Thanks and good luck,
Scott



On Fri, May 31, 2013 at 5:58 AM, Marcel Kerkveld <m.kerkveld< at >rijkzwaan.nl>wrote:

Re: Error running load_ncbi_taxonomy.pl with inputfile

Naama Menda — 2013-06-03T17:35:04

It sounds from your description that you generated manually the input file
with a number of taxons. I don't think the loader can work if
you selectively pick a number of taxons. Your input file is for loading
part of the NCBI taxonomy tree, so it must include a parent taxon and all
the nodes when you climb the tree all the way to the leaves (it is OK to
exclude a leaf, but not any of the nodes in the way.  this is because each
node in the tree is stored with a right and left indices, which makes
reconstructing trees very quick , since you don't have to climb up and down
the tree each time you query. This means if you excluded a parent node, you
will be missing one of the indices.

If you want to load a number of branches, you will need to load them
separately, unless you go up to their common root.


You are also using the -t option, for a test run, but looking at  the error
message it does not look like this is the problem.

Can you try to load a single tree with the full lineage and let me know if
that works?

thanks
-Naama




Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
nm249< at >cornell.edu


On Mon, Jun 3, 2013 at 7:41 AM, Nicolas Joannin
<nicolas.joannin< at >gmail.com>wrote:

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Re: Error running load_ncbi_taxonomy.pl with inputfile

Nicolas Joannin — 2013-06-03T11:41:07

Hi Naama,

I generated the file through the NCBI Taxonomy webpage: I searched for all
the taxons I wanted and downloaded their ids to a file. The input file is
has one txid per line and ends with an empty line.
The script was run with like this:
perl load_ncbi_taxonomy.pl -H host -D dbname -u username -d Pg -p password
-i path/to/infile -v -t

Let me know if you need more info!

Best regards,
Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Mon, Jun 3, 2013 at 7:27 PM, Naama Menda <naama.menda< at >cornell.edu> wrote:

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Re: Error running load_ncbi_taxonomy.pl with inputfile

Naama Menda — 2013-06-03T10:27:22

Hi Nicolas

How did you generate your input file, and which options did you use for
running the script?

Naama



On Monday, June 3, 2013, Nicolas Joannin wrote:

Error running load_ncbi_taxonomy.pl with input file

Nicolas Joannin — 2013-06-03T05:40:18

Hello,

I have encountered an error running load_ncbi_taxonomy.pl with in input
file of txids.
You'll find the last few lines of the output below.

Do you have any idea what I might have done wrong?

Best regards,
Nicolas

Command line output:

### MUCH MORE BEFORE THIS ###
Found child_id 14104 (organism_id = 14132)
walking the tree for id 14104, index count is 241
Setting left index= 242 for parent 14104

Found child_id 15654 (organism_id = 15682)
walking the tree for id 15654, index count is 242
Setting left index= 243 for parent 15654

Setting right index= 244 for phylonode id 15654

Setting right index= 245 for phylonode id 14104

Setting right index= 246 for phylonode id 25556

Setting right index= 247 for phylonode id 25068

Updating the phylonode and phylonode_organism tables

An error occured! Rolling back!
 DBIx::Class::Storage::DBI::__ANON__(): DBI Exception: DBD::Pg::db do
failed: ERROR:  null value in column "left_idx" violates not-null
constraint at load_ncbi_taxonomy.pl line 528

 Resetting database sequences...



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan
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Re: Problem loading NCBI taxonomy

Nicolas Joannin — 2013-06-03T05:34:54

Hi Naama,

Thanks for your quick reply!

I just realized that your reply was only addressed to me, so I've added the
gmod-schema mailing list :)
This seems to fix the problem. At least I could launch the program, but
it's still running now so I don't know if it'll complete or not.
Crossing my fingers (it's such a long process to include all NCBI Taxonomy
;)!

I now have a new problem though, but I will start a new thread for it...

Cheers,
Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Thu, May 30, 2013 at 1:38 AM, Naama Menda <naama.menda< at >cornell.edu>wrote:

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