gmod-schema — For discussion of GMOD schema development

Re: [Gmod-schema] Chado 1.31 released

[Siddhartha B. <bi...@gm...>]

Congrats to Scott and to all the chado contributors, seems like the pine tree 
is a good motivation.

Quick question though, is it available through a github checkout or
through any tag/branch. It's also possible to tarball the chado release
and make it available through release page.

thanks,
-sidd

On Thu, 21 Jan 2016, Scott Cain wrote:

>    Hello,
> 
>    You have no idea how happy it makes me to announce the release of Chado
>    1.31:
> 
>    https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/
> 
>    This release marks the first schema change in Chado in 5 years, and
>    incorporates several changes, including
> 
>    * Converting all primary and foreign keys from integers to BigInts
>    * Converting feature.seqlen and featureloc.fmin and fmax from integers to
>    BigInts (darn pine trees!)
>    * Several added linking tables.
>    * Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of" term is not
>    found (thanks Eric Rasche).
>    * Fixed the ncbi_taxonomy loader to load the entire NCBI taxonomy (thanks
>    Naama Menda).
>    * Fixed the "organism by data" functionality of gmod_bulk_load_gff3.pl
>    (thanks Alexie Papanicolaou).
>    * Removed much of the initialization data included with Chado that is
>    considered out of date.
> 
>    For details on what changed in the schema, you can find the sql diff in
>    chado/schemas/1.23-1.31/diff.sql or atA 
>    https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/schemas/1.23-1.31/diff.sql
>    (note that this file is fairly large, due to the large number of
>    statements required to convert all of the primary keys to BigInts.)
>    Note that if you are a Tripal user, you will want to wait until Tripal has
>    been updated to support the new schema. A 
>    Finally, I want to give a very big "THANK YOU!!" to Stephen Ficklin and
>    Lacey Sanderson, without whom I never would have gotten this release out.
>    Thanks,
>    Scott
> 
>    --
>    ------------------------------------------------------------------------
>    Scott Cain, Ph. D. A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A 
>    scott at scottcain dot net
>    GMOD Coordinator (http://gmod.org/) A  A  A  A  A  A  A  A  A  A 
>    216-392-3087
>    Ontario Institute for Cancer Research

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Re: [Gmod-schema] gmod hardware requirements

[Iulia C. <I.C...@bh...>]

Dear Stephen,

Thank you so much for the details ! I am very grateful for all the information you shared.


Kind regards,

Iulia Cimpan

Research Software Support Specialist

IT Services, Room 108

Phone: 0121 4144072

Email: Ci...@ad...

________________________________
From: Stephen Ficklin [spf...@gm...]
Sent: 21 January 2016 19:42
To: Iulia Cimpan; Lacey Sanderson; gmo...@li...; GMOD Schema/Chado List
Subject: Re: gmod hardware requirements

Hi Iulia,

I'm CC'ing my response to both the Tripal and Chado mailing list in case others have the same question or want to add additional input.

The deciding factor for selection of appropriate hardware really depends on the amount of data you'll need to share and store, any analytical tools you might want to make available online and of course your budget.  And unfortunately it's hard to give you a good estimate.  But I can share some experience.  I've worked on setups that include Tripal and therefore Chado, GBrowse, JBrowse and houses transcriptomic, genomic, genetic (markers, variant data, phenotypes), and germplasm data. For one site in particular, the Tripal/Chado databases together are about 250GB in size with another 16GB for GBRowse.  The site has about 5Tb of files for download and also provides some analytical tools.    For this site we use separate web, file and database server.   This way analytical jobs that run on the web server do not impact performance of the database server, and downloading of files doesn't impact the web server.   For the database server we have 256 Gb of RAM to support joins and sorts on large record sets.   If the database can perform these operations in memory it runs much better.  But we find the major bottleneck on the database server is pulling data from the disk.  So, the faster the disks the better performance you'll have (SSD if you can afford it or 15K RPM drives).  We setup our database server to have a separate bank of disks to house the OS and all programs, and a second much larger bank of disks dedicated for database files.  This way other programs and the database don't have to compete for the spin cycles on the drives.  If you can afford to buy enough disks for a RAID 10 configuration then you should get the best performance.   The web server just needs enough RAM and processors/cores for the expected load you'll have.    Also, be sure to consider how you want to mange your backup and disaster recover strategy.

This example is for what I would consider a large site, but depending on your expected needs you may not need all of what I described.   As Scott mentioned, if your database is small enough and your user base is small you could use a much smaller configuration.

And perhaps others might be able to give more insightful thoughts...

Hope that helps a little,
Stephen

On 1/21/2016 8:48 AM, Iulia Cimpan wrote:
Dear Stephen and Lacey,

We are Research Computing Team at University of Birmingham and we want to install GMOD and components (including Tripal).
We are aware of the documentation http://gmod.org/wiki/Computing_Requirements and also about different requirements to install different components http://gmod.org/wiki/GMOD_Components

I need your help in figuring out the hardware architecture we need for Tripal, in terms of: memory usage, cpu usage for different tasks when using different applications, serial/parallel job executions etc. when about 30-50 users are accessing this entire GMOD install. Can you guide me towards such documentation or groups who already have installed most of your components, such that I get a bit of help ?

Thank you very much for all your help and I apologise if I'm a bit unclear in my request.


Kind regards,

Iulia Cimpan

Research Software Support Specialist

IT Services, Room 108

Phone: 0121 4144072

Email: Ci...@ad...<mailto:Ci...@ad...>

________________________________
From: Scott Cain [sc...@sc...<mailto:sc...@sc...>]
Sent: 20 January 2016 16:44
To: Iulia Cimpan; Monica Munoz-Torres; Stephen Ficklin; Lacey Sanderson
Cc: he...@gm...<mailto:he...@gm...>
Subject: Re: gmod hardware requirements

Hi Iulia,

Sorry for the delay; I was at a conference last week so I missed you initial email.

Of course, it can be quite difficult to nail down what sort of hardware you need.  For example, I have a test installation of JBrowse for WormBase (not a lot of users, but quite a bit of data and over 800 tracks) on a AWS t2.nano machine, which has only 1 CPU and 512 MB of ram, and it is quite responsive.  Of course, running a database on that would be not terribly realistic.  The AWS machine that is running http://cloud.gmod.org/ (Again, not a lot of users, but it has GBrowse, JBrowse, Apollo, Tripal and Chado) is an m1.small (1 CPU and 3.75 GB ram) is is generally pretty responsive.  The only thing would not be inclined to do with that machine as is is to hold something like an annotation jamboree where many users are using Apollo at the same time.

For more info on individual components, I'll direct you to Moni Munoz-Torres at Apollo, who does things like workshops where many users are accessing Apollo, so she can give you an idea of what sort of hardware is needed for that, and Stephen Ficklin and Lacey Sanderson who are the lead developers of Tripal and have been involved in many installations of it over the past few years.

Good luck!
Scott


On Thu, Jan 14, 2016 at 10:57 AM, Iulia Cimpan <I.C...@bh...<mailto:I.C...@bh...>> wrote:
Dear All,

I am putting together a "GMOD project overview" for my IT team. We want to install many of the tools and databases that GMOD provides.

We are aware of the documentation <http://gmod.org/wiki/Computing_Requirements> http://gmod.org/wiki/Computing_Requirements and also about different requirements to install different components <http://gmod.org/wiki/GMOD_Components> http://gmod.org/wiki/GMOD_Components

I need your help in figuring out the hardware architecture we need, in terms of: memory usage, cpu usage for different tasks when using different applications, serial/parallel job executions etc. when about 30-50 users are accessing this entire GMOD install. Can you guide me towards such documentation or groups who already have installed most of your components, such that I get a bit of help ?

Thank you very much for all your help and I apologise if I'm a bit unclear in my request.


Kind regards,

Iulia Cimpan

Research Software Support Specialist

IT Services, Room 108

Phone: 0121 4144072

Email: <mailto:Ci...@ad...> Ci...@ad...<mailto:Ci...@ad...>



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

[Gmod-schema] Chado 1.31 released

[Scott C. <sc...@sc...>]

Hello,

You have no idea how happy it makes me to announce the release of Chado
1.31:

https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/

This release marks the first schema change in Chado in 5 years, and
incorporates several changes, including

* Converting all primary and foreign keys from integers to BigInts
* Converting feature.seqlen and featureloc.fmin and fmax from integers to
BigInts (darn pine trees!)
* Several added linking tables.
* Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of" term is not
found (thanks Eric Rasche).
* Fixed the ncbi_taxonomy loader to load the entire NCBI taxonomy (thanks
Naama Menda).
* Fixed the "organism by data" functionality of gmod_bulk_load_gff3.pl
(thanks Alexie Papanicolaou).
* Removed much of the initialization data included with Chado that is
considered out of date.

For details on what changed in the schema, you can find the sql diff in
chado/schemas/1.23-1.31/diff.sql or at

https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/schemas/1.23-1.31/diff.sql

(note that this file is fairly large, due to the large number of statements
required to convert all of the primary keys to BigInts.)

Note that if you are a Tripal user, you will want to wait until Tripal has
been updated to support the new schema.

Finally, I want to give a very big "THANK YOU!!" to Stephen Ficklin and
Lacey Sanderson, without whom I never would have gotten this release out.

Thanks,
Scott




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

Re: [Gmod-schema] gmod hardware requirements

[Stephen F. <spf...@gm...>]

Hi Iulia,

I'm CC'ing my response to both the Tripal and Chado mailing list in case 
others have the same question or want to add additional input.

The deciding factor for selection of appropriate hardware really depends 
on the amount of data you'll need to share and store, any analytical 
tools you might want to make available online and of course your 
budget.  And unfortunately it's hard to give you a good estimate.  But I 
can share some experience.  I've worked on setups that include Tripal 
and therefore Chado, GBrowse, JBrowse and houses transcriptomic, 
genomic, genetic (markers, variant data, phenotypes), and germplasm 
data. For one site in particular, the Tripal/Chado databases together 
are about 250GB in size with another 16GB for GBRowse.  The site has 
about 5Tb of files for download and also provides some analytical tools. 
    For this site we use separate web, file and database server.   This 
way analytical jobs that run on the web server do not impact performance 
of the database server, and downloading of files doesn't impact the web 
server. For the database server we have 256 Gb of RAM to support joins 
and sorts on large record sets.   If the database can perform these 
operations in memory it runs much better.  But we find the major 
bottleneck on the database server is pulling data from the disk. So, the 
faster the disks the better performance you'll have (SSD if you can 
afford it or 15K RPM drives).  We setup our database server to have a 
separate bank of disks to house the OS and all programs, and a second 
much larger bank of disks dedicated for database files.  This way other 
programs and the database don't have to compete for the spin cycles on 
the drives.  If you can afford to buy enough disks for a RAID 10 
configuration then you should get the best performance.   The web server 
just needs enough RAM and processors/cores for the expected load you'll 
have.    Also, be sure to consider how you want to mange your backup and 
disaster recover strategy.

This example is for what I would consider a large site, but depending on 
your expected needs you may not need all of what I described.   As Scott 
mentioned, if your database is small enough and your user base is small 
you could use a much smaller configuration.

And perhaps others might be able to give more insightful thoughts...

Hope that helps a little,
Stephen

On 1/21/2016 8:48 AM, Iulia Cimpan wrote:
> Dear Stephen and Lacey,
>
> We are Research Computing Team at University of Birmingham and we want 
> to install GMOD and components (including Tripal).
> We are aware of the documentation 
> http://gmod.org/wiki/Computing_Requirements and also about different 
> requirements to install different components 
> http://gmod.org/wiki/GMOD_Components
>
> I need your help in figuring out the hardware architecture we need for 
> Tripal, in terms of: memory usage, cpu usage for different tasks when 
> using different applications, serial/parallel job executions etc. when 
> about 30-50 users are accessing this entire GMOD install. Can you 
> guide me towards such documentation or groups who already have 
> installed most of your components, such that I get a bit of help ?
>
> Thank you very much for all your help and I apologise if I'm a bit 
> unclear in my request.
>
> Kind regards,
>
> Iulia Cimpan
>
> Research Software Support Specialist
>
> IT Services, Room 108
>
> Phone: 0121 4144072
>
> Email: Ci...@ad...
>
> ------------------------------------------------------------------------
> *From:* Scott Cain [sc...@sc...]
> *Sent:* 20 January 2016 16:44
> *To:* Iulia Cimpan; Monica Munoz-Torres; Stephen Ficklin; Lacey Sanderson
> *Cc:* he...@gm...
> *Subject:* Re: gmod hardware requirements
>
> Hi Iulia,
>
> Sorry for the delay; I was at a conference last week so I missed you 
> initial email.
>
> Of course, it can be quite difficult to nail down what sort of 
> hardware you need.  For example, I have a test installation of JBrowse 
> for WormBase (not a lot of users, but quite a bit of data and over 800 
> tracks) on a AWS t2.nano machine, which has only 1 CPU and 512 MB of 
> ram, and it is quite responsive. Of course, running a database on that 
> would be not terribly realistic.  The AWS machine that is running 
> http://cloud.gmod.org/ (Again, not a lot of users, but it has GBrowse, 
> JBrowse, Apollo, Tripal and Chado) is an m1.small (1 CPU and 3.75 GB 
> ram) is is generally pretty responsive.  The only thing would not be 
> inclined to do with that machine as is is to hold something like an 
> annotation jamboree where many users are using Apollo at the same time.
>
> For more info on individual components, I'll direct you to Moni 
> Munoz-Torres at Apollo, who does things like workshops where many 
> users are accessing Apollo, so she can give you an idea of what sort 
> of hardware is needed for that, and Stephen Ficklin and Lacey 
> Sanderson who are the lead developers of Tripal and have been involved 
> in many installations of it over the past few years.
>
> Good luck!
> Scott
>
>
> On Thu, Jan 14, 2016 at 10:57 AM, Iulia Cimpan <I.C...@bh... 
> <mailto:I.C...@bh...>> wrote:
>
>     Dear All,
>
>     I am putting together a "GMOD project overview" for my IT team. We
>     want to install many of the tools and databases that GMOD provides.
>
>     We are aware of the documentation
>     http://gmod.org/wiki/Computing_Requirements and also about
>     different requirements to install different components
>     http://gmod.org/wiki/GMOD_Components
>
>     I need your help in figuring out the hardware architecture we
>     need, in terms of: memory usage, cpu usage for different tasks
>     when using different applications, serial/parallel job executions
>     etc. when about 30-50 users are accessing this entire GMOD
>     install. Can you guide me towards such documentation or groups who
>     already have installed most of your components, such that I get a
>     bit of help ?
>
>     Thank you very much for all your help and I apologise if I'm a bit
>     unclear in my request.
>
>     Kind regards,
>
>     Iulia Cimpan
>
>     Research Software Support Specialist
>
>     IT Services, Room 108
>
>     Phone: 0121 4144072
>
>     Email: Ci...@ad... <mailto:Ci...@ad...>
>
>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                    216-392-3087
> Ontario Institute for Cancer Research

Re: [Gmod-schema] requested indexes for Chado

[Scott C. <sc...@sc...>]

Hi Karl,

Sorry, that's what I get for looking at code changes first thing in the
morning with very little sleep the night before.  For some reason, I
thought this index was for feature_dbxref.  It makes much more sense as an
index on feature :-)

Thanks,
Scott


On Tue, Jan 19, 2016 at 12:14 PM, Karl O. Pinc <ko...@me...> wrote:

> Hi Scott,
>
> On Tue, 19 Jan 2016 11:26:55 -0500
> Scott Cain <sc...@sc...> wrote:
>
> > I'm going through the requested additions for Chado, and I have a
> > question for you about this index:
> >
> > create index feature_idx1b
> >  on feature (feature_id, dbxref_id)
> >  where dbxref_id is not null;
> >
> > In what context do you imagine this index being helpful?  I wonder
> > for two reasons: one, dbxref_id is defined as not null for the table,
> > so the where clause doesn't appear to do anything,
>
> feature.dbxref_id is allowed to be NULL, as far as I can tell.
> It's allowed to be null in our version of chado, and
> see line 22 of
>
> https://github.com/GMOD/Chado/blob/master/chado/modules/sequence/sequence.sql
>
> If you don't say "not null" then you're allowed nulls.
>
> > and B, the
> > majority of the time, you would be querying for one item (either the
> > feature_id or the dbxref_id) in order to get a list of the other
> > items, in which case the existing indexes on the individual foreign
> > keys would be used.  When would I be querying for both at the same
> > time such that this index would help?
>
> I can't tell you off the top of my head.  I'm pretty sure we
> had to add the index to get something we do that's important
> to perform decently -- or at all.  Our revison control system
> says we made the index to support our VCF loading process,
> which can take days and days.  For some reason the optimizer
> wanted the index.  We spent some time doing this sort of
> tuning.
>
> One use case that's off the top of my head is when joining feature
> just to get a dbxref_id.  You don't really want anything on feature,
> but you've got the feature_id and want something on dbxref.
> In our case it's possible that we might have both; having
> made a dbxref and having looked up a feature we want to know if they
> are paired so that we can make a new feature to go with the
> dbxref if necessary.  (With VCF files I think we are creating
> features for each baboon sequenced, although not for each
> sequencing of each baboon.  But it's been a while since
> I've touched this and could be wrong.  Anyway, one
> loci could have several features with different dbxrefs --
> the dbxref.accession containing the baboon's identifier.)
>
> Regards,
>
> Karl <ko...@me...>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>



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

Re: [Gmod-schema] requested indexes for Chado

[Karl O. P. <ko...@me...>]

Hi Scott,

On Tue, 19 Jan 2016 11:26:55 -0500
Scott Cain <sc...@sc...> wrote:

> I'm going through the requested additions for Chado, and I have a
> question for you about this index:
> 
> create index feature_idx1b
>  on feature (feature_id, dbxref_id)
>  where dbxref_id is not null;
> 
> In what context do you imagine this index being helpful?  I wonder
> for two reasons: one, dbxref_id is defined as not null for the table,
> so the where clause doesn't appear to do anything,

feature.dbxref_id is allowed to be NULL, as far as I can tell.
It's allowed to be null in our version of chado, and
see line 22 of
https://github.com/GMOD/Chado/blob/master/chado/modules/sequence/sequence.sql

If you don't say "not null" then you're allowed nulls.

> and B, the
> majority of the time, you would be querying for one item (either the
> feature_id or the dbxref_id) in order to get a list of the other
> items, in which case the existing indexes on the individual foreign
> keys would be used.  When would I be querying for both at the same
> time such that this index would help?

I can't tell you off the top of my head.  I'm pretty sure we
had to add the index to get something we do that's important
to perform decently -- or at all.  Our revison control system
says we made the index to support our VCF loading process,
which can take days and days.  For some reason the optimizer
wanted the index.  We spent some time doing this sort of
tuning.

One use case that's off the top of my head is when joining feature
just to get a dbxref_id.  You don't really want anything on feature,
but you've got the feature_id and want something on dbxref.
In our case it's possible that we might have both; having
made a dbxref and having looked up a feature we want to know if they
are paired so that we can make a new feature to go with the
dbxref if necessary.  (With VCF files I think we are creating
features for each baboon sequenced, although not for each
sequencing of each baboon.  But it's been a while since
I've touched this and could be wrong.  Anyway, one
loci could have several features with different dbxrefs --
the dbxref.accession containing the baboon's identifier.)

Regards,

Karl <ko...@me...>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

[Gmod-schema] requested indexes for Chado

[Scott C. <sc...@sc...>]

Hi Karl,

I'm going through the requested additions for Chado, and I have a question
for you about this index:

create index feature_idx1b
 on feature (feature_id, dbxref_id)
 where dbxref_id is not null;

In what context do you imagine this index being helpful?  I wonder for two
reasons: one, dbxref_id is defined as not null for the table, so the where
clause doesn't appear to do anything, and B, the majority of the time, you
would be querying for one item (either the feature_id or the dbxref_id) in
order to get a list of the other items, in which case the existing indexes
on the individual foreign keys would be used.  When would I be querying for
both at the same time such that this index would help?

Thanks,
Scott


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

[Gmod-schema] Using features from one schema in another schema

[Matija B. <mat...@cr...>]

Hello,

I'm trying to resolve a problem in the CHADO database which I would like 
to share on this forum to be sure on the implications of my possible 
solution in terms of not breaking too many rules of how the database is 
structured.

THE PROBLEM:
I need to be able to use features(in this case DNA constructs) from one 
schema within a different schema.
This request is justified as the DNA constructs from one species(schema) 
can be used to test the regulation of the gene in other species(schema).
- each species has it's own schema(this is how the database was 
initially designed) +  public things that are in common like 
publications etc.


THE SOLUTION:
The solution I'm trying to implement works properly with the custom CMS 
we're using, but I want to be sure I'm not breaking the rules so the 
database still remains CHADO compatible.

construct relations schema
This is a small schema just to describe the relations between the 
features in our feature_relationship table

What I did is I copied all the features which are constructs into the 
public schema so they can be available to all other schemas, but the 
main problem then is the FK(foreign key) constraint within the 
feature_relationship, featureprop, feature_pub and feature_expression 
tables, which is then trying to reference a feature_id not present 
within the particular schema because it's copied to public.

So first I created a function which returns true or false and does 
mostly what a FK constraint would do except it would look in the 
particular schema plus public schema, and in that way return true or 
false if the record is present within schema_name or public(for 
constructs), this way the constructs would also be referenced being in 
the public schema

------------------------------------------------------------------FUNCTION 
CHECK FEATURES----------------------------------------------------------
CREATE FUNCTION schema_name.check_features(integer)
RETURNS boolean
AS $$
DECLARE
key       ALIAS FOR  $1;

BEGIN
     IF     EXISTS (SELECT feature_id FROM schema_name.feature WHERE 
feature_id=key) OR EXISTS (SELECT feature_id FROM public.feature WHERE 
feature_id=key) THEN
         RETURN true;
     ELSE
         RETURN false;
     END IF;
END;
$$
LANGUAGE plpgsql;
--------------------------------------------------------------------------------------------------------------------------------------------------------------------

After that I would remove the foreign keys referencing schema.feature_id 
from the tables linked to feature within the particular schema, and add 
a CHECK constraint calling the previously defined function check_features

------------------------------------------------------------------------------------------------------
1. FEATURE RELATIONSHIP
ALTER TABLE schema_name.feature_relationship
DROP CONSTRAINT feature_relationship_subject_id_fkey
DROP CONSTRAINT feature_relationship_object_id_fkey
ADD CONSTRAINT feature_relationship_subject_id_check CHECK 
(schema_name.check_features(subject_id))
ADD CONSTRAINT feature_relationship_object_id_check CHECK 
(schema_name.check_features(object_id))

2. FEATUREPROP
ALTER TABLE schema_name.featureprop
DROP CONSTRAINT featureprop_feature_id_fkey
ADD CONSTRAINT featureprop_feature_id_fkey_check CHECK 
(schema_name.check_features(feature_id))

3. FEATURE_PUB
ALTER TABLE schema_name.feature_pub
DROP CONSTRAINT feature_pub_feature_id_fkey
ADD CONSTRAINT feature_pub_feature_id_fkey_check CHECK 
(schema_name.check_features(feature_id))

4. FEATURE_EXPRESSION
ALTER TABLE schema_name.feature_expression
DROP CONSTRAINT feature_expression_feature_id_fkey
ADD CONSTRAINT feature_expression_feature_id_fkey_check CHECK 
(schema_name.check_features(feature_id))
------------------------------------------------------------------------------------------------------

In this way all the records would stay connected and the links between 
tables more or less the same, there is no need to add extra tables or 
views, which makes it an easy solution in terms of not touching the 
"model" layer above in the CMS.

There are of course alternative solutions , for example making an extra 
table in the public schema containing all feature_ids(with triggers on 
INPUT UPDATE DELETE) from all species and then pointing the foreign keys 
to that table, but as the feature table is one of the most populated in 
the whole CHADO schema that would make a bit of extra load.

Another alternative would be making a whole layer of views and then 
querying the views instead of the underneath tables which would be ok at 
the database level but would require significant changes in the layers 
above.

I'd be thankful on your thoughts and suggestions on this problem and 
solution(s).

If some of my descriptions are not clear feel free to ask.

all the best,
Matija

[Gmod-schema] loading proteins

[Moseley, R. C. <mos...@or...>]

Hi,

I've loaded a fasta file containing protein sequences and synced them.  Everything seems to have worked fine, the right number of polypeptide features shows up in the feature composition graph, the polypeptide is linked to the appropriate mRNA feature, etc.  However, The feature name and unique name are shown as the same for the polypeptide even though I didn't specify that. The description line for each protein sequence looks like this:


>Kalax.1326s0009.1.p pacid=32530537 transcript=Kalax.1326s0009.1 locus=Kalax.1326s0009 ID=Kalax.1326s0009.1.v1.1 annot-version=v1.1


My advanced options where filled out like this:

-------------------------------------------------------


Regular expression for the name: >(.*?)\s   "Kalax.1326s0009.1.p"


Regular expression for the unique name:  >.*?ID=(.*?)\s     "Kalax.1326s0009.1.v1.1"


Relationship type: produced by


Regular expression for the parent:  >.*?ID=(.*?)\s     "Kalax.1326s0009.1.v1.1"


Parent type:  mRNA

--------------------------------------------------------


The mRNA name would be Kalax.1326s0009.1 and the unique name would be Kalax.1326s0009.1.v1.1.

The polypeptide name should be Kalax.1326s0009.1.p and the unique name should be Kalax.1326s0009.1.v1.1 but instead the name is Kalax.1326s0009.1.v1.1 and the unique name is Kalax.1326s0009.1.v1.1.


I looked into this with another Tripal user (Cc'ed) and we looked through the code of the fasta loader and I think we found an error but I can't remember what we found as it was two weeks ago when we looked into this.  Hopefully he can recall better what we found and respond.


Regards,


Rob Moseley

Re: [Gmod-schema] [GMOD-devel] Trouble with Chado installation

[Scott C. <sc...@sc...>]

Hi Haritha,

I'm cc'ing the schema mailing list, since that's where we discuss Chado
issues.  I haven't installed DBIx::DBStag on the command line/via cpan in a
really long time.  Since you're using Ubuntu, I'd suggest that you use
apt-get:

  sudo apt-get install libdbix-dbstag-perl

Virtually all (or actually all, I don't remember) prerequisites can be
installed with apt-get on Debian and Ubuntu systems.  There is also a
Debian package for Chado, but as I recall, it's pretty flawed, so I'd
suggest not using it.

Also, if you plan on using Tripal at all, I'd suggest installing Chado with
Tripal anyway, as it's easier.

Scott


On Thu, Nov 12, 2015 at 11:46 AM, Haritha Veeraghanta <hv...@co...>
wrote:

> Hello,
>
>
>
> I am working on a genome project for BTI. I am trying to install Chado on
> my Ubuntu machine on postgres. I followed all the steps of the GMOD
> installation verbatim. I got the GMOD bundle installed. I am running into
> trouble with the DBIs::DBStag (DBIx::DBSchema is installed). When I reach
> the step “make” after the makefile.pl, I get repeated error at the same
> line in the script at:
>
>
>
> t/cvterm.t ...... Cannot quote a reference at
> /home/hv66/Downloads/DBIx-DBStag-0.10/blib/lib/DBIx/DBStag.pm line 3736.
>
> t/cvterm.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)
>
>
>
> I am not sure what I am missing. When I checked for the bundle installs,
> all others are up to date.
>
>
>
> The result is FAIL, but I am pretty sure d it yesterday night, it showed
> me a PASS. I might be severely mistaken.
>
>
>
> Please help me out,
>
>
>
> Thanks
>
> Haritha
>
>
>
> --
>
>
>
> Haritha Veeraghanta
>
> Data Architect
>
> Genomics & Open-source Breeding Informatics Initiative (GOBII)
>
> hv...@co...
>
> (607) 254-2734
>
> [image: logo] <http://bti.cornell.edu>
>
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>


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

Re: [Gmod-schema] Error while installing CVs -Relationship Ontology (ro.obo)

[Scott C. <sc...@sc...>]

Hi Adawiah,

Sorry about that; this is a known problem.

You can use the link I provided in this issue report:

https://github.com/GMOD/Chado/issues/17

and then use the commands in the INSTALL.Chado document for loading them
manually.

Scott


On Thu, Nov 5, 2015 at 6:42 PM, Adawiah Zainal <rab...@gm...
> wrote:

> Dear Scott,
>
> I was getting an error when submitting the Relationship Ontology using
> Tripal 2.0 Web Interface.
> But it is fine for other ontologies.
> Here I attached the snapshot of error.
>
> It looks like the URL (http://www.obofoundry.org/ro/ro.obo) doesn't has
> the .obo file.
>
> How can I do it manually?
>
> Thanks & Regards,
>



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

[Gmod-schema] Time is short: GMOD related talks at PAG

[Scott C. <sc...@sc...>]

Hi All,

I realize time is short for this: there is a hard deadline of November 6
for entering speakers for the Plant and Animal Genomes meeting in January
2016.  If you would like to give a talk in the GMOD section of the meeting,
please get me a title and brief description (an abstract would be good but
not required) by November 5.  The talk can take the form of a project
update, user "story" or interpretive dance.  Speakers get early
registration discount no matter when they register, so if you haven't
registered yet, it would be like getting $100 off.

Sorry for the short notice, and I look forward to seeing in San Diego!
Scott


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

Re: [Gmod-schema] [Gmod-tripal] GMOD expression data

[Scott C. <sc...@sc...>]

Hi Meg,

So what do you do now, store the data in a custom schema, or do you
shoe-horn it into Chado?  I assume the goal is to gather information about
the experiment and then link it to an external data file (presumably BAM or
BigWig).

Thanks,
Scott



On Tue, Nov 3, 2015 at 7:34 AM, Meg Staton <me...@gm...> wrote:

> Hi, Yasir,
> There are a number of groups working on this right now; I hope to have an
> expression data module publicly launched by spring.
>
> Andrew Farmer and I have discussed the incompatibility of chado with
> RNASEq expression data - its really designed for microarray data (ie the
> MAGE module). The current code from my lab will use the MAGE module, but in
> the long term it would be nice to update the schema.
>
> Meg
>
> On Mon, Nov 2, 2015 at 11:47 AM, Scott Cain <sc...@sc...> wrote:
>
>> Hi Yasir,
>>
>> There is a module for storing expression data, but there isn't a
>> dedicated command line tool for storing expression data.  I cc'ed both the
>> Chado and Tripal mailing lists to get input from users for how they deal
>> with expression data like this.  Perhaps you could also flesh out a little
>> what organism you're working with and what sort of data you have.
>>
>> Scott
>>
>>
>> On Mon, Nov 2, 2015 at 10:55 AM, Yasir Suhail <yas...@gm...>
>> wrote:
>>
>>> Dear Scott,
>>>
>>> Thank you for your help on Chado. Is there a chado module for expression
>>> data? I want to load my RNAseq expression results on a GMOD website. Could
>>> you please point me in the right direction?
>>>
>>> Best,
>>> yasir
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-tripal mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>
> --
> Margaret Staton
> Assistant Professor
> Department of Entomology and Plant Pathology
> 370 PBB, 2505 EJ Chapman Drive
> Knoxville, TN 37996-4560
>
> 864-506-4515 Mobile
> mst...@ut...
>
>
>
>
>


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

Re: [Gmod-schema] [Gmod-tripal] GMOD expression data

[Meg S. <me...@gm...>]

Hi, Yasir,
There are a number of groups working on this right now; I hope to have an
expression data module publicly launched by spring.

Andrew Farmer and I have discussed the incompatibility of chado with RNASEq
expression data - its really designed for microarray data (ie the MAGE
module). The current code from my lab will use the MAGE module, but in the
long term it would be nice to update the schema.

Meg

On Mon, Nov 2, 2015 at 11:47 AM, Scott Cain <sc...@sc...> wrote:

> Hi Yasir,
>
> There is a module for storing expression data, but there isn't a dedicated
> command line tool for storing expression data.  I cc'ed both the Chado and
> Tripal mailing lists to get input from users for how they deal with
> expression data like this.  Perhaps you could also flesh out a little what
> organism you're working with and what sort of data you have.
>
> Scott
>
>
> On Mon, Nov 2, 2015 at 10:55 AM, Yasir Suhail <yas...@gm...>
> wrote:
>
>> Dear Scott,
>>
>> Thank you for your help on Chado. Is there a chado module for expression
>> data? I want to load my RNAseq expression results on a GMOD website. Could
>> you please point me in the right direction?
>>
>> Best,
>> yasir
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>


-- 
Margaret Staton
Assistant Professor
Department of Entomology and Plant Pathology
370 PBB, 2505 EJ Chapman Drive
Knoxville, TN 37996-4560

864-506-4515 Mobile
mst...@ut...

Re: [Gmod-schema] GMOD expression data

[Yasir S. <yas...@gm...>]

Hi Scott,

I am working on Brassica napus RNAseq data for one treatment, 2 time
points.

I have some syntenic homologs, and pathways of interest of a related
species (Arabidopsis). I will be happy with any tools that may provide
users with a way to select and visualize the gene expression data and look
at genes of interest.

Best,
yasir

On Mon, Nov 2, 2015 at 11:47 AM, Scott Cain <sc...@sc...> wrote:

> Hi Yasir,
>
> There is a module for storing expression data, but there isn't a dedicated
> command line tool for storing expression data.  I cc'ed both the Chado and
> Tripal mailing lists to get input from users for how they deal with
> expression data like this.  Perhaps you could also flesh out a little what
> organism you're working with and what sort of data you have.
>
> Scott
>
>
> On Mon, Nov 2, 2015 at 10:55 AM, Yasir Suhail <yas...@gm...>
> wrote:
>
>> Dear Scott,
>>
>> Thank you for your help on Chado. Is there a chado module for expression
>> data? I want to load my RNAseq expression results on a GMOD website. Could
>> you please point me in the right direction?
>>
>> Best,
>> yasir
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

Re: [Gmod-schema] GMOD expression data

[Scott C. <sc...@sc...>]

Hi Yasir,

There is a module for storing expression data, but there isn't a dedicated
command line tool for storing expression data.  I cc'ed both the Chado and
Tripal mailing lists to get input from users for how they deal with
expression data like this.  Perhaps you could also flesh out a little what
organism you're working with and what sort of data you have.

Scott


On Mon, Nov 2, 2015 at 10:55 AM, Yasir Suhail <yas...@gm...>
wrote:

> Dear Scott,
>
> Thank you for your help on Chado. Is there a chado module for expression
> data? I want to load my RNAseq expression results on a GMOD website. Could
> you please point me in the right direction?
>
> Best,
> yasir
>



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

Re: [Gmod-schema] Chado/GMOD doesn't parse OBO

[Yasir S. <yas...@gm...>]

So I found that the stag-storenode scripts name was wrong. After changing
line 352 of  from
my $stag_string = "stag-storenode.pl -d
'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
to
my $stag_string = "stag-storenode -d
'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
The previous error goes away but I get:
Maybe DBIx::DBSchema does not work with your database? at
/usr/share/perl5/DBIx/DBStag.pm line 427
    DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x20c4b78)', 'cv') called
at /usr/share/perl5/DBIx/DBStag.pm line 1265
    DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x20c4b78)',
'Data::Stag::StagImpl=ARRAY(0x2e058e8)') called at
/usr/share/perl5/DBIx/DBStag.pm line 1180
    DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x20c4b78)',
'Data::Stag::StagImpl=ARRAY(0x2ccc6f0)') called at /usr/bin/stag-storenode
line 88
    eval {...} called at /usr/bin/stag-storenode line 87
    main::store('Data::Stag::BaseHandler=HASH(0x2bafa20)',
'Data::Stag::StagImpl=ARRAY(0x2ccc6f0)') called at /usr/bin/stag-storenode
line 137
    main::__ANON__('Data::Stag::BaseHandler=HASH(0x2bafa20)',
'Data::Stag::StagImpl=ARRAY(0x2ccc6f0)') called at
/usr/share/perl5/Data/Stag/BaseHandler.pm line 594

Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2bafa20)',
'cv') called at /usr/share/perl5/Data/Stag/BaseHandler.pm line 742

Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2bafa20)',
'HASH(0x2ccc378)') called at /usr/share/perl5/XML/Parser/PerlSAX.pm line 239

XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x2c9f6c8)',
'XML::Parser::Expat=HASH(0x2bf09a0)', 'cv') called at
/usr/share/perl5/XML/Parser/PerlSAX.pm line 79
    XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x2bf09a0)',
'cv') called at /usr/lib/perl5/XML/Parser/Expat.pm line 470
    XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x2bf09a0)',
'FileHandle=GLOB(0x2ce7970)') called at /usr/lib/perl5/XML/Parser.pm line
187
    eval {...} called at /usr/lib/perl5/XML/Parser.pm line 186
    XML::Parser::parse('XML::Parser=HASH(0x2bd9cd0)',
'FileHandle=GLOB(0x2ce7970)') called at
/usr/share/perl5/XML/Parser/PerlSAX.pm line 146
    XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x2c9f6c8)',
'Handler', 'Data::Stag::BaseHandler=HASH(0x2bafa20)', 'Source',
'HASH(0x2c9fa88)') called at /usr/share/perl5/Data/Stag/XMLParser.pm line 69

Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2bd94c0)',
'FileHandle=GLOB(0x2ce7970)') called at
/usr/share/perl5/Data/Stag/BaseGenerator.pm line 476

Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2bd94c0)',
'-file', 'tmp/load/etc/feature_property.oboxml', '-str', undef, '-fh',
undef) called at /usr/share/perl5/Data/Stag/XMLParser.pm line 58
    Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2bd94c0)',
'-file', 'tmp/load/etc/feature_property.oboxml', '-str', undef, '-fh',
undef) called at /usr/share/perl5/Data/Stag/StagImpl.pm line 275
    Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, '-file',
'tmp/load/etc/feature_property.oboxml', '-handler',
'Data::Stag::BaseHandler=HASH(0x2bafa20)') called at
/usr/share/perl5/Data/Stag.pm line 181
    Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file',
'tmp/load/etc/feature_property.oboxml', '-handler',
'Data::Stag::BaseHandler=HASH(0x2bafa20)') called at
/usr/bin/stag-storenode line 143
System call 'stag-storenode -d
'dbi:Pg:dbname=drupal;host=localhost;port=5432' --user ubuntu
tmp/load/etc/feature_property.oboxml' failed: 256
failed: 256 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
make: *** [ontologies] Error 1


On Sun, Nov 1, 2015 at 1:47 AM, Yasir Suhail <yas...@gm...> wrote:

> Dear GMOD devs and users,
>
> I am trying to follow the GMOD 2013 tutorial (
> http://gmod.org/wiki/Chado_Tutorial) and used the latest AMI to start an
> instance in AWS. It seems that Chado::Builder fails to parse OBO files.
> Please let me know what I could be doing wrong or other suggestions.
> When I try to run make ontologies, this is what I see:
>
> ubuntu@ip-10-170-117-101:~/sources/chado/chado$ make ontologies
> ./Build ontologies
> Available ontologies:
> [1] Relationship Ontology
> [2] Sequence Ontology
> [3] Gene Ontology
> [4] Chado Feature Properties
> [5] Plant Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0]  3,4,5
> fetching files for Gene Ontology
>   +http://www.geneontology.org/ontology/gene_ontology.obo
>     ./tmp/go/go.obo is up to date
> fetching files for Chado Feature Properties
>   +load/etc/feature_property.obo
>     loading...sh: 1: stag-storenode.pl: not found
> System call 'stag-storenode.pl -d
> 'dbi:Pg:dbname=drupal;host=localhost;port=5432' --user ubuntu
> tmp/load/etc/feature_property.oboxml' failed: 32512
> failed: 32512 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
> make: *** [ontologies] Error 127
> ubuntu@ip-10-170-117-101:~/sources/chado/chado$
>
> Best,
> yasir
>

[Gmod-schema] Chado/GMOD doesn't parse OBO

[Yasir S. <yas...@gm...>]

Dear GMOD devs and users,

I am trying to follow the GMOD 2013 tutorial (
http://gmod.org/wiki/Chado_Tutorial) and used the latest AMI to start an
instance in AWS. It seems that Chado::Builder fails to parse OBO files.
Please let me know what I could be doing wrong or other suggestions.
When I try to run make ontologies, this is what I see:

ubuntu@ip-10-170-117-101:~/sources/chado/chado$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  3,4,5
fetching files for Gene Ontology
  +http://www.geneontology.org/ontology/gene_ontology.obo
    ./tmp/go/go.obo is up to date
fetching files for Chado Feature Properties
  +load/etc/feature_property.obo
    loading...sh: 1: stag-storenode.pl: not found
System call 'stag-storenode.pl -d
'dbi:Pg:dbname=drupal;host=localhost;port=5432' --user ubuntu
tmp/load/etc/feature_property.oboxml' failed: 32512
failed: 32512 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
make: *** [ontologies] Error 127
ubuntu@ip-10-170-117-101:~/sources/chado/chado$

Best,
yasir

Re: [Gmod-schema] What sequence ontology to get?

[Karl O. P. <ko...@me...>]

On Mon, 27 Jul 2015 13:44:36 -0700
Chris Mungall <cjm...@lb...> wrote:

> Yes, that's right (it may point to something else in the future, it
> shouldn't really be exposing the 'so-xp' filename, but this shouldn't
> affect anything)
> 
> On Wed, Jul 22, 2015 at 5:21 PM, Karl O. Pinc <ko...@me...> wrote:

> > So the correct SO to download is the so-xp.obo, right?

Thanks!





Karl <ko...@me...>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

Re: [Gmod-schema] What sequence ontology to get?

[Chris M. <cjm...@lb...>]

Yes, that's right (it may point to something else in the future, it
shouldn't really be exposing the 'so-xp' filename, but this shouldn't
affect anything)

On Wed, Jul 22, 2015 at 5:21 PM, Karl O. Pinc <ko...@me...> wrote:

> On Wed, 22 Jul 2015 16:50:56 -0700
> "Chris Mungall" <cjm...@lb...> wrote:
>
> > I recommend using purls for all ontologies
> >
> > E.g.
> >
> > http://purl.obolibrary.org/obo/so.obo
> >
> > These should remain stable allowing the underlying delivery system to
> > change
>
> Ok.  Thanks.
>
> So the correct SO to download is the so-xp.obo, right?
> (That's what the prul points to.)
>
> >
> > On 22 Jul 2015, at 16:04, Karl O. Pinc wrote:
> >
> > > Hi,
> > >
> > > Looks like the sequence ontology has moved from sourceforge
> > > to github.  The url in chado/load/tt2/load.conf.tt2
> > > no longer works.
> > >
> > > What is the corresponding url on github?
> > > Is it the first so download link of:
> > >
> https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo
> > >
> > > ?
> > >
> > > The various choices are at:
> > > https://github.com/The-Sequence-Ontology/SO-Ontologies
> > >
> > > Thanks.
> > >
> > > Karl <ko...@me...>
> > > Free Software:  "You don't pay back, you pay forward."
> > >               -- Robert A. Heinlein
> > >
> > >
> ------------------------------------------------------------------------------
> > > _______________________________________________
> > > Gmod-schema mailing list
> > > Gmo...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
>
>
>
>
>
> Karl <ko...@me...>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>

[Gmod-schema] Docker images for Tripal

[Eric R. <es...@ta...>]

Howdy all,

Quick release announcement; I've built Docker images for Chado
<https://hub.docker.com/u/erasche/chado/>/WebApollo
<https://hub.docker.com/u/erasche/webapollo/> 1.0/JBrowse
<https://hub.docker.com/u/erasche/jbrowse/> in the past, and wanted to
mention the addition of a Tripal
<https://registry.hub.docker.com/u/erasche/tripal/> image to that set.

For those who just want to play around quickly with a lightweight instance,
Docker images offer a nice alternative to full VMs.

   - https://github.com/erasche/docker-tripal
   - https://registry.hub.docker.com/u/erasche/tripal/

If you have suggestions/comments/concerns, please let me know!

Known Issues: Currently the tripal image installs one of my precompiled
chado schemas with all 5 built-in ontologies on first-run, I'm working on
changing that to depend on my chado image, such that connecting WebApollo
to the same chado image is possible.
Ciao,
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
es...@ta...
ras...@ya...

Re: [Gmod-schema] Ontologies and Chado

[Siddhartha B. <bi...@gm...>]

On Thu, 23 Jul 2015, Chris Mungall wrote:

>    All the relation IDs in RO are standard OBO-style RO:nnnnnn, this would be
>    stored in dbxref table in the usual way. The labels are human readable
>    (and chado shouldn't care about the labels)
So my application code that search by name have to be changed after
switching to new RO(name with space and no more underscores). Does it
also means that search by name is not recommended.

-siddhartha

> 
>    Haven't checked the stag issue not sure when I would get a chance to
>    On Thu, Jul 23, 2015 at 10:12 AM, Scott Cain <sc...@sc...> wrote:
> 
>      Hi Chris,
>      I'm fine with creating a "Chado edition" of RO; the other thing we would
>      certainly need is a 'derives_from', but it looks like that is present in
>      RO, though I'm noticing that the names of all of the features in RO lack
>      underscores--is that how they'd get stored in Chado as well?A  Or is
>      that part of what would be in the Chado edition?
>      Of course, it must also be loadable in Chado, and RO currently fails to
>      load using xsltproc/DBIx::DBStag in Chado, but that may be due to the
>      missing is_a or something else, I haven't looked closely at what the
>      problem is.A  If another method is preferable, that needs to be worked
>      in to the build procedure.
>      Thanks,
>      Scott
>      (cross posted from the github issue, and bfo-devel removed, since it
>      will bounce.)
>      On Thu, Jul 23, 2015 at 12:43 PM, Chris Mungall <cjm...@lb...>
>      wrote:
> 
>        On 23 Jul 2015, at 8:56, Scott Cain wrote:
> 
>          Hi all,
> 
>          As a few of us are working on new release of Chado, I've discovered
>          the
>          wonder of BFO (Big F'ing Ontology, right?)
> 
>          So here's my very vague question: what do I need to know?A  It seems
>          that
>          OBO_REL no longer exists, which is going to be a hassle for many
>          Chado-related tools, which considered it fairly fundamental (with
>          its is_a
>          and part_of and a consistent cv.name of 'relationship').A  I'm
>          guessing BFO
>          should completely replace OBO_REL, and RO is not really going to be
>          needed
>          in general instances of Chado (though obviously some users may want
>          it, it
>          isn't fundamental in the same way).
> 
>        Hi Scott,
> 
>        I recommend that Chado uses RO, you can get the .obo from here:
>        http://purl.obolibrary.org/obo/ro.obo
> 
>        Note this includes some classes from BFO, it should be possible to
>        produce a more minimal relation only edition/subset.
> 
>        There are two pain points for you:
> 
>        A 1. Chado needs an edge label for "is_a"
>        A 2. There is code that makes an assumption that there will be a
>        relation with OBO-Format ID "OBO_REL:part_of"
> 
>        We can make a special edition just for Chado. For 1, we would add a
>        special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really
>        make any sense in terms of the mapping to OWL, where SubClass is a
>        builtin construct. But we can ignore this, as this edition is just for
>        Chado.
> 
>        For 2, it's up to you. You can try and coordinate the move for Chado
>        to use BFO:0000050 (which is in RO). Or we can have the Chado edition
>        have the old OBO_REL:part_of as well, with some documentation that the
>        goal is to eventually move away from this, and an equivalent
>        properties axiom (not something we'd normally do, but this is a
>        specific edition designed to solve a particular problem)
> 
>        I filed a ticket for this:
>        https://github.com/oborel/obo-relations/issues/68
> 
>          Anything else?A  Also, what is the obo purl for BFO? I tried to
>          guess it a
>          few times and failed.
> 
>          Thanks,
>          Scott
> 
>          --
>          ------------------------------------------------------------------------
>          Scott Cain, Ph. D.A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A 
>          A scott at scottcain dot
>          net
>          GMOD Coordinator (http://gmod.org/)A  A  A  A  A  A  A  A  A  A 
>          A 216-392-3087
>          Ontario Institute for Cancer Research
>          ------------------------------------------------------------------------------
>          _______________________________________________
>          Gmod-schema mailing list
>          Gmo...@li...
>          https://lists.sourceforge.net/lists/listinfo/gmod-schema
> 
>      --
>      ------------------------------------------------------------------------
>      Scott Cain, Ph. D.A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A  A A 
>      scott at scottcain dot net
>      GMOD Coordinator (http://gmod.org/)A  A  A  A  A  A  A  A  A  A A 
>      216-392-3087
>      Ontario Institute for Cancer Research

> ------------------------------------------------------------------------------

> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

Re: [Gmod-schema] Ontologies and Chado

[Scott C. <sc...@sc...>]

"shouldn't care about the labels"--nice sentiment, that. :-)

I'll worry about stag after I have a RO I can use.

On Thu, Jul 23, 2015 at 2:05 PM, Chris Mungall <cjm...@lb...> wrote:

> All the relation IDs in RO are standard OBO-style RO:nnnnnn, this would be
> stored in dbxref table in the usual way. The labels are human readable (and
> chado shouldn't care about the labels)
>
> Haven't checked the stag issue not sure when I would get a chance to
>
> On Thu, Jul 23, 2015 at 10:12 AM, Scott Cain <sc...@sc...> wrote:
>
>> Hi Chris,
>>
>> I'm fine with creating a "Chado edition" of RO; the other thing we would
>> certainly need is a 'derives_from', but it looks like that is present in
>> RO, though I'm noticing that the names of all of the features in RO lack
>> underscores--is that how they'd get stored in Chado as well?  Or is that
>> part of what would be in the Chado edition?
>>
>> Of course, it must also be loadable in Chado, and RO currently fails to
>> load using xsltproc/DBIx::DBStag in Chado, but that may be due to the
>> missing is_a or something else, I haven't looked closely at what the
>> problem is.  If another method is preferable, that needs to be worked in to
>> the build procedure.
>>
>> Thanks,
>> Scott
>>
>> (cross posted from the github issue, and bfo-devel removed, since it will
>> bounce.)
>>
>> On Thu, Jul 23, 2015 at 12:43 PM, Chris Mungall <cjm...@lb...>
>> wrote:
>>
>>>
>>>
>>> On 23 Jul 2015, at 8:56, Scott Cain wrote:
>>>
>>>  Hi all,
>>>>
>>>> As a few of us are working on new release of Chado, I've discovered the
>>>> wonder of BFO (Big F'ing Ontology, right?)
>>>>
>>>> So here's my very vague question: what do I need to know?  It seems that
>>>> OBO_REL no longer exists, which is going to be a hassle for many
>>>> Chado-related tools, which considered it fairly fundamental (with its
>>>> is_a
>>>> and part_of and a consistent cv.name of 'relationship').  I'm guessing
>>>> BFO
>>>> should completely replace OBO_REL, and RO is not really going to be
>>>> needed
>>>> in general instances of Chado (though obviously some users may want it,
>>>> it
>>>> isn't fundamental in the same way).
>>>>
>>>
>>> Hi Scott,
>>>
>>> I recommend that Chado uses RO, you can get the .obo from here:
>>> http://purl.obolibrary.org/obo/ro.obo
>>>
>>> Note this includes some classes from BFO, it should be possible to
>>> produce a more minimal relation only edition/subset.
>>>
>>> There are two pain points for you:
>>>
>>>  1. Chado needs an edge label for "is_a"
>>>  2. There is code that makes an assumption that there will be a relation
>>> with OBO-Format ID "OBO_REL:part_of"
>>>
>>> We can make a special edition just for Chado. For 1, we would add a
>>> special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really make
>>> any sense in terms of the mapping to OWL, where SubClass is a builtin
>>> construct. But we can ignore this, as this edition is just for Chado.
>>>
>>> For 2, it's up to you. You can try and coordinate the move for Chado to
>>> use BFO:0000050 (which is in RO). Or we can have the Chado edition have the
>>> old OBO_REL:part_of as well, with some documentation that the goal is to
>>> eventually move away from this, and an equivalent properties axiom (not
>>> something we'd normally do, but this is a specific edition designed to
>>> solve a particular problem)
>>>
>>> I filed a ticket for this:
>>> https://github.com/oborel/obo-relations/issues/68
>>>
>>>
>>>> Anything else?  Also, what is the obo purl for BFO? I tried to guess it
>>>> a
>>>> few times and failed.
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot
>>>> net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>> ------------------------------------------------------------------------------
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> Gmo...@li...
>>>> 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
>>
>
>


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

Re: [Gmod-schema] Ontologies and Chado

[Chris M. <cjm...@lb...>]

On 23 Jul 2015, at 8:56, Scott Cain wrote:

> Hi all,
>
> As a few of us are working on new release of Chado, I've discovered 
> the
> wonder of BFO (Big F'ing Ontology, right?)
>
> So here's my very vague question: what do I need to know?  It seems 
> that
> OBO_REL no longer exists, which is going to be a hassle for many
> Chado-related tools, which considered it fairly fundamental (with its 
> is_a
> and part_of and a consistent cv.name of 'relationship').  I'm guessing 
> BFO
> should completely replace OBO_REL, and RO is not really going to be 
> needed
> in general instances of Chado (though obviously some users may want 
> it, it
> isn't fundamental in the same way).

Hi Scott,

I recommend that Chado uses RO, you can get the .obo from here: 
http://purl.obolibrary.org/obo/ro.obo

Note this includes some classes from BFO, it should be possible to 
produce a more minimal relation only edition/subset.

There are two pain points for you:

  1. Chado needs an edge label for "is_a"
  2. There is code that makes an assumption that there will be a 
relation with OBO-Format ID "OBO_REL:part_of"

We can make a special edition just for Chado. For 1, we would add a 
special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really 
make any sense in terms of the mapping to OWL, where SubClass is a 
builtin construct. But we can ignore this, as this edition is just for 
Chado.

For 2, it's up to you. You can try and coordinate the move for Chado to 
use BFO:0000050 (which is in RO). Or we can have the Chado edition have 
the old OBO_REL:part_of as well, with some documentation that the goal 
is to eventually move away from this, and an equivalent properties axiom 
(not something we'd normally do, but this is a specific edition designed 
to solve a particular problem)

I filed a ticket for this:
https://github.com/oborel/obo-relations/issues/68

>
> Anything else?  Also, what is the obo purl for BFO? I tried to guess 
> it a
> few times and failed.
>
> Thanks,
> Scott
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at 
> scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

Re: [Gmod-schema] Ontologies and Chado

[Chris M. <cjm...@lb...>]

All the relation IDs in RO are standard OBO-style RO:nnnnnn, this would be
stored in dbxref table in the usual way. The labels are human readable (and
chado shouldn't care about the labels)

Haven't checked the stag issue not sure when I would get a chance to

On Thu, Jul 23, 2015 at 10:12 AM, Scott Cain <sc...@sc...> wrote:

> Hi Chris,
>
> I'm fine with creating a "Chado edition" of RO; the other thing we would
> certainly need is a 'derives_from', but it looks like that is present in
> RO, though I'm noticing that the names of all of the features in RO lack
> underscores--is that how they'd get stored in Chado as well?  Or is that
> part of what would be in the Chado edition?
>
> Of course, it must also be loadable in Chado, and RO currently fails to
> load using xsltproc/DBIx::DBStag in Chado, but that may be due to the
> missing is_a or something else, I haven't looked closely at what the
> problem is.  If another method is preferable, that needs to be worked in to
> the build procedure.
>
> Thanks,
> Scott
>
> (cross posted from the github issue, and bfo-devel removed, since it will
> bounce.)
>
> On Thu, Jul 23, 2015 at 12:43 PM, Chris Mungall <cjm...@lb...> wrote:
>
>>
>>
>> On 23 Jul 2015, at 8:56, Scott Cain wrote:
>>
>>  Hi all,
>>>
>>> As a few of us are working on new release of Chado, I've discovered the
>>> wonder of BFO (Big F'ing Ontology, right?)
>>>
>>> So here's my very vague question: what do I need to know?  It seems that
>>> OBO_REL no longer exists, which is going to be a hassle for many
>>> Chado-related tools, which considered it fairly fundamental (with its
>>> is_a
>>> and part_of and a consistent cv.name of 'relationship').  I'm guessing
>>> BFO
>>> should completely replace OBO_REL, and RO is not really going to be
>>> needed
>>> in general instances of Chado (though obviously some users may want it,
>>> it
>>> isn't fundamental in the same way).
>>>
>>
>> Hi Scott,
>>
>> I recommend that Chado uses RO, you can get the .obo from here:
>> http://purl.obolibrary.org/obo/ro.obo
>>
>> Note this includes some classes from BFO, it should be possible to
>> produce a more minimal relation only edition/subset.
>>
>> There are two pain points for you:
>>
>>  1. Chado needs an edge label for "is_a"
>>  2. There is code that makes an assumption that there will be a relation
>> with OBO-Format ID "OBO_REL:part_of"
>>
>> We can make a special edition just for Chado. For 1, we would add a
>> special stanza with OBO-Format ID "OBO_REL:is_a". This doesn't really make
>> any sense in terms of the mapping to OWL, where SubClass is a builtin
>> construct. But we can ignore this, as this edition is just for Chado.
>>
>> For 2, it's up to you. You can try and coordinate the move for Chado to
>> use BFO:0000050 (which is in RO). Or we can have the Chado edition have the
>> old OBO_REL:part_of as well, with some documentation that the goal is to
>> eventually move away from this, and an equivalent properties axiom (not
>> something we'd normally do, but this is a specific edition designed to
>> solve a particular problem)
>>
>> I filed a ticket for this:
>> https://github.com/oborel/obo-relations/issues/68
>>
>>
>>> Anything else?  Also, what is the obo purl for BFO? I tried to guess it a
>>> few times and failed.
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot
>>> net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> Gmo...@li...
>>> 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
>