gmod-schema — For discussion of GMOD schema development

Re: [Gmod-schema] Vocabularies with terms from other ontologies

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

Hi Stephen,
For my solution, 
As discussed in the github issue mentioned below
https://github.com/oborel/obo-relations/issues/68
I took a much low key approach(standing on shoulder of giant) by try to
solve it on the file level. Using owltools,  the makefile here
https://github.com/oborel/obo-relations/pull/95/commits/966f0826cf139396766f48c7ea51754dd09915cf 
serializes(import/merge etc) all terms to *ro* namespace along with
removing cross ontology terms. The resultant obo file is loadable in
in current chado. I did some minor modifications in my fork for the time
being until the piece get merged in master.
Now to understand your direct owl based approach i wonder what are 
key differences ....
* ro.owl gets terms from bfo.owl(defined in core.owl). Which namespace
  you are using for that, *ro* or something else. owltools merge process brings
  everything to a unified *ro* namespace.
* Are you filtering or keeping the cross-ontology terms(GO/PATO). If you
  are keeping them what advantages does it provide or in other words
  what am i going to miss if i don't have them loaded with *ro*.
  I am asking this because in my process,  owltools filter them out.
And frankly, your approach(particularly 2) is interesting for me and
which in turn actually touches a broader problem. As lot of the
ontologies are switching to a semantic owl path(obo is just for compatibility),
how much of it we really need to represent them in chado.
* Cross importing of other ontology in owl. How do i know which ontology
  is needed for data representation in chado(need to load) and which
  one in needed for ontology development(need to discard).
* If we somehow figure that out, how do i solve the dependencies at
  runtime.
* Last but not least, what kind of tools/lib support we have for
  managing this. From the top of my head, json-ld is a good
  representation of rdf that has multiple language bindings, but i don't
  how much of it help it could provide in case of handling owl.

thanks,
-siddhartha


  
 




On Tue, 12 Apr 2016, Chris Mungall wrote:

> Hi Stephen,
> 
> A couple of pointers to OWL parsers:
> 
>   - don't target the XML, this is 2 levels of abstraction too low. I can 
> guarantee anything you write here will likely break
>   - targeting the RDF level of abstraction is better and there are RDF 
> parsers for every language. Still, it can be a low level way to view OWL 
> and there are many gotchas
>   - using an OWL API is best. Unfortunately there is only the java 
> OWLAPI, so if you aren't in a JVM language this is harder
> 
> We may have a standard JSON/YAML that is OWL-complete in the future that 
> would be a better target. Having said that, a JVM language is a good 
> choice for a Chado ontology loader due to access to reasoners (e.g. 
> cvtermpath).
> 
> With the syntactic issues aside, there is still the issue of how to map 
> different kinds of OWL axioms to relationships. I recommend following 
> the same mapping we do for graph databases documented here:
> https://github.com/SciCrunch/SciGraph/wiki/
> 
> As for RO, there is always the solution of tailoring the RO release for 
> Chado, thanks for contributing to the discussion here:
> https://github.com/oborel/obo-relations/issues/68
> 
> For your solutions below, I like 2 best.
> 
> On 12 Apr 2016, at 8:48, Stephen Ficklin wrote:
> 
> > Hi All,
> >
> > We're working on an OWL parser for Tripal.  Specifically we are trying
> > to load the new Relationship Ontology (RO).   This ontology includes
> > terms from other ontologies.  There's no problem importing these
> > dependent ontologies.   But, Chado does not have a direct way to 
> > include
> > terms from one vocabulary in another.   Here are some options I came 
> > up
> > with:
> >
> > 1) Make note of the inclusion in the cvtermprop table
> > 2) Create a new custom cvterm_cv table to associate terms from one
> > vocabulary with another
> > 3) Duplicate the term in both vocabularies.
> >
> > There are issues with all 3 methods.  I don't care for option 1 as the
> > association isn't really a property of the term.  I also don't like
> > option 3 because if the term is updated in the parent vocabulary the
> > changes are not reflected in the copy.  My favorite option is 2 but 
> > the
> > fill_cvtermpath() function will not create a complete representation 
> > of
> > the vocabulary in the cvtermpath table. We could replace this function
> > with a version that can use a new cvterm_cv table.
> >
> > Are there any objections to using option2?  Does anyone have other 
> > ideas
> > that may work?
> >
> > Thanks,
> > Stephen
> >
> > ------------------------------------------------------------------------------
> > Find and fix application performance issues faster with Applications 
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Re: [Gmod-schema] Vocabularies with terms from other ontologies

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

Hi Stephen,

A couple of pointers to OWL parsers:

  - don't target the XML, this is 2 levels of abstraction too low. I can 
guarantee anything you write here will likely break
  - targeting the RDF level of abstraction is better and there are RDF 
parsers for every language. Still, it can be a low level way to view OWL 
and there are many gotchas
  - using an OWL API is best. Unfortunately there is only the java 
OWLAPI, so if you aren't in a JVM language this is harder

We may have a standard JSON/YAML that is OWL-complete in the future that 
would be a better target. Having said that, a JVM language is a good 
choice for a Chado ontology loader due to access to reasoners (e.g. 
cvtermpath).

With the syntactic issues aside, there is still the issue of how to map 
different kinds of OWL axioms to relationships. I recommend following 
the same mapping we do for graph databases documented here:
https://github.com/SciCrunch/SciGraph/wiki/

As for RO, there is always the solution of tailoring the RO release for 
Chado, thanks for contributing to the discussion here:
https://github.com/oborel/obo-relations/issues/68

For your solutions below, I like 2 best.

On 12 Apr 2016, at 8:48, Stephen Ficklin wrote:

> Hi All,
>
> We're working on an OWL parser for Tripal.  Specifically we are trying
> to load the new Relationship Ontology (RO).   This ontology includes
> terms from other ontologies.  There's no problem importing these
> dependent ontologies.   But, Chado does not have a direct way to 
> include
> terms from one vocabulary in another.   Here are some options I came 
> up
> with:
>
> 1) Make note of the inclusion in the cvtermprop table
> 2) Create a new custom cvterm_cv table to associate terms from one
> vocabulary with another
> 3) Duplicate the term in both vocabularies.
>
> There are issues with all 3 methods.  I don't care for option 1 as the
> association isn't really a property of the term.  I also don't like
> option 3 because if the term is updated in the parent vocabulary the
> changes are not reflected in the copy.  My favorite option is 2 but 
> the
> fill_cvtermpath() function will not create a complete representation 
> of
> the vocabulary in the cvtermpath table. We could replace this function
> with a version that can use a new cvterm_cv table.
>
> Are there any objections to using option2?  Does anyone have other 
> ideas
> that may work?
>
> Thanks,
> Stephen
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications 
> Manager
> Applications Manager provides deep performance insights into multiple 
> tiers of
> your business applications. It resolves application problems quickly 
> and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> _______________________________________________
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Re: [Gmod-schema] Vocabularies with terms from other ontologies

[valentin.guignon <gu...@ci...>]

Hi Stephen and the list,



Solution 3) does not require any change in the existing schema 
(cvterm_relationship table could be used for the link) but as you 
mentionned, vocabulary updates may rise some issues. However, we can 
think of a table trigger that could automatically propagate such an 
update of the relationship between those terms when its type is 'copy 
of' (or whatever you want to name that relation type).
Here is my idea of such a trigger (not tested):
----------
CREATE OR REPLACE FUNCTION cvterm_multicv_update() RETURNS TRIGGER AS
$code$
   DECLARE
     copy_cvterm RECORD;
   BEGIN
     UPDATE cvterm cvt
       SET name = NEW.name
       FROM cvterm_relationship cr
         JOIN cvterm rtype ON rtype.cvterm_id = cr.type_id AND 
rtype.name = 'copy of'
       WHERE cvt.name != NEW.name
         AND ((cr.subject_id = NEW.cvterm_id AND cr.object_id = 
cvt.cvterm_id)
              OR (cr.subject_id = cvt.cvterm_id AND cr.object_id = 
NEW.cvterm_id))
       ;
     RETURN NEW;
   END
$code$
LANGUAGE plpgsql SECURITY DEFINER;

CREATE TRIGGER cvterm_multicv_update_u
   AFTER UPDATE ON cvterm
   FOR EACH ROW
   EXECUTE PROCEDURE cvterm_multicv_update();
----------
But this would not solve other issues like the redundancy of the term in 
the database and when you want to check if a feature is tagged with a 
term of a given cv through feature_cvterm, you won't find feature that 
are tagged with a copy of terms of that cv. You would have to use a more 
tricky query that would include copies...


About solution 2), I don't like to have a field cv_id in the 
cvterm_table then. It would be confusing: is the member "cv_id" means 
there is a "main" CV for a cvterm and other CV associated with cvterm_cv 
are just "secondaries" CV? What if you would like to update such a 
secondary CV? How would it work/how would it deal with the cvterm_cv table?
IMNSHO, I'm ok with solution 2 if we remove the field cv_id from the 
cvterm table. But it would mean we loose backward compatibility.



Another solution could be to change the cvterm field "cv_id" type from 
integer to integer[]. Once again, we loose backward compatibility and 
people who do not know how to deal with PostgreSQL arrays would have to 
learn it! http://www.postgresql.org/docs/9.3/static/arrays.html



As discussed at PAG2016, I think Chado schema needs a global rethinking. 
Chado v2.0? ;-p



    Val


Le 12/04/2016 17:48, Stephen Ficklin a écrit :
> Hi All,
>
> We're working on an OWL parser for Tripal.  Specifically we are trying
> to load the new Relationship Ontology (RO).   This ontology includes
> terms from other ontologies.  There's no problem importing these
> dependent ontologies.   But, Chado does not have a direct way to include
> terms from one vocabulary in another.   Here are some options I came up
> with:
>
> 1) Make note of the inclusion in the cvtermprop table
> 2) Create a new custom cvterm_cv table to associate terms from one
> vocabulary with another
> 3) Duplicate the term in both vocabularies.
>
> There are issues with all 3 methods.  I don't care for option 1 as the
> association isn't really a property of the term.  I also don't like
> option 3 because if the term is updated in the parent vocabulary the
> changes are not reflected in the copy.  My favorite option is 2 but the
> fill_cvtermpath() function will not create a complete representation of
> the vocabulary in the cvtermpath table. We could replace this function
> with a version that can use a new cvterm_cv table.
>
> Are there any objections to using option2?  Does anyone have other ideas
> that may work?
>
> Thanks,
> Stephen
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

[Gmod-schema] Vocabularies with terms from other ontologies

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

Hi All,

We're working on an OWL parser for Tripal.  Specifically we are trying 
to load the new Relationship Ontology (RO).   This ontology includes 
terms from other ontologies.  There's no problem importing these 
dependent ontologies.   But, Chado does not have a direct way to include 
terms from one vocabulary in another.   Here are some options I came up 
with:

1) Make note of the inclusion in the cvtermprop table
2) Create a new custom cvterm_cv table to associate terms from one 
vocabulary with another
3) Duplicate the term in both vocabularies.

There are issues with all 3 methods.  I don't care for option 1 as the 
association isn't really a property of the term.  I also don't like 
option 3 because if the term is updated in the parent vocabulary the 
changes are not reflected in the copy.  My favorite option is 2 but the 
fill_cvtermpath() function will not create a complete representation of 
the vocabulary in the cvtermpath table. We could replace this function 
with a version that can use a new cvterm_cv table.

Are there any objections to using option2?  Does anyone have other ideas 
that may work?

Thanks,
Stephen

Re: [Gmod-schema] [GMOD-devel] [go-discuss] GAFs, GPADs, LEGO and GMOD

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

On 7 Apr 2016, at 9:30, Siddhartha Basu wrote:

> Hi Chris,
> I have a quick look and using owl for modeling GO
> annotations makes more sense. GO annotations now a days have linked
> data(annotation extensions) and the flat file format is really getting
> stretched. The implicit dependencies and connections in the flat file 
> is just impossible
> to express.

Exactly

> So, this is something i would like to revisit
> in detail besides modeling GPAD into chado. For the time being just 
> want
> to brainstorm few ideas/questions that comes from the first look.
> * Unless we go full owl for modeling annotations, we have to use 
> owltools command to
>   convert gpad into lego compatible owl.

you mean (lossy) lego->gpad,gaf?

Yes, you can use our converter to do that --- but you won't have to. The 
GOC is committed to continued support for annotations in GAF/GPAD. You 
should just be aware that this will not capture the richness of the lego 
model. But we're not forcing anyone to do any extra work.

Note that for particular kinds of bioinformatics application, other 
kinds of lossy transformation may be fine - e.g. getting files for use 
in cytoscape.

I would say that GMOD ultimately has a broader picture though.

> * How do we store these owl model for querying it.
>   Could we just shove it in a triple store like Jena TDB. Is there any
>   other options.

There are a variety of options - LEGO fits naturally into a graph or RDF 
store (as its native form is RDF/OWL). We are also storing the graph 
blobs in a Solr index for fast access and querying via AmiGO. This isn't 
intended to support rich queries involving pathway connections, but 
rather for things like "which models have mouse genes with kinase 
activity"

And you could use a relational store if you really wanted to. You don't 
need to express all of OWL. You could design a datamodel around the 
types we use in LEGO - functions, processes, components, molecular 
entities, causal links. But we'd probably both be in agreement that it 
would be more natural to use a graph-level abstraction.

The question for GMOD is do we want to consolidate everything into one 
store, or have a federated approach, with different data types in 
different kinds of store, optimized for that datatype? If things are 
consolidated, is that via incremental extensions of existing schemas, or 
through of a redesign, with (for example) a rdf/graph store front and 
center?

There are multiple possibilities here. For example, a GMOD application 
like Tripal could integrate the AmiGO LEGO widget, and have that 
communicate with our service. Or we could explore the route of having a 
tighter coupling.

> * How do we query that model. Is sparql an option. Or there is an high
>   level api.

Within GO, there will be a mixture of both. For retrieval purposes, we 
have an unpublished very high level API for fetching entire models based 
on what genes they contain etc, for this use case: 
https://github.com/geneontology/noctua/issues/221

> * How does noctua fits here. It seems to have its own customized 
> stack.
>   Does it play well with other generic rdf/semantic/linked data tool.

It's primarily an editing tool so it has its own custom stack for 
handing distributed simultaneous editing of models. But the back-end 
component is mostly a layer on top of OWL. So it depends exactly what 
you mean, but one thing to note is that as the native form is rdf/owl, 
so anything in the semweb stack will work on it out of the box.

Hope this answers some of your questions,
Chris

> thanks,
> -sidd
>
>
> On Tue, 05 Apr 2016, Chris Mungall wrote:
>
>> Dear GMODders,
>>
>> Following on from a recent discussion on gmod-schema involving Eric
>> and Siddhartha, I thought this would be a good opportunity to
>> clarify some differences between some existing GO association
>> formats, and to give you a heads-up about a new more expressive way
>> of doing GO annotation you'll be seeing soon.
>>
>> I posted some details here:
>> http://geneontology.org/article/gaf-gpad-and-lego
>>
>> In particular, I wanted to draw your attention to the more
>> expressive form of LEGO annotations. The best way to grok this is by
>> having a look at some existing annotations and documentation here:
>> http://noctua.berkeleybop.org/
>>
>> Although I think it's too early to start thinking about integrating
>> this into the GMOD stack, we can still have a conversation about how
>> this might work. For example, WormBase are exploring the addition of
>> a Noctua widget into their pages. What we learn from this could feed
>> into generic GMOD tools like Tripal - it would be great to see LEGO
>> diagrams in there.
>>
>> I'd be happy to answer any questions over on the GMOD lists. Also,
>> if any of you are at ISB/Biocuration then there will be many GO
>> experts there, as well as the Noctua developer, Seth. Paul Thomas
>> will be giving a talk about the modeling paradigm. Feel free to ask
>> us questions!
>>
>> Cheers,
>> Chris
>> _______________________________________________
>> go-discuss mailing list
>> go-...@li...
>> https://mailman.stanford.edu/mailman/listinfo/go-discuss
>
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Re: [Gmod-schema] [go-discuss] GAFs, GPADs, LEGO and GMOD

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

Hi Chris,
I have a quick look and using owl for modeling GO
annotations makes more sense. GO annotations now a days have linked
data(annotation extensions) and the flat file format is really getting
stretched. The implicit dependencies and connections in the flat file is just impossible
to express. 
So, this is something i would like to revisit
in detail besides modeling GPAD into chado. For the time being just want
to brainstorm few ideas/questions that comes from the first look.
* Unless we go full owl for modeling annotations, we have to use owltools command to
  convert gpad into lego compatible owl.
* How do we store these owl model for querying it.
  Could we just shove it in a triple store like Jena TDB. Is there any
  other options.
* How do we query that model. Is sparql an option. Or there is an high
  level api.
* How does noctua fits here. It seems to have its own customized stack.
  Does it play well with other generic rdf/semantic/linked data tool.

thanks,
-sidd


On Tue, 05 Apr 2016, Chris Mungall wrote:

> Dear GMODders,
> 
> Following on from a recent discussion on gmod-schema involving Eric
> and Siddhartha, I thought this would be a good opportunity to
> clarify some differences between some existing GO association
> formats, and to give you a heads-up about a new more expressive way
> of doing GO annotation you'll be seeing soon.
> 
> I posted some details here:
> http://geneontology.org/article/gaf-gpad-and-lego
> 
> In particular, I wanted to draw your attention to the more
> expressive form of LEGO annotations. The best way to grok this is by
> having a look at some existing annotations and documentation here:
> http://noctua.berkeleybop.org/
> 
> Although I think it's too early to start thinking about integrating
> this into the GMOD stack, we can still have a conversation about how
> this might work. For example, WormBase are exploring the addition of
> a Noctua widget into their pages. What we learn from this could feed
> into generic GMOD tools like Tripal - it would be great to see LEGO
> diagrams in there.
> 
> I'd be happy to answer any questions over on the GMOD lists. Also,
> if any of you are at ISB/Biocuration then there will be many GO
> experts there, as well as the Noctua developer, Seth. Paul Thomas
> will be giving a talk about the modeling paradigm. Feel free to ask
> us questions!
> 
> Cheers,
> Chris
> _______________________________________________
> go-discuss mailing list
> go-...@li...
> https://mailman.stanford.edu/mailman/listinfo/go-discuss

[Gmod-schema] GAFs, GPADs, LEGO and GMOD

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

Dear GMODders,

Following on from a recent discussion on gmod-schema involving Eric and 
Siddhartha, I thought this would be a good opportunity to clarify some 
differences between some existing GO association formats, and to give 
you a heads-up about a new more expressive way of doing GO annotation 
you'll be seeing soon.

I posted some details here:
http://geneontology.org/article/gaf-gpad-and-lego

In particular, I wanted to draw your attention to the more expressive 
form of LEGO annotations. The best way to grok this is by having a look 
at some existing annotations and documentation here: 
http://noctua.berkeleybop.org/

Although I think it's too early to start thinking about integrating this 
into the GMOD stack, we can still have a conversation about how this 
might work. For example, WormBase are exploring the addition of a Noctua 
widget into their pages. What we learn from this could feed into generic 
GMOD tools like Tripal - it would be great to see LEGO diagrams in 
there.

I'd be happy to answer any questions over on the GMOD lists. Also, if 
any of you are at ISB/Biocuration then there will be many GO experts 
there, as well as the Noctua developer, Seth. Paul Thomas will be giving 
a talk about the modeling paradigm. Feel free to ask us questions!

Cheers,
Chris

Re: [Gmod-schema] Chado Extensions: GAF / Sequencing Data / etc?

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

You can read about GPAD/GPI here:
http://geneontology.org/page/go-annotation-file-formats

Note that the GO will be moving towards a more expressive OWL-based 
representation that will allow annotations to be connected into pathways 
and pathway fragments, called LEGO. You can see the editor here: 
http://noctua.berkeleybop.org/

We will continue to make annotations available in GAF/GPAD, but this 
will not be expressive enough to capture the full details of a LEGO 
model. This would require either a new Chado module, or storage outside 
Chado. WormBase are taking the latter approach.

I'll post more details here, but if any of you will be at the ISB 
Biocuration meeting in Geneva, lots of GO people will be present, 
including Seth Carbon (cc'd), the Noctua developer - he would be happy 
to chat with any GMOD folks about technical details.


On 5 Apr 2016, at 10:16, Eric Rasche wrote:

> Hi Siddhartha,
>
> On 04. april 2016 20:55, Siddhartha Basu wrote:
>> Hi Eric,
>>
>> On Thu, 31 Mar 2016, Eric Rasche wrote:
>>
>>>    Just wanted to ping other Chado people and see if anyone is:
>>>      * storing full GAF2.0 annotations in Chado?
>> My ex-colleague did but on a oracle instance of chado. Here is the
>> starting part of legacy code
>> https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/dictygaf2chado.pm
> Huh, good to know.
>> Kim Rutherford(pombase) has done work with GPAD(latest format for GO
>> annotations) and here is a helpful discussion
>> http://generic-model-organism-system-database.450254.n5.nabble.com/Storing-GO-annotation-extensions-in-Chado-td4564896.html#a4581460
> That is a helpful discussion. Good to know that GPAD (will?) 
> superseded
> GAF at some point. I'd never heard of it before.
>> I have an unfinished loader for GPAD, written in golang, the testing
>> sqlite backend works but the pg backed yet to be completed. Here is a 
>> my
>> visual interpretation of the data model that i developed after a 
>> email
>> conversation with kim.
>> https://github.com/dictyBase/gochado/issues/6
>> And some thought process that might help
>> https://github.com/dictyBase/gochado/issues/7
> Thanks for sharing this work! This will be very helpful, hopefully we
> can implement something like this.
>>
>> thanks,
>> -siddhartha
>>
>>
>>>      * storing sequencing data nearby the database in any way?
>>>           * e.g. filenames pointing to bam/bigwig/cram/etc in a cell 
>>> that you
>>>             could pull out for automated analyses
>>>      * storing any other interesting datasets?
>>>
>>>    We're building out our infrastructure for genome database. I saw 
>>> these as
>>>    possible future problems for us, and wanted to see if the 
>>> community was
>>>    doing anything cool that they would be willing to share?
>>>
>>>    Cheers,
>>>    Eric
>>>
>>>    --
>>>    Eric Rasche
>>>    Programmer II
>>>
>>>    Center for Phage Technology
>>>    Rm 312A, BioBio
>>>    Texas A&M University
>>>    College Station, TX 77843
>>>    es...@ta...
>>> ------------------------------------------------------------------------------
>>> Transform Data into Opportunity.
>>> Accelerate data analysis in your applications with
>>> Intel Data Analytics Acceleration Library.
>>> Click to learn more.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> Gmo...@li...
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>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
> Thanks again,
> Eric
>
> -- 
> Eric Rasche
> Programmer II
>
> Center for Phage Technology
> Rm 312A, BioBio
> Texas A&M University
> College Station, TX 77843
> es...@ta... <mailto:es...@ta...>
> ------------------------------------------------------------------------------
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Re: [Gmod-schema] Chado Extensions: GAF / Sequencing Data / etc?

[Eric R. <ras...@gm...>]

Hi Siddhartha,

On 04. april 2016 20:55, Siddhartha Basu wrote:
> Hi Eric,
>
> On Thu, 31 Mar 2016, Eric Rasche wrote:
>
>>    Just wanted to ping other Chado people and see if anyone is:
>>      * storing full GAF2.0 annotations in Chado?
> My ex-colleague did but on a oracle instance of chado. Here is the
> starting part of legacy code 
> https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/dictygaf2chado.pm
Huh, good to know.
> Kim Rutherford(pombase) has done work with GPAD(latest format for GO
> annotations) and here is a helpful discussion
> http://generic-model-organism-system-database.450254.n5.nabble.com/Storing-GO-annotation-extensions-in-Chado-td4564896.html#a4581460
That is a helpful discussion. Good to know that GPAD (will?) superseded
GAF at some point. I'd never heard of it before.
> I have an unfinished loader for GPAD, written in golang, the testing
> sqlite backend works but the pg backed yet to be completed. Here is a my
> visual interpretation of the data model that i developed after a email
> conversation with kim.
> https://github.com/dictyBase/gochado/issues/6
> And some thought process that might help
> https://github.com/dictyBase/gochado/issues/7
Thanks for sharing this work! This will be very helpful, hopefully we
can implement something like this.
>
> thanks,
> -siddhartha
>
>
>>      * storing sequencing data nearby the database in any way?
>>           * e.g. filenames pointing to bam/bigwig/cram/etc in a cell that you
>>             could pull out for automated analyses
>>      * storing any other interesting datasets?
>>
>>    We're building out our infrastructure for genome database. I saw these as
>>    possible future problems for us, and wanted to see if the community was
>>    doing anything cool that they would be willing to share?
>>
>>    Cheers,
>>    Eric
>>
>>    --
>>    Eric Rasche
>>    Programmer II
>>
>>    Center for Phage Technology
>>    Rm 312A, BioBio
>>    Texas A&M University
>>    College Station, TX 77843
>>    es...@ta...
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
Thanks again,
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
es...@ta... <mailto:es...@ta...>

Re: [Gmod-schema] Chado Extensions: GAF / Sequencing Data / etc?

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

Hi Eric,

On Thu, 31 Mar 2016, Eric Rasche wrote:

>    Just wanted to ping other Chado people and see if anyone is:
>      * storing full GAF2.0 annotations in Chado?
My ex-colleague did but on a oracle instance of chado. Here is the
starting part of legacy code 
https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/dictygaf2chado.pm
Kim Rutherford(pombase) has done work with GPAD(latest format for GO
annotations) and here is a helpful discussion
http://generic-model-organism-system-database.450254.n5.nabble.com/Storing-GO-annotation-extensions-in-Chado-td4564896.html#a4581460
I have an unfinished loader for GPAD, written in golang, the testing
sqlite backend works but the pg backed yet to be completed. Here is a my
visual interpretation of the data model that i developed after a email
conversation with kim.
https://github.com/dictyBase/gochado/issues/6
And some thought process that might help
https://github.com/dictyBase/gochado/issues/7

thanks,
-siddhartha


>      * storing sequencing data nearby the database in any way?
>           * e.g. filenames pointing to bam/bigwig/cram/etc in a cell that you
>             could pull out for automated analyses
>      * storing any other interesting datasets?
> 
>    We're building out our infrastructure for genome database. I saw these as
>    possible future problems for us, and wanted to see if the community was
>    doing anything cool that they would be willing to share?
> 
>    Cheers,
>    Eric
> 
>    --
>    Eric Rasche
>    Programmer II
> 
>    Center for Phage Technology
>    Rm 312A, BioBio
>    Texas A&M University
>    College Station, TX 77843
>    es...@ta...

> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140

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

[Gmod-schema] Chado Extensions: GAF / Sequencing Data / etc?

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

Just wanted to ping other Chado people and see if anyone is:

  * storing full GAF2.0 annotations in Chado?
  * storing sequencing data nearby the database in any way?
      o e.g. filenames pointing to bam/bigwig/cram/etc in a cell that
        you could pull out for automated analyses
  * storing any other interesting datasets?

We're building out our infrastructure for genome database. I saw these
as possible future problems for us, and wanted to see if the community
was doing anything cool that they would be willing to share?

Cheers,
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
es...@ta... <mailto:es...@ta...>

[Gmod-schema] Chado & github

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

I'm seeing slightly different data on svn vs github (i.e. in
chado-1.31.sql svn uses bigint, github uses int), which prompted a
couple questions:

  * Is that the future home of Chado or merely a mirror?
  * if future home would there be interest in PRs for cleanups? E.g.:
      o cleaning out things like the TODO which hasn't been touched in a
        decade.
      o cleaning out + refactoring docs
      o separating out perl code from sql schema
      o separating out the top level folders into separate projects?
        (JavaTools, XMLTools, hackathon_2007, from the "main" chado project)
      o removing ancient code that hasn't been touched in some N years.
  * else
      o are PRs minded there that do things like cleanups? I don't want
        to impose significant overhead patching back into SVN for the
        maintainers.

v/r
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
es...@ta... <mailto:es...@ta...>

Re: [Gmod-schema] Tripal/Chado Web Services Update

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

Hi Joe,
Great for chipping in about postgrest, really neat piece of software
to httpify postgresql access. Will be great to tame chado access with
this tool and have a great developer experience. Love those curl
snippets!

Hi Eric,
Well done with Jbrowse REST interface, the enjoyable part is that it's
written in golang which is my preferred choice for server side. 
I think developing web services(REST/unREST anything..) in golang is really
straight forward and combining it with postgrest just put you in a no
excuse zone. Once again thanks for sharing the code, have quite a bit to
learn and code for myself.

thanks,
-siddhartha

On Thu, 10 Mar 2016, Eric Rasche wrote:

>    Hiya Joe,
> 
>    Now that you've mentioned this I suppose it's time to share what I've been
>    working on.
>    I was going to keep it under wraps until I was further along but ... oh
>    well ;)
> 
>    On 03/10/2016 05:33 PM, Joe Carlson wrote:
> 
>  I haven't been aware of what - if anything - has been happening on the
>  chado API scene. (the web_services link in this mail no longer works. I
>  take this as not a good sign.)
> 
>    I'm actually using this since there was going to be a month lead on the
>    "official" one. I was a bit excited to get started.
> 
>  But I wanted to pass along to the group some info of a project that I've
>  just learned about in case it is useful. postgrest (www.postgrest.com
>  and https://github.com/begriffs/postgrest) is a project that provides an
>  one-stop REST service for a postgres db.
> 
>  The project is at an early stage and it looks that there much to be
>  done. (I don't know if I trust the authentication just yet.) And the
>  querying seems to be limited to single tables (or views) and stored
>  procedures. I realize there are other similar projects out there. This
>  is just one that I've tried out. (No other involvement in the project,
>  though.)
> 
>    I haven't figured out the auth yet to be honest. I'm fond of JWT, it's
>    easy to use, etc. Just haven't thrown time at it yet.
> 
>    That said, between:
>      * postgrest
>      * ng-admin's example postgrest project
> 
>    It's insanely easy to throw together a responsive/fast Chado admin
>    interface.
>    If y'all will be kind to my servers (writing back doesn't work due to
>    CORS, otherwise "save" would work), I have a demo here:
>    Demo: https://erasche.github.io/chado-angular-admin
>    Source: https://github.com/erasche/chado-angular-admin
> 
>    Just hit login :)
> 
>    I wrote a small API server to expose a chado database as a JBrowse REST
>    compatible API.
>    Demo: http://erasche.github.io/chado-angular-admin/browser.html
>    Source: https://github.com/erasche/chado-jbrowse-connector
> 
>    The postgrest server is available here with the yeast data from one
>    tutorial on the GMOD wiki.
>    http://shed.hx42.org:8300/
> 
>    I'm actually using a couple of docker images to do this in case anyone
>    else wants to play with it locally
> 
>  launching is easy:
> 
>  ./postgrest postgres://<database role>:<password>@<dbserver>/<dbname> -a
>  <database role for anonymous connections>
> 
>  A couple examples. A query for a single table (or view):
> 
>  curl 'localhost:3000/organism?species=eq.sapiens'
>  [{"organism_id":1,"abbreviation":"H.sapiens","genus":"Homo","species":"sapiens","common_name":"human","comment":null}]
> 
>  A query on a table uses the endpoint /<table name>. Column constraints
>  on the query are given as "<column>=<operator>.<value>"; in this case
>  species='sapiens'
> 
>  And a stored procedure. genomic_slice is one that I have for returning a
>  segment of a chromosome sequence. ('proteome'  is a dbxref... don't
>  worry about that)
> 
>  curl -d
>  '{"proteome":"210","chromosome":"Chr01","fmin":"1000000","len":"10"}' -X
>  POST -H "Content-Type: application/json"
>  'http://localhost:3000/rpc/genomic_slice'
>  [{"genomic_slice":"TACCAAGGTA"}]
> 
>  (specifying the application/json in the POST headers is important!)
> 
>  I wanted to try the queries on the public flybase db. But that server is
>  running postgres 8.4 and this requires at least 9.0.3
> 
>    I tried the same, would be great if there were other publicly exposed
>    chado databases.
>    (I'd love to know how other people store their data. How do people
>    reference intermediate samples that they track? Sequencing files on disk?
>    Etc?)
> 
> 
>  Part of the reason for sending the email is that there will be a meetup
>  with the developer in San Fran next week for those that are local.
> 
>  http://www.meetup.com/postgresql-1/events/229237351
> 
>  The talk will be video taped and available later, I've heard.
> 
>  Joe
> 
>  On 01/29/2015 08:57 AM, Stephen Ficklin wrote:
> 
>  Dear Tripal/Chado Community,
> 
>  Some progress has been made on the "low-level" Chado API that will
>  provide access to data in a Chado-centric manner, but does not include a
>  design for specific use cases.   The current state of this web service
>  API can be found on the Tripal 2.x demo site:
> 
>  http://demo.tripal.info/2.x/web_services
> 
>  Currently, the web services are very simple.  As progress is made we
>  will update the web services on that page.  There is still much work to
>  do, so what you see is not finalized but is made available in an effort
>  to solicit feedback for suggested changes.  Please let us know what you
>  do or don't like so far.
> 
>  Also, on Saturday, Jan 10th at the Plant and Animal Genome Conference
>  (PAG) in San Deigo, several folks interested in the development of web
>  services for Tripal/Chado met for our second meeting to discuss design
>  of the web services as funded by the NSF DIBBs grant.   The goal of
>  these meetings is to solicit input in the design of web services such
>  that they can support the needs of a broad set of Tripal sites.  Below
>  is a Google doc containing a summary of that meeting. The section
>  containing attendee comments was drawn from memory as we failed to
>  designate an official note taker.
> 
>  https://docs.google.com/document/d/1gdL7Xo-Xoq2ztBVY0FVAHWPv5kNz_ajyNtAlYjCzC4U/edit
> 
>  For anyone interested in web services for Tripal/Chado, please contact
>  me directly if you have comments as the way we have approached
>  soliciting input during the design phase (positive or negative-- I'm
>  happy to hear all) as we want to ensure stake-holders feel heard and the
>  design fits the broadest needs.
> 
>  Thanks much to all who are participating in this!
>  Stephen
> 
> 
> 
>  ------------------------------------------------------------------------------
>  Dive into the World of Parallel Programming. The Go Parallel Website,
>  sponsored by Intel and developed in partnership with Slashdot Media, is your
>  hub for all things parallel software development, from weekly thought
>  leadership blogs to news, videos, case studies, tutorials and more. Take a
>  look and join the conversation now. http://goparallel.sourceforge.net/
>  _______________________________________________
>  Gmod-schema mailing list
>  Gmo...@li...
>  https://lists.sourceforge.net/lists/listinfo/gmod-schema
> 
> 
>  ------------------------------------------------------------------------------
>  Transform Data into Opportunity.
>  Accelerate data analysis in your applications with
>  Intel Data Analytics Acceleration Library.
>  Click to learn more.
>  http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140
>  _______________________________________________
>  Gmod-schema mailing list
>  Gmo...@li...
>  https://lists.sourceforge.net/lists/listinfo/gmod-schema
> 
>    --
>    Eric Rasche
>    Programmer II
> 
>    Center for Phage Technology
>    Rm 312A, BioBio
>    Texas A&M University
>    College Station, TX 77843
>    404-692-2048
>    es...@ta...

> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140

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

Re: [Gmod-schema] Tripal/Chado Web Services Update

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

Hi Joe,

To provide an update as to where we are with web services and Chado...

Yes, the link in the earlier email below has been removed.   When we 
first started on the project we had intended to create RESTful web 
services with direct access to Chado.  The link that was in that 
original email from early last year was a demo of that work. 
Essentially, you could find genomic features by using the 'feature' 
resource, and the 'stock' resource for germplasm, etc.  However, in 
meetings that we had with the community of Chado users it was clear that 
there was a preference for a web services that were not Chado-centric.  
Folks weren't interested in requiring their users to understand Chado 
table structure in order to query for information. Some tables, such as 
the stock table, can be very confusing to users as it's not always clear 
what's stored in that table.  Additionally, some of the sites that use 
Tripal and Chado have a set of authentication and access rules that 
would be difficult to enforce via Chado-centric web services.  For 
example, some data is private and only available to specific users, and 
Chado itself has no account of that access information.  Tripal / Drupal 
does, so we wanted tighter integration with web services and 
Tripal/Drupal authentication support.   Third, it is increasingly common 
for some data to not be housed in Chado (i.e. BAM alignments, all info 
in a VCF file, images, etc.), and we wanted those non-Chado (linked to 
Chado data) to also be available via web services.  This ensures we have 
consistency between the data that is shown on a page (i.e. gene page) 
and the same data that is available via web services for the same content.

Our goal is to provide web services for data in Chado, but we also have 
the goal of providing web services for the "community database" as well, 
so we have these additional constraints that need to be built into the 
web services, and hence they necessitated a change from our original 
plans.  There was some interest in also having Chado-centric web 
services, but we just didn't have the time to more fully develop both 
more robust web services and the Chado-centric version at the same time.

To meet the requirements described above we redesigned how we are going 
to offer data in Chado via web services for Tripal v3 (coming soon).  It 
will offer data in a more intuitive manner (e.g. via data types: genes, 
germplasm, genetic_marker, etc.), and ensures privacy of data.  It does 
support Chado but incorporates non-Chado data as well.   So, long 
story.... we took down the link to the original Chado-based web services 
we were working on, and unfortunately that added confusion because we 
failed to replace it with additional information.

Our work is progressing and we are close to offering a meeting to 
provide a demo of our current implementation for web services and to 
solicit more feedback on our web services design.  That should occur in 
April, and I'll send out a Doodle poll by email soon to schedule a time 
for interested groups.

Stephen


On 3/10/2016 9:33 AM, Joe Carlson wrote:
>
> I haven't been aware of what - if anything - has been happening on the 
> chado API scene. (the web_services link in this mail no longer works. 
> I take this as not a good sign.)
>
> But I wanted to pass along to the group some info of a project that 
> I've just learned about in case it is useful. postgrest 
> (www.postgrest.com and https://github.com/begriffs/postgrest) is a 
> project that provides an one-stop REST service for a postgres db.
>
> The project is at an early stage and it looks that there much to be 
> done. (I don't know if I trust the authentication just yet.) And the 
> querying seems to be limited to single tables (or views) and stored 
> procedures. I realize there are other similar projects out there. This 
> is just one that I've tried out. (No other involvement in the project, 
> though.)
>
> launching is easy:
>
> ./postgrest postgres://<database role>:<password>@<dbserver>/<dbname> 
> -a <database role for anonymous connections>
>
> A couple examples. A query for a single table (or view):
>
> curl 'localhost:3000/organism?species=eq.sapiens'
> [{"organism_id":1,"abbreviation":"H.sapiens","genus":"Homo","species":"sapiens","common_name":"human","comment":null}] 
>
>
> A query on a table uses the endpoint /<table name>. Column constraints 
> on the query are given as "<column>=<operator>.<value>"; in this case 
> species='sapiens'
>
> And a stored procedure. genomic_slice is one that I have for returning 
> a segment of a chromosome sequence. ('proteome'  is a dbxref... don't 
> worry about that)
>
> curl -d 
> '{"proteome":"210","chromosome":"Chr01","fmin":"1000000","len":"10"}' 
> -X POST -H "Content-Type: application/json" 
> 'http://localhost:3000/rpc/genomic_slice'
> [{"genomic_slice":"TACCAAGGTA"}]
>
> (specifying the application/json in the POST headers is important!)
>
> I wanted to try the queries on the public flybase db. But that server 
> is running postgres 8.4 and this requires at least 9.0.3
>
> Part of the reason for sending the email is that there will be a 
> meetup with the developer in San Fran next week for those that are local.
>
> http://www.meetup.com/postgresql-1/events/229237351
>
> The talk will be video taped and available later, I've heard.
>
> Joe
>
> On 01/29/2015 08:57 AM, Stephen Ficklin wrote:
>> Dear Tripal/Chado Community,
>>
>> Some progress has been made on the "low-level" Chado API that will
>> provide access to data in a Chado-centric manner, but does not include a
>> design for specific use cases.   The current state of this web service
>> API can be found on the Tripal 2.x demo site:
>>
>> http://demo.tripal.info/2.x/web_services
>>
>> Currently, the web services are very simple.  As progress is made we
>> will update the web services on that page.  There is still much work to
>> do, so what you see is not finalized but is made available in an effort
>> to solicit feedback for suggested changes.  Please let us know what you
>> do or don't like so far.
>>
>> Also, on Saturday, Jan 10th at the Plant and Animal Genome Conference
>> (PAG) in San Deigo, several folks interested in the development of web
>> services for Tripal/Chado met for our second meeting to discuss design
>> of the web services as funded by the NSF DIBBs grant.   The goal of
>> these meetings is to solicit input in the design of web services such
>> that they can support the needs of a broad set of Tripal sites. Below
>> is a Google doc containing a summary of that meeting. The section
>> containing attendee comments was drawn from memory as we failed to
>> designate an official note taker.
>>
>> https://docs.google.com/document/d/1gdL7Xo-Xoq2ztBVY0FVAHWPv5kNz_ajyNtAlYjCzC4U/edit 
>>
>>
>> For anyone interested in web services for Tripal/Chado, please contact
>> me directly if you have comments as the way we have approached
>> soliciting input during the design phase (positive or negative-- I'm
>> happy to hear all) as we want to ensure stake-holders feel heard and the
>> design fits the broadest needs.
>>
>> Thanks much to all who are participating in this!
>> Stephen
>>
>>
>>
>> ------------------------------------------------------------------------------ 
>>
>> Dive into the World of Parallel Programming. The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, 
>> is your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. 
>> Take a
>> look and join the conversation now. http://goparallel.sourceforge.net/
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

Re: [Gmod-schema] Tripal/Chado Web Services Update

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

Hiya Joe,

Now that you've mentioned this I suppose it's time to share what I've
been working on.
I was going to keep it under wraps until I was further along but ... oh
well ;)

On 03/10/2016 05:33 PM, Joe Carlson wrote:
> I haven't been aware of what - if anything - has been happening on the 
> chado API scene. (the web_services link in this mail no longer works. I 
> take this as not a good sign.)
I'm actually using this since there was going to be a month lead on the
"official" one. I was a bit excited to get started.
> But I wanted to pass along to the group some info of a project that I've 
> just learned about in case it is useful. postgrest (www.postgrest.com 
> and https://github.com/begriffs/postgrest) is a project that provides an 
> one-stop REST service for a postgres db.
>
> The project is at an early stage and it looks that there much to be 
> done. (I don't know if I trust the authentication just yet.) And the 
> querying seems to be limited to single tables (or views) and stored 
> procedures. I realize there are other similar projects out there. This 
> is just one that I've tried out. (No other involvement in the project, 
> though.)
I haven't figured out the auth yet to be honest. I'm fond of JWT, it's
easy to use, etc. Just haven't thrown time at it yet.

That said, between:

  * postgrest
  * ng-admin's example postgrest project
    <https://github.com/marmelab/ng-admin-postgrest>

It's insanely easy to throw together a responsive/fast Chado admin
interface.
If y'all will be kind to my servers (writing back doesn't work due to
CORS, otherwise "save" would work), I have a demo here:
Demo: https://erasche.github.io/chado-angular-admin
Source: https://github.com/erasche/chado-angular-admin

Just hit login :)

I wrote a small API server to expose a chado database as a JBrowse REST
compatible API.
Demo: http://erasche.github.io/chado-angular-admin/browser.html
Source: https://github.com/erasche/chado-jbrowse-connector

The postgrest server is available here with the yeast data from one
tutorial on the GMOD wiki.
http://shed.hx42.org:8300/

I'm actually using a couple of docker images
<https://github.com/erasche/docker-chado-postgrest/blob/master/docker-compose.yml>
to do this in case anyone else wants to play with it locally

> launching is easy:
>
> ./postgrest postgres://<database role>:<password>@<dbserver>/<dbname> -a 
> <database role for anonymous connections>
>
> A couple examples. A query for a single table (or view):
>
> curl 'localhost:3000/organism?species=eq.sapiens'
> [{"organism_id":1,"abbreviation":"H.sapiens","genus":"Homo","species":"sapiens","common_name":"human","comment":null}]
>
> A query on a table uses the endpoint /<table name>. Column constraints 
> on the query are given as "<column>=<operator>.<value>"; in this case 
> species='sapiens'
>
> And a stored procedure. genomic_slice is one that I have for returning a 
> segment of a chromosome sequence. ('proteome'  is a dbxref... don't 
> worry about that)
>
> curl -d 
> '{"proteome":"210","chromosome":"Chr01","fmin":"1000000","len":"10"}' -X 
> POST -H "Content-Type: application/json" 
> 'http://localhost:3000/rpc/genomic_slice'
> [{"genomic_slice":"TACCAAGGTA"}]
>
> (specifying the application/json in the POST headers is important!)
>
> I wanted to try the queries on the public flybase db. But that server is 
> running postgres 8.4 and this requires at least 9.0.3
I tried the same, would be great if there were other publicly exposed
chado databases.
(I'd love to know how other people store their data. How do people
reference intermediate samples that they track? Sequencing files on
disk? Etc?)
>
> Part of the reason for sending the email is that there will be a meetup 
> with the developer in San Fran next week for those that are local.
>
> http://www.meetup.com/postgresql-1/events/229237351
>
> The talk will be video taped and available later, I've heard.
>
> Joe
>
> On 01/29/2015 08:57 AM, Stephen Ficklin wrote:
>> Dear Tripal/Chado Community,
>>
>> Some progress has been made on the "low-level" Chado API that will
>> provide access to data in a Chado-centric manner, but does not include a
>> design for specific use cases.   The current state of this web service
>> API can be found on the Tripal 2.x demo site:
>>
>> http://demo.tripal.info/2.x/web_services
>>
>> Currently, the web services are very simple.  As progress is made we
>> will update the web services on that page.  There is still much work to
>> do, so what you see is not finalized but is made available in an effort
>> to solicit feedback for suggested changes.  Please let us know what you
>> do or don't like so far.
>>
>> Also, on Saturday, Jan 10th at the Plant and Animal Genome Conference
>> (PAG) in San Deigo, several folks interested in the development of web
>> services for Tripal/Chado met for our second meeting to discuss design
>> of the web services as funded by the NSF DIBBs grant.   The goal of
>> these meetings is to solicit input in the design of web services such
>> that they can support the needs of a broad set of Tripal sites.  Below
>> is a Google doc containing a summary of that meeting. The section
>> containing attendee comments was drawn from memory as we failed to
>> designate an official note taker.
>>
>> https://docs.google.com/document/d/1gdL7Xo-Xoq2ztBVY0FVAHWPv5kNz_ajyNtAlYjCzC4U/edit
>>
>> For anyone interested in web services for Tripal/Chado, please contact
>> me directly if you have comments as the way we have approached
>> soliciting input during the design phase (positive or negative-- I'm
>> happy to hear all) as we want to ensure stake-holders feel heard and the
>> design fits the broadest needs.
>>
>> Thanks much to all who are participating in this!
>> Stephen
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming. The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
>> look and join the conversation now. http://goparallel.sourceforge.net/
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> ------------------------------------------------------------------------------
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> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
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--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048 <tel:404-692-2048>
es...@ta... <mailto:es...@ta...>

Re: [Gmod-schema] Tripal/Chado Web Services Update

[Joe C. <jwc...@lb...>]

I haven't been aware of what - if anything - has been happening on the 
chado API scene. (the web_services link in this mail no longer works. I 
take this as not a good sign.)

But I wanted to pass along to the group some info of a project that I've 
just learned about in case it is useful. postgrest (www.postgrest.com 
and https://github.com/begriffs/postgrest) is a project that provides an 
one-stop REST service for a postgres db.

The project is at an early stage and it looks that there much to be 
done. (I don't know if I trust the authentication just yet.) And the 
querying seems to be limited to single tables (or views) and stored 
procedures. I realize there are other similar projects out there. This 
is just one that I've tried out. (No other involvement in the project, 
though.)

launching is easy:

./postgrest postgres://<database role>:<password>@<dbserver>/<dbname> -a 
<database role for anonymous connections>

A couple examples. A query for a single table (or view):

curl 'localhost:3000/organism?species=eq.sapiens'
[{"organism_id":1,"abbreviation":"H.sapiens","genus":"Homo","species":"sapiens","common_name":"human","comment":null}]

A query on a table uses the endpoint /<table name>. Column constraints 
on the query are given as "<column>=<operator>.<value>"; in this case 
species='sapiens'

And a stored procedure. genomic_slice is one that I have for returning a 
segment of a chromosome sequence. ('proteome'  is a dbxref... don't 
worry about that)

curl -d 
'{"proteome":"210","chromosome":"Chr01","fmin":"1000000","len":"10"}' -X 
POST -H "Content-Type: application/json" 
'http://localhost:3000/rpc/genomic_slice'
[{"genomic_slice":"TACCAAGGTA"}]

(specifying the application/json in the POST headers is important!)

I wanted to try the queries on the public flybase db. But that server is 
running postgres 8.4 and this requires at least 9.0.3

Part of the reason for sending the email is that there will be a meetup 
with the developer in San Fran next week for those that are local.

http://www.meetup.com/postgresql-1/events/229237351

The talk will be video taped and available later, I've heard.

Joe

On 01/29/2015 08:57 AM, Stephen Ficklin wrote:
> Dear Tripal/Chado Community,
>
> Some progress has been made on the "low-level" Chado API that will
> provide access to data in a Chado-centric manner, but does not include a
> design for specific use cases.   The current state of this web service
> API can be found on the Tripal 2.x demo site:
>
> http://demo.tripal.info/2.x/web_services
>
> Currently, the web services are very simple.  As progress is made we
> will update the web services on that page.  There is still much work to
> do, so what you see is not finalized but is made available in an effort
> to solicit feedback for suggested changes.  Please let us know what you
> do or don't like so far.
>
> Also, on Saturday, Jan 10th at the Plant and Animal Genome Conference
> (PAG) in San Deigo, several folks interested in the development of web
> services for Tripal/Chado met for our second meeting to discuss design
> of the web services as funded by the NSF DIBBs grant.   The goal of
> these meetings is to solicit input in the design of web services such
> that they can support the needs of a broad set of Tripal sites.  Below
> is a Google doc containing a summary of that meeting. The section
> containing attendee comments was drawn from memory as we failed to
> designate an official note taker.
>
> https://docs.google.com/document/d/1gdL7Xo-Xoq2ztBVY0FVAHWPv5kNz_ajyNtAlYjCzC4U/edit
>
> For anyone interested in web services for Tripal/Chado, please contact
> me directly if you have comments as the way we have approached
> soliciting input during the design phase (positive or negative-- I'm
> happy to hear all) as we want to ensure stake-holders feel heard and the
> design fits the broadest needs.
>
> Thanks much to all who are participating in this!
> Stephen
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

[Gmod-schema] Call for Abstracts for BOSC

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

Hi All,

I'm forwarding this call for abstracts for BOSC (Bioinformatics Open Source
Conference) this year in Orlando, Florida:

>From Peter Cock (p.j.a.cock at googlemail.com):

As BOSC co-chair I would like to encourage you all to think about
attending BOSC 2016, and if you are working on your own open
source software for bioinformatics please consider submitting an
abstract. See the email below and:

http://news.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/

Also, as a member of the Open Bioinformatics Foundation (OBF)
Board of Directors, I am delighted to let you know about the new
OBF Travel Fellowship which could be used to attend BOSC:

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

In case you missed the earlier announcement last year, we finally
got rid of the paper forms for OBF membership, see:

http://news.open-bio.org/2015/12/10/online-membership-form/

Thank you,

Peter

[Biopython developer, BOSC co-chair, OBF Secretary, etc.]


--
------------------------------------------------------------------------
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] [apollo] GMOD in Google Summer of Code 2016

[Fields, C. J <cjf...@il...>]

Woohoo!  Congratulations, that’s awesome news!

chris

On Mar 1, 2016, at 9:37 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:

Hello,

Very good news!  GMOD (as part of the Open Genome Informatics group along with Reactome) has been accepted into Google Summer of Code this year.  If you are or know of a student that might like to participate, please take a look at

  http://gmod.org/wiki/GSOC_Project_Ideas_2016<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_wiki_GSOC-5FProject-5FIdeas-5F2016&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=tDGDphAO6NEimtzLSSmQFGvp83Nv4of3Q091GUeBRjE&m=Eb_ZrfR3Xc51lteT_Inle_8o0jZZLUD2We_AnIKbBLs&s=d2Mb3nPsluquON7h548pjpEuZOTj33QhTJRfyLg7A54&e=>

where there are several really interesting project ideas.  It is also possible for students to suggest their own ideas and we will try hard to find them a mentor.

Please let me know if you have any questions about GSoC.

Scott

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=tDGDphAO6NEimtzLSSmQFGvp83Nv4of3Q091GUeBRjE&m=Eb_ZrfR3Xc51lteT_Inle_8o0jZZLUD2We_AnIKbBLs&s=RpOGhmECJxidFEEp4hCh307q6AlstopqVaLdfXfbM_g&e=>)                     216-392-3087
Ontario Institute for Cancer Research



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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[Gmod-schema] GMOD in Google Summer of Code 2016

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

Hello,

Very good news!  GMOD (as part of the Open Genome Informatics group along
with Reactome) has been accepted into Google Summer of Code this year.  If
you are or know of a student that might like to participate, please take a
look at

  http://gmod.org/wiki/GSOC_Project_Ideas_2016

where there are several really interesting project ideas.  It is also
possible for students to suggest their own ideas and we will try hard to
find them a mentor.

Please let me know if you have any questions about GSoC.

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] GMOD 2016 meeting

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

Hello all,

I am pleased to announce that details have been finalized for the 2016 GMOD
meeting.  It will take place immediately following the Galaxy Community
Conference at Indiana University in Bloomington, IN on June 30 and July 1.
We're still working on agenda details, so if you have suggestions or would
like to present, please let me know.

For registration information, please see:

  https://gmod2016.eventbrite.com

And for other information about the meeting, keep an eye on:

  http://gmod.org/wiki/Jun_2016_GMOD_Meeting

I look forward to seeing you there!
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] Chado 1.31 released

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

Scott (and Joe), you are awesome :-)

-sidd

On Fri, 22 Jan 2016, Scott Cain wrote:

>    OK, now it's available via the the 1.31-release tag:
>    https://github.com/GMOD/Chado/releases/tag/1.31-release
>    (Thanks Joe Carlson!)
>    On Fri, Jan 22, 2016 at 10:54 AM, Scott Cain <sc...@sc...> wrote:
> 
>      Hi Sid,
>      Yes, Chado is available on the 1.31 branch of GMOD/Chado at Github:
>      https://github.com/GMOD/Chado/tree/1.31
>      Though I suppose I should tag it in someway now that I've released it.A 
>      Time to read about how to do that in git :-)
>      Scott
>      On Fri, Jan 22, 2016 at 10:49 AM, Siddhartha Basu <bi...@gm...>
>      wrote:
> 
>        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:
> 
>        >A  A  Hello,
>        >
>        >A  A  You have no idea how happy it makes me to announce the release
>        of Chado
>        >A  A  1.31:
>        >
>        >A  A  https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/
>        >
>        >A  A  This release marks the first schema change in Chado in 5 years,
>        and
>        >A  A  incorporates several changes, including
>        >
>        >A  A  * Converting all primary and foreign keys from integers to
>        BigInts
>        >A  A  * Converting feature.seqlen and featureloc.fmin and fmax from
>        integers to
>        >A  A  BigInts (darn pine trees!)
>        >A  A  * Several added linking tables.
>        >A  A  * Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of"
>        term is not
>        >A  A  found (thanks Eric Rasche).
>        >A  A  * Fixed the ncbi_taxonomy loader to load the entire NCBI
>        taxonomy (thanks
>        >A  A  Naama Menda).
>        >A  A  * Fixed the "organism by data" functionality of
>        gmod_bulk_load_gff3.pl
>        >A  A  (thanks Alexie Papanicolaou).
>        >A  A  * Removed much of the initialization data included with Chado
>        that is
>        >A  A  considered out of date.
>        >
>        >A  A  For details on what changed in the schema, you can find the sql
>        diff in
>        >A  A  chado/schemas/1.23-1.31/diff.sql or atA
>        >A  A 
>        https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/schemas/1.23-1.31/diff.sql
>        >A  A  (note that this file is fairly large, due to the large number
>        of
>        >A  A  statements required to convert all of the primary keys to
>        BigInts.)
>        >A  A  Note that if you are a Tripal user, you will want to wait until
>        Tripal has
>        >A  A  been updated to support the new schema. A
>        >A  A  Finally, I want to give a very big "THANK YOU!!" to Stephen
>        Ficklin and
>        >A  A  Lacey Sanderson, without whom I never would have gotten this
>        release out.
>        >A  A  Thanks,
>        >A  A  Scott
>        >
>        >A  A  --
>        >A  A 
>        ------------------------------------------------------------------------
>        >A  A  Scott Cain, Ph. D. AA  AA  AA  AA  AA  AA  AA  AA  AA  AA  AA 
>        AA  AA  AA  AA  AA  A
>        >A  A  scott at scottcain dot net
>        >A  A  GMOD Coordinator (http://gmod.org/) AA  AA  AA  AA  AA  AA  AA 
>        AA  AA  A
>        >A  A  216-392-3087
>        >A  A  Ontario Institute for Cancer Research
> 
>        >
>        ------------------------------------------------------------------------------
>        > Site24x7 APM Insight: Get Deep Visibility into Application
>        Performance
>        > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>        > Monitor end-to-end web transactions and take corrective actions now
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> 
>        > _______________________________________________
>        > Gmod-schema mailing list
>        > Gmo...@li...
>        > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> 
>        ------------------------------------------------------------------------------
>        Site24x7 APM Insight: Get Deep Visibility into Application Performance
>        APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>        Monitor end-to-end web transactions and take corrective actions now
>        Troubleshoot faster and improve end-user experience. Signup Now!
>        http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>        _______________________________________________
>        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
> 
>    --
>    ------------------------------------------------------------------------
>    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

> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140

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

Re: [Gmod-schema] gmod hardware requirements

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

Thank you very much Karl ! I appreciate your help.



Kind regards,

Iulia Cimpan

Research Software Support Specialist

IT Services, Room 108

Phone: 0121 4144072

Email: Ci...@ad...

________________________________________
From: Karl O. Pinc [ko...@me...]
Sent: 23 January 2016 17:50
To: Iulia Cimpan
Cc: Stephen Ficklin; Lacey Sanderson; gmo...@li...; GMOD Schema/Chado List
Subject: Re: [Gmod-schema] gmod hardware requirements

On Fri, 22 Jan 2016 09:40:39 +0000
Iulia Cimpan <I.C...@bh...> wrote:

> 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 ?

FWIW, we ran just Chado with 2G of RAM and about 100G of disk.
Did fine, but we did really nothing much but load the reference
genome and poke around.


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

Re: [Gmod-schema] gmod hardware requirements

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

On Fri, 22 Jan 2016 09:40:39 +0000
Iulia Cimpan <I.C...@bh...> wrote:

> 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 ?

FWIW, we ran just Chado with 2G of RAM and about 100G of disk.
Did fine, but we did really nothing much but load the reference
genome and poke around.


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

Re: [Gmod-schema] Chado 1.31 released

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

OK, now it's available via the the 1.31-release tag:

https://github.com/GMOD/Chado/releases/tag/1.31-release

(Thanks Joe Carlson!)


On Fri, Jan 22, 2016 at 10:54 AM, Scott Cain <sc...@sc...> wrote:

> Hi Sid,
>
> Yes, Chado is available on the 1.31 branch of GMOD/Chado at Github:
>
> https://github.com/GMOD/Chado/tree/1.31
>
> Though I suppose I should tag it in someway now that I've released it.
> Time to read about how to do that in git :-)
>
> Scott
>
>
> On Fri, Jan 22, 2016 at 10:49 AM, Siddhartha Basu <bi...@gm...>
> wrote:
>
>> 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
>>
>> >
>> ------------------------------------------------------------------------------
>> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> > Monitor end-to-end web transactions and take corrective actions now
>> > Troubleshoot faster and improve end-user experience. Signup Now!
>> > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > Gmo...@li...
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> 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] Chado 1.31 released

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

Hi Sid,

Yes, Chado is available on the 1.31 branch of GMOD/Chado at Github:

https://github.com/GMOD/Chado/tree/1.31

Though I suppose I should tag it in someway now that I've released it.
Time to read about how to do that in git :-)

Scott


On Fri, Jan 22, 2016 at 10:49 AM, Siddhartha Basu <bi...@gm...> wrote:

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