Implementing GMOD Restful API in Tripal

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Implementing GMOD Restful API in Tripal

Lacey-Anne Sanderson
I am interested in implementing the GMOD Restful API as a Tripal module making all Tripal sites able to expose their data in a cross-MOD friendly fashion. The idea is that you can enable a Tripal module and any public data available through your website (stored in chado) is made available at http://yourtripalsite/gmodrpc/v<api version>... as described by the API. 

I'm wondering if the API described at http://gmod.org/wiki/GMOD_REST_API is in a stable enough state for me to start coding this module? Also, how close are the other versions to being ready for deployment on non-Tripal MODs?

My Design Plans:
Stage 1: Use the Drupal menu system to manage generating the URLs and the Tripal Chado API to supply the data for those pages.
Stage 2: Implement dynamically generated Tripal pages (organism/feature) based on data pulled from other MODs using the GMOD Restful API. This will allow Tripal sites to display data from other MODs in a seamless manner (Of course these pages will give credit and link to the MODs storing the data). An administration page will allow you to configure which MOD's you want to query -full web-address specification or selecting options from a form.

Thanks,
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan


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Re: Implementing GMOD Restful API in Tripal

Lacey-Anne Sanderson
So in spite of the lack of response, I've started working on this module. I need some clarification:

GMOD RPC Questions:
- When you say "Gene Full text Search" is this a full text searching of all records in the chado feature table or are you restricting it to those of type gene?
- When you refer to type (Gene Full Text Search), I assume you mean feature.type_id exclusively? 
- In Gene Location, does the type refer to the type of features located on that chromosome to return

Chado Storage Questions:
- Where in chado is the taxid normally stored? is this an organismprop?
- Are gene orthologs normally stored in chado using feature_relationship with a cvterm of orthologous (SO:0000858)?

I know some of these questions might seem like I think I know the answer but I don't want to assume anything or we might end up with a non-standard implementation.
Thanks in advance for the help!
~Lacey

PS. My implementation is at http://knowpulse2.usask.ca/devel/ if anyone wants to go look at examples. Currently I only have organisms (http://knowpulse2.usask.ca/devel/gmodrpc/v1.1/organisms) done.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-01-10, at 4:35 PM, Lacey-Anne Sanderson wrote:

I am interested in implementing the GMOD Restful API as a Tripal module making all Tripal sites able to expose their data in a cross-MOD friendly fashion. The idea is that you can enable a Tripal module and any public data available through your website (stored in chado) is made available at http://yourtripalsite/gmodrpc/v<api version>... as described by the API. 

I'm wondering if the API described at http://gmod.org/wiki/GMOD_REST_API is in a stable enough state for me to start coding this module? Also, how close are the other versions to being ready for deployment on non-Tripal MODs?

My Design Plans:
Stage 1: Use the Drupal menu system to manage generating the URLs and the Tripal Chado API to supply the data for those pages.
Stage 2: Implement dynamically generated Tripal pages (organism/feature) based on data pulled from other MODs using the GMOD Restful API. This will allow Tripal sites to display data from other MODs in a seamless manner (Of course these pages will give credit and link to the MODs storing the data). An administration page will allow you to configure which MOD's you want to query -full web-address specification or selecting options from a form.

Thanks,
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan



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Re: Implementing GMOD Restful API in Tripal

Josh Goodman
Hi Lacey,

My apologies, your initial reply slipped past my inbox.  Alex
Kalderimis (InterMine) and I had a flurry of activity after GMOD last
year, but that has died off as the holidays kicked in.

Alex did quite a bit of nice work refractoring code and you are free
to take a look at
https://github.com/GMOD/GMOD-RPC-perl/tree/templateless.  I've been
meaning to get back to this, but I haven't quite cleared my TODO list
enough.

I'd say that the API is stable enough for you to start drafting
something.  I don't know how close other MODs are but I've set a goal
for having this deployed at FlyBase by this summer.

The full text search service is currently limited to only features of
type gene (SO:0000704).  The type field is there to allow for adding
additional features in the future.  The same goes for location.  Yes,
the type indicates the type of feature to return.

I think the proper place for a taxid on an organism would be a link to
dbxref in organism_dbxref.

Your orthology implementation seems reasonable.

Josh




On Fri, Jan 20, 2012 at 11:57 AM, Lacey-Anne Sanderson
<[hidden email]> wrote:

> So in spite of the lack of response, I've started working on this module. I
> need some clarification:
>
> GMOD RPC Questions:
> - When you say "Gene Full text Search" is this a full text searching of all
> records in the chado feature table or are you restricting it to those of
> type gene?
> - When you refer to type (Gene Full Text Search), I assume you mean
> feature.type_id exclusively?
> - In Gene Location, does the type refer to the type of features located on
> that chromosome to return
>
> Chado Storage Questions:
> - Where in chado is the taxid normally stored? is this an organismprop?
> - Are gene orthologs normally stored in chado using feature_relationship
> with a cvterm of orthologous (SO:0000858)?
>
> I know some of these questions might seem like I think I know the answer but
> I don't want to assume anything or we might end up with a non-standard
> implementation.
> Thanks in advance for the help!
> ~Lacey
>
> PS. My implementation is at http://knowpulse2.usask.ca/devel/ if anyone
> wants to go look at examples. Currently I only have organisms
> (http://knowpulse2.usask.ca/devel/gmodrpc/v1.1/organisms) done.
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-2430
> Email: [hidden email]
> Room 3D10 Agriculture
> Department of Plant Sciences
> University of Saskatchewan
>
> On 2012-01-10, at 4:35 PM, Lacey-Anne Sanderson wrote:
>
> I am interested in implementing the GMOD Restful API as a Tripal module
> making all Tripal sites able to expose their data in a cross-MOD friendly
> fashion. The idea is that you can enable a Tripal module and any public data
> available through your website (stored in chado) is made available at
> http://yourtripalsite/gmodrpc/v<api version>... as described by the API.
>
> I'm wondering if the API described at http://gmod.org/wiki/GMOD_REST_API is
> in a stable enough state for me to start coding this module? Also, how close
> are the other versions to being ready for deployment on non-Tripal MODs?
>
> My Design Plans:
> Stage 1: Use the Drupal menu system to manage generating the URLs and the
> Tripal Chado API to supply the data for those pages.
> Stage 2: Implement dynamically generated Tripal pages (organism/feature)
> based on data pulled from other MODs using the GMOD Restful API. This will
> allow Tripal sites to display data from other MODs in a seamless manner (Of
> course these pages will give credit and link to the MODs storing the data).
> An administration page will allow you to configure which MOD's you want to
> query -full web-address specification or selecting options from a form.
>
> Thanks,
> ~Lacey
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-2430
> Email: [hidden email]
> Room 3D10 Agriculture
> Department of Plant Sciences
> University of Saskatchewan
>
>
>
> ------------------------------------------------------------------------------
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> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>

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Re: Implementing GMOD Restful API in Tripal

Lacey-Anne Sanderson
Hi Josh,

I think for the Tripal implementation, I'm not going to limit the full text search and location services to gene. Our website doesn't currently have any gene models due to the species being orphan legume crops (Pea, Lentil, Chickpea, Bean) which don't yet have these resources and if the gene limit is enforced this service wouldn't be useful to us. Since the Tripal module won't use the API directly but rather expose the results in the same format, I don't think this should be a problem. What are your thoughts?

Also, I have been in contact with the Legume Information System (LIS) and Soybase about using this API for cross-communication between all legume informatic websites. We have a need to export data in addition to sequences including QTL, genetic map, genotypic and phenotypic data. What do you think of expanding the current API with our help to include some/all of these type of data in version 1.2? I would be willing to spearhead determining what the URLs and returned results should look like.

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-01-20, at 1:41 PM, Josh Goodman wrote:

Hi Lacey,

My apologies, your initial reply slipped past my inbox.  Alex
Kalderimis (InterMine) and I had a flurry of activity after GMOD last
year, but that has died off as the holidays kicked in.

Alex did quite a bit of nice work refractoring code and you are free
to take a look at
https://github.com/GMOD/GMOD-RPC-perl/tree/templateless.  I've been
meaning to get back to this, but I haven't quite cleared my TODO list
enough.

I'd say that the API is stable enough for you to start drafting
something.  I don't know how close other MODs are but I've set a goal
for having this deployed at FlyBase by this summer.

The full text search service is currently limited to only features of
type gene (SO:0000704).  The type field is there to allow for adding
additional features in the future.  The same goes for location.  Yes,
the type indicates the type of feature to return.

I think the proper place for a taxid on an organism would be a link to
dbxref in organism_dbxref.

Your orthology implementation seems reasonable.

Josh




On Fri, Jan 20, 2012 at 11:57 AM, Lacey-Anne Sanderson
<[hidden email]> wrote:
So in spite of the lack of response, I've started working on this module. I
need some clarification:

GMOD RPC Questions:
- When you say "Gene Full text Search" is this a full text searching of all
records in the chado feature table or are you restricting it to those of
type gene?
- When you refer to type (Gene Full Text Search), I assume you mean
feature.type_id exclusively?
- In Gene Location, does the type refer to the type of features located on
that chromosome to return

Chado Storage Questions:
- Where in chado is the taxid normally stored? is this an organismprop?
- Are gene orthologs normally stored in chado using feature_relationship
with a cvterm of orthologous (SO:0000858)?

I know some of these questions might seem like I think I know the answer but
I don't want to assume anything or we might end up with a non-standard
implementation.
Thanks in advance for the help!
~Lacey

PS. My implementation is at http://knowpulse2.usask.ca/devel/ if anyone
wants to go look at examples. Currently I only have organisms
(http://knowpulse2.usask.ca/devel/gmodrpc/v1.1/organisms) done.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Email: [hidden email]
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-01-10, at 4:35 PM, Lacey-Anne Sanderson wrote:

I am interested in implementing the GMOD Restful API as a Tripal module
making all Tripal sites able to expose their data in a cross-MOD friendly
fashion. The idea is that you can enable a Tripal module and any public data
available through your website (stored in chado) is made available at
http://yourtripalsite/gmodrpc/v<api version>... as described by the API.

I'm wondering if the API described at http://gmod.org/wiki/GMOD_REST_API is
in a stable enough state for me to start coding this module? Also, how close
are the other versions to being ready for deployment on non-Tripal MODs?

My Design Plans:
Stage 1: Use the Drupal menu system to manage generating the URLs and the
Tripal Chado API to supply the data for those pages.
Stage 2: Implement dynamically generated Tripal pages (organism/feature)
based on data pulled from other MODs using the GMOD Restful API. This will
allow Tripal sites to display data from other MODs in a seamless manner (Of
course these pages will give credit and link to the MODs storing the data).
An administration page will allow you to configure which MOD's you want to
query -full web-address specification or selecting options from a form.

Thanks,
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Email: [hidden email]
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan



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Re: Implementing GMOD Restful API in Tripal

Alex Kalderimis-2
In reply to this post by Lacey-Anne Sanderson
Just thought I should say that our development efforts have taken a back seat to the work on the current InterMine release, but we plan to have a working implementation for the GMOD meeting in April.

Alex



-------- Original message --------
Subject: Re: [GMOD-devel] Implementing GMOD Restful API in Tripal
From: Lacey-Anne Sanderson <[hidden email]>
To: Josh Goodman <[hidden email]>
CC: [hidden email]


Hi Josh,

I think for the Tripal implementation, I'm not going to limit the full text search and location services to gene. Our website doesn't currently have any gene models due to the species being orphan legume crops (Pea, Lentil, Chickpea, Bean) which don't yet have these resources and if the gene limit is enforced this service wouldn't be useful to us. Since the Tripal module won't use the API directly but rather expose the results in the same format, I don't think this should be a problem. What are your thoughts?

Also, I have been in contact with the Legume Information System (LIS) and Soybase about using this API for cross-communication between all legume informatic websites. We have a need to export data in addition to sequences including QTL, genetic map, genotypic and phenotypic data. What do you think of expanding the current API with our help to include some/all of these type of data in version 1.2? I would be willing to spearhead determining what the URLs and returned results should look like.

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-01-20, at 1:41 PM, Josh Goodman wrote:

Hi Lacey,

My apologies, your initial reply slipped past my inbox.  Alex
Kalderimis (InterMine) and I had a flurry of activity after GMOD last
year, but that has died off as the holidays kicked in.

Alex did quite a bit of nice work refractoring code and you are free
to take a look at
https://github.com/GMOD/GMOD-RPC-perl/tree/templateless.  I've been
meaning to get back to this, but I haven't quite cleared my TODO list
enough.

I'd say that the API is stable enough for you to start drafting
something.  I don't know how close other MODs are but I've set a goal
for having this deployed at FlyBase by this summer.

The full text search service is currently limited to only features of
type gene (SO:0000704).  The type field is there to allow for adding
additional features in the future.  The same goes for location.  Yes,
the type indicates the type of feature to return.

I think the proper place for a taxid on an organism would be a link to
dbxref in organism_dbxref.

Your orthology implementation seems reasonable.

Josh




On Fri, Jan 20, 2012 at 11:57 AM, Lacey-Anne Sanderson
<[hidden email]> wrote:
So in spite of the lack of response, I've started working on this module. I
need some clarification:

GMOD RPC Questions:
- When you say "Gene Full text Search" is this a full text searching of all
records in the chado feature table or are you restricting it to those of
type gene?
- When you refer to type (Gene Full Text Search), I assume you mean
feature.type_id exclusively?
- In Gene Location, does the type refer to the type of features located on
that chromosome to return

Chado Storage Questions:
- Where in chado is the taxid normally stored? is this an organismprop?
- Are gene orthologs normally stored in chado using feature_relationship
with a cvterm of orthologous (SO:0000858)?

I know some of these questions might seem like I think I know the answer but
I don't want to assume anything or we might end up with a non-standard
implementation.
Thanks in advance for the help!
~Lacey

PS. My implementation is at http://knowpulse2.usask.ca/devel/ if anyone
wants to go look at examples. Currently I only have organisms
(http://knowpulse2.usask.ca/devel/gmodrpc/v1.1/organisms) done.

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Email: [hidden email]
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-01-10, at 4:35 PM, Lacey-Anne Sanderson wrote:

I am interested in implementing the GMOD Restful API as a Tripal module
making all Tripal sites able to expose their data in a cross-MOD friendly
fashion. The idea is that you can enable a Tripal module and any public data
available through your website (stored in chado) is made available at
http://yourtripalsite/gmodrpc/v<api version>... as described by the API.

I'm wondering if the API described at http://gmod.org/wiki/GMOD_REST_API is
in a stable enough state for me to start coding this module? Also, how close
are the other versions to being ready for deployment on non-Tripal MODs?

My Design Plans:
Stage 1: Use the Drupal menu system to manage generating the URLs and the
Tripal Chado API to supply the data for those pages.
Stage 2: Implement dynamically generated Tripal pages (organism/feature)
based on data pulled from other MODs using the GMOD Restful API. This will
allow Tripal sites to display data from other MODs in a seamless manner (Of
course these pages will give credit and link to the MODs storing the data).
An administration page will allow you to configure which MOD's you want to
query -full web-address specification or selecting options from a form.

Thanks,
~Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Email: [hidden email]
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan



------------------------------------------------------------------------------
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Re: Implementing GMOD Restful API in Tripal

Josh Goodman
In reply to this post by Lacey-Anne Sanderson
Hi Lacey,

I see nothing wrong with your first paragraph.

I'm a bit hesitant to agree to your second paragraph because I think
it goes beyond the scope of this API.  Previous efforts to improve
cross MOD integration have failed when they tried to go beyond the
"Gene" concept.  The concepts and services might work well across your
legume crops but might not translate very well when applied to other
organisms.

Having said that, I don't want to be the sole voice that gives a
thumbs up or down to this proposal, so I think your group should put
together a proposal and send it to gmod-devel for discussion.

Cheers,
Josh




On Wed, Jan 25, 2012 at 3:11 PM, Lacey-Anne Sanderson
<[hidden email]> wrote:

> Hi Josh,
>
> I think for the Tripal implementation, I'm not going to limit the full text
> search and location services to gene. Our website doesn't currently have any
> gene models due to the species being orphan legume crops (Pea, Lentil,
> Chickpea, Bean) which don't yet have these resources and if the gene limit
> is enforced this service wouldn't be useful to us. Since the Tripal module
> won't use the API directly but rather expose the results in the same format,
> I don't think this should be a problem. What are your thoughts?
>
> Also, I have been in contact with the Legume Information System (LIS) and
> Soybase about using this API for cross-communication between all legume
> informatic websites. We have a need to export data in addition to sequences
> including QTL, genetic map, genotypic and phenotypic data. What do you think
> of expanding the current API with our help to include some/all of these type
> of data in version 1.2? I would be willing to spearhead determining what the
> URLs and returned results should look like.
>
> ~Lacey
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-2430
> Email: [hidden email]
> Room 3D10 Agriculture
> Department of Plant Sciences
> University of Saskatchewan
>
> On 2012-01-20, at 1:41 PM, Josh Goodman wrote:
>
> Hi Lacey,
>
> My apologies, your initial reply slipped past my inbox.  Alex
> Kalderimis (InterMine) and I had a flurry of activity after GMOD last
> year, but that has died off as the holidays kicked in.
>
> Alex did quite a bit of nice work refractoring code and you are free
> to take a look at
> https://github.com/GMOD/GMOD-RPC-perl/tree/templateless.  I've been
> meaning to get back to this, but I haven't quite cleared my TODO list
> enough.
>
> I'd say that the API is stable enough for you to start drafting
> something.  I don't know how close other MODs are but I've set a goal
> for having this deployed at FlyBase by this summer.
>
> The full text search service is currently limited to only features of
> type gene (SO:0000704).  The type field is there to allow for adding
> additional features in the future.  The same goes for location.  Yes,
> the type indicates the type of feature to return.
>
> I think the proper place for a taxid on an organism would be a link to
> dbxref in organism_dbxref.
>
> Your orthology implementation seems reasonable.
>
> Josh
>
>
>
>
> On Fri, Jan 20, 2012 at 11:57 AM, Lacey-Anne Sanderson
> <[hidden email]> wrote:
>
> So in spite of the lack of response, I've started working on this module. I
>
> need some clarification:
>
>
> GMOD RPC Questions:
>
> - When you say "Gene Full text Search" is this a full text searching of all
>
> records in the chado feature table or are you restricting it to those of
>
> type gene?
>
> - When you refer to type (Gene Full Text Search), I assume you mean
>
> feature.type_id exclusively?
>
> - In Gene Location, does the type refer to the type of features located on
>
> that chromosome to return
>
>
> Chado Storage Questions:
>
> - Where in chado is the taxid normally stored? is this an organismprop?
>
> - Are gene orthologs normally stored in chado using feature_relationship
>
> with a cvterm of orthologous (SO:0000858)?
>
>
> I know some of these questions might seem like I think I know the answer but
>
> I don't want to assume anything or we might end up with a non-standard
>
> implementation.
>
> Thanks in advance for the help!
>
> ~Lacey
>
>
> PS. My implementation is at http://knowpulse2.usask.ca/devel/ if anyone
>
> wants to go look at examples. Currently I only have organisms
>
> (http://knowpulse2.usask.ca/devel/gmodrpc/v1.1/organisms) done.
>
>
> ------------------------------------------------------
>
> Lacey-Anne Sanderson
>
> Bioinformaticist
>
> Pulse Crop Breeding and Genetics
>
> Phone: (306) 966-2430
>
> Email: [hidden email]
>
> Room 3D10 Agriculture
>
> Department of Plant Sciences
>
> University of Saskatchewan
>
>
> On 2012-01-10, at 4:35 PM, Lacey-Anne Sanderson wrote:
>
>
> I am interested in implementing the GMOD Restful API as a Tripal module
>
> making all Tripal sites able to expose their data in a cross-MOD friendly
>
> fashion. The idea is that you can enable a Tripal module and any public data
>
> available through your website (stored in chado) is made available at
>
> http://yourtripalsite/gmodrpc/v<api version>... as described by the API.
>
>
> I'm wondering if the API described at http://gmod.org/wiki/GMOD_REST_API is
>
> in a stable enough state for me to start coding this module? Also, how close
>
> are the other versions to being ready for deployment on non-Tripal MODs?
>
>
> My Design Plans:
>
> Stage 1: Use the Drupal menu system to manage generating the URLs and the
>
> Tripal Chado API to supply the data for those pages.
>
> Stage 2: Implement dynamically generated Tripal pages (organism/feature)
>
> based on data pulled from other MODs using the GMOD Restful API. This will
>
> allow Tripal sites to display data from other MODs in a seamless manner (Of
>
> course these pages will give credit and link to the MODs storing the data).
>
> An administration page will allow you to configure which MOD's you want to
>
> query -full web-address specification or selecting options from a form.
>
>
> Thanks,
>
> ~Lacey
>
> ------------------------------------------------------
>
> Lacey-Anne Sanderson
>
> Bioinformaticist
>
> Pulse Crop Breeding and Genetics
>
> Phone: (306) 966-2430
>
> Email: [hidden email]
>
> Room 3D10 Agriculture
>
> Department of Plant Sciences
>
> University of Saskatchewan
>
>
>
>
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