Fwd: Health module info for GMOD teleconf

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Fwd: Health module info for GMOD teleconf

Scott Cain
Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




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

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Re: Fwd: Health module info for GMOD teleconf

Daniel Quest
Forgive my ignorance... But doesn't it make sense to link this data you will be collecting to SNOWMED/ICD9 codes/OMIM/ect?  Drugs are also important.  I can't look at the schema on my iPad right now, but my feeling is if you really want to make stuff impact the clinic, you will want to start with a set of (human) cohorts that share genetic features (e.g. Variants) where there is a model in Fly/worm ect.  The link could go through any of the data sources mentioned (e.g. Drug, SNOWMED, ect)... Most valuable is a collection of literature verifying mechanism/treatment in the model organism that would be the basis for a clinical trial.  Prioritization of clinically significant mechanisms in model organisms could be based on the size of the human cohort group, the strength of the source evidence, ect.  If we (Mayo Clinic) tried to use such a thing we would need the ability to extract-transform+load the Chado database and link it to our clinical/research database systems.  

Hope this is helpful
Dan


Sent from my iPad

On Dec 12, 2013, at 10:49 AM, Scott Cain <[hidden email]> wrote:

Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
<health.sql>
<HHproformaspecs.pdf>
------------------------------------------------------------------------------
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Re: Fwd: Health module info for GMOD teleconf

David Emmert
Hi Dan,

If you have a look at the second document Scott sent around you'll get an idea of what FlyBase curators are currently planning to curate (obviously including links to external databases as appropriate).   The curators' plan is the result of extensive discussions within the group and review by scientific advisors and other interested parties, but as I told Scott, there are liable to be some changes as we move to implementation.

Of course, none of these details are going to be directly reflected in the chado tables, which are deliberately designed to be generic, to support the wide range of data and external links disparate MODs are likely to want to curate, and to support as much as possible new developments going forward in data to be curated and in linkable external databases.

Best,

-Dave




On Thu, Dec 12, 2013 at 8:17 PM, Daniel Quest <[hidden email]> wrote:
Forgive my ignorance... But doesn't it make sense to link this data you will be collecting to SNOWMED/ICD9 codes/OMIM/ect?  Drugs are also important.  I can't look at the schema on my iPad right now, but my feeling is if you really want to make stuff impact the clinic, you will want to start with a set of (human) cohorts that share genetic features (e.g. Variants) where there is a model in Fly/worm ect.  The link could go through any of the data sources mentioned (e.g. Drug, SNOWMED, ect)... Most valuable is a collection of literature verifying mechanism/treatment in the model organism that would be the basis for a clinical trial.  Prioritization of clinically significant mechanisms in model organisms could be based on the size of the human cohort group, the strength of the source evidence, ect.  If we (Mayo Clinic) tried to use such a thing we would need the ability to extract-transform+load the Chado database and link it to our clinical/research database systems.  

Hope this is helpful
Dan


Sent from my iPad

On Dec 12, 2013, at 10:49 AM, Scott Cain <[hidden email]> wrote:

Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
<health.sql>
<HHproformaspecs.pdf>
------------------------------------------------------------------------------
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Re: Fwd: Health module info for GMOD teleconf

Daniel Quest
Hey Dave,

Sorry, I did not see the OMIM links.  That is good.  Our clinical systems have SNOMED/ICD9 codes, so if you can link to those, I think it would help adoption. I think scientific advisors are important, but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

Best wishes
Daniel


On Fri, Dec 13, 2013 at 8:49 AM, David Emmert <[hidden email]> wrote:
Hi Dan,

If you have a look at the second document Scott sent around you'll get an idea of what FlyBase curators are currently planning to curate (obviously including links to external databases as appropriate).   The curators' plan is the result of extensive discussions within the group and review by scientific advisors and other interested parties, but as I told Scott, there are liable to be some changes as we move to implementation.

Of course, none of these details are going to be directly reflected in the chado tables, which are deliberately designed to be generic, to support the wide range of data and external links disparate MODs are likely to want to curate, and to support as much as possible new developments going forward in data to be curated and in linkable external databases.

Best,

-Dave




On Thu, Dec 12, 2013 at 8:17 PM, Daniel Quest <[hidden email]> wrote:
Forgive my ignorance... But doesn't it make sense to link this data you will be collecting to SNOWMED/ICD9 codes/OMIM/ect?  Drugs are also important.  I can't look at the schema on my iPad right now, but my feeling is if you really want to make stuff impact the clinic, you will want to start with a set of (human) cohorts that share genetic features (e.g. Variants) where there is a model in Fly/worm ect.  The link could go through any of the data sources mentioned (e.g. Drug, SNOWMED, ect)... Most valuable is a collection of literature verifying mechanism/treatment in the model organism that would be the basis for a clinical trial.  Prioritization of clinically significant mechanisms in model organisms could be based on the size of the human cohort group, the strength of the source evidence, ect.  If we (Mayo Clinic) tried to use such a thing we would need the ability to extract-transform+load the Chado database and link it to our clinical/research database systems.  

Hope this is helpful
Dan


Sent from my iPad

On Dec 12, 2013, at 10:49 AM, Scott Cain <[hidden email]> wrote:

Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
<health.sql>
<HHproformaspecs.pdf>
------------------------------------------------------------------------------
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Re: Health module info for GMOD teleconf

Scott Cain
In reply to this post by Scott Cain
Hi,

This is a reminder about the call today at 12:30 EST where we'll discuss FlyBase's proposed addition to Chado, what they are calling the health module.  If you would like to join the call, please let me know and I'll send you call in info.

Thanks,
Scott



On Thu, Dec 12, 2013 at 11:49 AM, Scott Cain <[hidden email]> wrote:
Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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

------------------------------------------------------------------------------
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organizations don't have a clear picture of how application performance
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Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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Re: Health module info for GMOD teleconf

Sook Jung
Hi Scott,
I would like to join the call. One thing I want to suggest is to make the name more general than human health. I think it will be useful for crop/animal databases, since data that are associated with plant/animal disease need to be stored as well. We were thinking about having very similar sets of custom tables and call it 'pathology' .. Pathology was the name of the table in CottonDB before we converted it into chado in CottonGEN.
Thanks
Sook


On Tue, Dec 17, 2013 at 9:47 AM, Scott Cain <[hidden email]> wrote:
Hi,

This is a reminder about the call today at 12:30 EST where we'll discuss FlyBase's proposed addition to Chado, what they are calling the health module.  If you would like to join the call, please let me know and I'll send you call in info.

Thanks,
Scott



On Thu, Dec 12, 2013 at 11:49 AM, Scott Cain <[hidden email]> wrote:
Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Re: Health module info for GMOD teleconf

Cannon, Steven
I agree with Sook about looking for ways to make this general, and applicable for crop species etc. Both "health" and "pathology" basically describe kinds of observable phenotypes – which may be genetic disease states or pathologies, or may be desirable (dwarf/determinate, early-flowering, delayed senescence, etc.). Several groups are working on ontology-based descriptions of phenotypes. So maybe the thing to do is to look for ways to extend the current phenotype table(s).

Steven

From: Sook Jung <[hidden email]>
Date: Tuesday, December 17, 2013 9:13 AM
To: Scott Cain <[hidden email]>
Cc: GMOD Schema/Chado List <[hidden email]>
Subject: Re: [Gmod-schema] Health module info for GMOD teleconf

Hi Scott,
I would like to join the call. One thing I want to suggest is to make the name more general than human health. I think it will be useful for crop/animal databases, since data that are associated with plant/animal disease need to be stored as well. We were thinking about having very similar sets of custom tables and call it 'pathology' .. Pathology was the name of the table in CottonDB before we converted it into chado in CottonGEN.
Thanks
Sook


On Tue, Dec 17, 2013 at 9:47 AM, Scott Cain <[hidden email]> wrote:
Hi,

This is a reminder about the call today at 12:30 EST where we'll discuss FlyBase's proposed addition to Chado, what they are calling the health module.  If you would like to join the call, please let me know and I'll send you call in info.

Thanks,
Scott



On Thu, Dec 12, 2013 at 11:49 AM, Scott Cain <[hidden email]> wrote:
Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Re: Health module info for GMOD teleconf

Naama Menda-2
I think this is a great opportunity to finally tackle the long-overdue phenotype module revision.
I believe with a few changes and new tables, health or pathology information could fit into a generic phenotype table.

After we finished designing the Natural Diversity module, nobody wanted to touch the phenotype module, since it was hard to get an agreement on what is a phenotype, and how traits should be separated from observations... 

-Naama



On Tue, Dec 17, 2013 at 10:42 AM, Cannon, Steven <[hidden email]> wrote:
I agree with Sook about looking for ways to make this general, and applicable for crop species etc. Both "health" and "pathology" basically describe kinds of observable phenotypes – which may be genetic disease states or pathologies, or may be desirable (dwarf/determinate, early-flowering, delayed senescence, etc.). Several groups are working on ontology-based descriptions of phenotypes. So maybe the thing to do is to look for ways to extend the current phenotype table(s).

Steven

From: Sook Jung <[hidden email]>
Date: Tuesday, December 17, 2013 9:13 AM
To: Scott Cain <[hidden email]>
Cc: GMOD Schema/Chado List <[hidden email]>
Subject: Re: [Gmod-schema] Health module info for GMOD teleconf

Hi Scott,
I would like to join the call. One thing I want to suggest is to make the name more general than human health. I think it will be useful for crop/animal databases, since data that are associated with plant/animal disease need to be stored as well. We were thinking about having very similar sets of custom tables and call it 'pathology' .. Pathology was the name of the table in CottonDB before we converted it into chado in CottonGEN.
Thanks
Sook


On Tue, Dec 17, 2013 at 9:47 AM, Scott Cain <[hidden email]> wrote:
Hi,

This is a reminder about the call today at 12:30 EST where we'll discuss FlyBase's proposed addition to Chado, what they are calling the health module.  If you would like to join the call, please let me know and I'll send you call in info.

Thanks,
Scott



On Thu, Dec 12, 2013 at 11:49 AM, Scott Cain <[hidden email]> wrote:
Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Re: Fwd: Health module info for GMOD teleconf

David Emmert
In reply to this post by Daniel Quest
Hi Daniel,

but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

I could not agree more.  

I'm particularly happy to have met you through this - I think you may have exactly the kind of understanding of human clinical data I've been worried our curators didn't have access to when they were developing their curation strategy.   If you'd be game, I'd love to bounce a few ideas off you from time to time as we go forward at FlyBase, to see whether what we're doing seems sensible from the human clinical data side.

Best,

-Dave


On Dec 14, 2013, at 9:57 PM, Daniel Quest <[hidden email]> wrote:

Hey Dave,

Sorry, I did not see the OMIM links.  That is good.  Our clinical systems have SNOMED/ICD9 codes, so if you can link to those, I think it would help adoption. I think scientific advisors are important, but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

Best wishes
Daniel


On Fri, Dec 13, 2013 at 8:49 AM, David Emmert <[hidden email]> wrote:
Hi Dan,

If you have a look at the second document Scott sent around you'll get an idea of what FlyBase curators are currently planning to curate (obviously including links to external databases as appropriate).   The curators' plan is the result of extensive discussions within the group and review by scientific advisors and other interested parties, but as I told Scott, there are liable to be some changes as we move to implementation.

Of course, none of these details are going to be directly reflected in the chado tables, which are deliberately designed to be generic, to support the wide range of data and external links disparate MODs are likely to want to curate, and to support as much as possible new developments going forward in data to be curated and in linkable external databases.

Best,

-Dave




On Thu, Dec 12, 2013 at 8:17 PM, Daniel Quest <[hidden email]> wrote:
Forgive my ignorance... But doesn't it make sense to link this data you will be collecting to SNOWMED/ICD9 codes/OMIM/ect?  Drugs are also important.  I can't look at the schema on my iPad right now, but my feeling is if you really want to make stuff impact the clinic, you will want to start with a set of (human) cohorts that share genetic features (e.g. Variants) where there is a model in Fly/worm ect.  The link could go through any of the data sources mentioned (e.g. Drug, SNOWMED, ect)... Most valuable is a collection of literature verifying mechanism/treatment in the model organism that would be the basis for a clinical trial.  Prioritization of clinically significant mechanisms in model organisms could be based on the size of the human cohort group, the strength of the source evidence, ect.  If we (Mayo Clinic) tried to use such a thing we would need the ability to extract-transform+load the Chado database and link it to our clinical/research database systems.  

Hope this is helpful
Dan


Sent from my iPad

On Dec 12, 2013, at 10:49 AM, Scott Cain <[hidden email]> wrote:

Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
<health.sql>
<HHproformaspecs.pdf>
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Re: Fwd: Health module info for GMOD teleconf

Daniel Quest
Sure, I am happy to be of help, and if I don't know the answer, there is a bunch of people I can put you in contact with.

Best,
Dan

Sent from my iPad

On Dec 17, 2013, at 4:32 PM, David Emmert <[hidden email]> wrote:

Hi Daniel,

but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

I could not agree more.  

I'm particularly happy to have met you through this - I think you may have exactly the kind of understanding of human clinical data I've been worried our curators didn't have access to when they were developing their curation strategy.   If you'd be game, I'd love to bounce a few ideas off you from time to time as we go forward at FlyBase, to see whether what we're doing seems sensible from the human clinical data side.

Best,

-Dave


On Dec 14, 2013, at 9:57 PM, Daniel Quest <[hidden email]> wrote:

Hey Dave,

Sorry, I did not see the OMIM links.  That is good.  Our clinical systems have SNOMED/ICD9 codes, so if you can link to those, I think it would help adoption. I think scientific advisors are important, but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

Best wishes
Daniel


On Fri, Dec 13, 2013 at 8:49 AM, David Emmert <[hidden email]> wrote:
Hi Dan,

If you have a look at the second document Scott sent around you'll get an idea of what FlyBase curators are currently planning to curate (obviously including links to external databases as appropriate).   The curators' plan is the result of extensive discussions within the group and review by scientific advisors and other interested parties, but as I told Scott, there are liable to be some changes as we move to implementation.

Of course, none of these details are going to be directly reflected in the chado tables, which are deliberately designed to be generic, to support the wide range of data and external links disparate MODs are likely to want to curate, and to support as much as possible new developments going forward in data to be curated and in linkable external databases.

Best,

-Dave




On Thu, Dec 12, 2013 at 8:17 PM, Daniel Quest <[hidden email]> wrote:
Forgive my ignorance... But doesn't it make sense to link this data you will be collecting to SNOWMED/ICD9 codes/OMIM/ect?  Drugs are also important.  I can't look at the schema on my iPad right now, but my feeling is if you really want to make stuff impact the clinic, you will want to start with a set of (human) cohorts that share genetic features (e.g. Variants) where there is a model in Fly/worm ect.  The link could go through any of the data sources mentioned (e.g. Drug, SNOWMED, ect)... Most valuable is a collection of literature verifying mechanism/treatment in the model organism that would be the basis for a clinical trial.  Prioritization of clinically significant mechanisms in model organisms could be based on the size of the human cohort group, the strength of the source evidence, ect.  If we (Mayo Clinic) tried to use such a thing we would need the ability to extract-transform+load the Chado database and link it to our clinical/research database systems.  

Hope this is helpful
Dan


Sent from my iPad

On Dec 12, 2013, at 10:49 AM, Scott Cain <[hidden email]> wrote:

Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
<health.sql>
<HHproformaspecs.pdf>
------------------------------------------------------------------------------
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Re: Fwd: Health module info for GMOD teleconf

Daniel Quest
In reply to this post by David Emmert
Thinking about this a bit more, I think the most direct approach from the clinical perspective is to identify a set of cohorts in the clinical space where there is poor/no therapeutic options and then curate/experiment in the model organism to better understand the fundamentals, assays (e.g. Sequencing) done in tandem in the clinical space and model organism.  Many such initiatives could be undertaken at the same time.  This way we don't try to populate all kinds of phenotypes with no clinical link, or populate phenotypes where there is a clinical link, but nothing can be done in the model/human (I.e. Aids does not infect mice or fly, but does infect Resus monkey and humans).  

Thoughts?

Dan

Sent from my iPad

On Dec 17, 2013, at 4:32 PM, David Emmert <[hidden email]> wrote:

Hi Daniel,

but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

I could not agree more.  

I'm particularly happy to have met you through this - I think you may have exactly the kind of understanding of human clinical data I've been worried our curators didn't have access to when they were developing their curation strategy.   If you'd be game, I'd love to bounce a few ideas off you from time to time as we go forward at FlyBase, to see whether what we're doing seems sensible from the human clinical data side.

Best,

-Dave


On Dec 14, 2013, at 9:57 PM, Daniel Quest <[hidden email]> wrote:

Hey Dave,

Sorry, I did not see the OMIM links.  That is good.  Our clinical systems have SNOMED/ICD9 codes, so if you can link to those, I think it would help adoption. I think scientific advisors are important, but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

Best wishes
Daniel


On Fri, Dec 13, 2013 at 8:49 AM, David Emmert <[hidden email]> wrote:
Hi Dan,

If you have a look at the second document Scott sent around you'll get an idea of what FlyBase curators are currently planning to curate (obviously including links to external databases as appropriate).   The curators' plan is the result of extensive discussions within the group and review by scientific advisors and other interested parties, but as I told Scott, there are liable to be some changes as we move to implementation.

Of course, none of these details are going to be directly reflected in the chado tables, which are deliberately designed to be generic, to support the wide range of data and external links disparate MODs are likely to want to curate, and to support as much as possible new developments going forward in data to be curated and in linkable external databases.

Best,

-Dave




On Thu, Dec 12, 2013 at 8:17 PM, Daniel Quest <[hidden email]> wrote:
Forgive my ignorance... But doesn't it make sense to link this data you will be collecting to SNOWMED/ICD9 codes/OMIM/ect?  Drugs are also important.  I can't look at the schema on my iPad right now, but my feeling is if you really want to make stuff impact the clinic, you will want to start with a set of (human) cohorts that share genetic features (e.g. Variants) where there is a model in Fly/worm ect.  The link could go through any of the data sources mentioned (e.g. Drug, SNOWMED, ect)... Most valuable is a collection of literature verifying mechanism/treatment in the model organism that would be the basis for a clinical trial.  Prioritization of clinically significant mechanisms in model organisms could be based on the size of the human cohort group, the strength of the source evidence, ect.  If we (Mayo Clinic) tried to use such a thing we would need the ability to extract-transform+load the Chado database and link it to our clinical/research database systems.  

Hope this is helpful
Dan


Sent from my iPad

On Dec 12, 2013, at 10:49 AM, Scott Cain <[hidden email]> wrote:

Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
<health.sql>
<HHproformaspecs.pdf>
------------------------------------------------------------------------------
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Re: Fwd: Health module info for GMOD teleconf

David Emmert
Hi Dan,

Thinking about this a bit more, I think the most direct approach from the clinical perspective is to identify a set of cohorts in the clinical space where there is poor/no therapeutic options and then curate/experiment in the model organism to better understand the fundamentals, assays (e.g. Sequencing) done in tandem in the clinical space and model organism.  Many such initiatives could be undertaken at the same time.  This way we don't try to populate all kinds of phenotypes with no clinical link, or populate phenotypes where there is a clinical link, but nothing can be done in the model/human (I.e. Aids does not infect mice or fly, but does infect Resus monkey and humans). 

I'd think FlyBase's efforts would be in support of what you describe.  The plan for the moment is to curate data on the few hundred cases in which there is a well characterized fly model for a human disease or condition, with the expectation that this will give both fly and human researchers a platform to expand their investigation in directions that will ultimately benefit human health...   tho I suppose if a few fly diseases were to get cured, that would be cool too!  ;)

FlyBase's plans for this are pretty modest at present, but the last few days I've been fretting about GWAS of complex diseases, and wondering whether down the line we're going to find ourselves wanting to manage associated GWAS data in flies, and what it would all look like...

Best,

-Dave


On Tue, Dec 17, 2013 at 9:26 PM, Daniel Quest <[hidden email]> wrote:
Thinking about this a bit more, I think the most direct approach from the clinical perspective is to identify a set of cohorts in the clinical space where there is poor/no therapeutic options and then curate/experiment in the model organism to better understand the fundamentals, assays (e.g. Sequencing) done in tandem in the clinical space and model organism.  Many such initiatives could be undertaken at the same time.  This way we don't try to populate all kinds of phenotypes with no clinical link, or populate phenotypes where there is a clinical link, but nothing can be done in the model/human (I.e. Aids does not infect mice or fly, but does infect Resus monkey and humans).  

Thoughts?

Dan

Sent from my iPad

On Dec 17, 2013, at 4:32 PM, David Emmert <[hidden email]> wrote:

Hi Daniel,

but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

I could not agree more.  

I'm particularly happy to have met you through this - I think you may have exactly the kind of understanding of human clinical data I've been worried our curators didn't have access to when they were developing their curation strategy.   If you'd be game, I'd love to bounce a few ideas off you from time to time as we go forward at FlyBase, to see whether what we're doing seems sensible from the human clinical data side.

Best,

-Dave


On Dec 14, 2013, at 9:57 PM, Daniel Quest <[hidden email]> wrote:

Hey Dave,

Sorry, I did not see the OMIM links.  That is good.  Our clinical systems have SNOMED/ICD9 codes, so if you can link to those, I think it would help adoption. I think scientific advisors are important, but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

Best wishes
Daniel


On Fri, Dec 13, 2013 at 8:49 AM, David Emmert <[hidden email]> wrote:
Hi Dan,

If you have a look at the second document Scott sent around you'll get an idea of what FlyBase curators are currently planning to curate (obviously including links to external databases as appropriate).   The curators' plan is the result of extensive discussions within the group and review by scientific advisors and other interested parties, but as I told Scott, there are liable to be some changes as we move to implementation.

Of course, none of these details are going to be directly reflected in the chado tables, which are deliberately designed to be generic, to support the wide range of data and external links disparate MODs are likely to want to curate, and to support as much as possible new developments going forward in data to be curated and in linkable external databases.

Best,

-Dave




On Thu, Dec 12, 2013 at 8:17 PM, Daniel Quest <[hidden email]> wrote:
Forgive my ignorance... But doesn't it make sense to link this data you will be collecting to SNOWMED/ICD9 codes/OMIM/ect?  Drugs are also important.  I can't look at the schema on my iPad right now, but my feeling is if you really want to make stuff impact the clinic, you will want to start with a set of (human) cohorts that share genetic features (e.g. Variants) where there is a model in Fly/worm ect.  The link could go through any of the data sources mentioned (e.g. Drug, SNOWMED, ect)... Most valuable is a collection of literature verifying mechanism/treatment in the model organism that would be the basis for a clinical trial.  Prioritization of clinically significant mechanisms in model organisms could be based on the size of the human cohort group, the strength of the source evidence, ect.  If we (Mayo Clinic) tried to use such a thing we would need the ability to extract-transform+load the Chado database and link it to our clinical/research database systems.  

Hope this is helpful
Dan


Sent from my iPad

On Dec 12, 2013, at 10:49 AM, Scott Cain <[hidden email]> wrote:

Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
<health.sql>
<HHproformaspecs.pdf>
------------------------------------------------------------------------------
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Re: Fwd: Health module info for GMOD teleconf

Daniel Quest
Interesting... VCF has stated to dominate here (perhaps because of 1000genomes)... I don't like putting the data into these files as it is very limiting but the bioinformatics core has gotten very creative in shoving all kinds of data into VCF.  We have reacted with good tooling for annotating, manipulating and filtering these files.  BioR is one of these tools - you can get it here:  http://bioinformaticstools.mayo.edu

The filtering tool, VCF-Miner will probably be out in Spring.  Open source tooling like tabix and vcf tools are all starting to create an ecosystem around this silly-limited format.  How one does deeper things like orthalogs for the type of thing you are talking about is anyone's guess.   Can you provide some concrete examples of things you want to represent in a file that you can't put in VCF?  We have done crazy stuff such as drilling out fields from this deeply nested drugbank.xml file and placed them in the VCF info field.  Flags for phenotype conditions can even be placed in the sample columns (as long as they are described in the Format field).

Thoughts?
Dan

Sent from my iPad

On Dec 19, 2013, at 3:09 PM, David Emmert <[hidden email]> wrote:

Hi Dan,

Thinking about this a bit more, I think the most direct approach from the clinical perspective is to identify a set of cohorts in the clinical space where there is poor/no therapeutic options and then curate/experiment in the model organism to better understand the fundamentals, assays (e.g. Sequencing) done in tandem in the clinical space and model organism.  Many such initiatives could be undertaken at the same time.  This way we don't try to populate all kinds of phenotypes with no clinical link, or populate phenotypes where there is a clinical link, but nothing can be done in the model/human (I.e. Aids does not infect mice or fly, but does infect Resus monkey and humans). 

I'd think FlyBase's efforts would be in support of what you describe.  The plan for the moment is to curate data on the few hundred cases in which there is a well characterized fly model for a human disease or condition, with the expectation that this will give both fly and human researchers a platform to expand their investigation in directions that will ultimately benefit human health...   tho I suppose if a few fly diseases were to get cured, that would be cool too!  ;)

FlyBase's plans for this are pretty modest at present, but the last few days I've been fretting about GWAS of complex diseases, and wondering whether down the line we're going to find ourselves wanting to manage associated GWAS data in flies, and what it would all look like...

Best,

-Dave


On Tue, Dec 17, 2013 at 9:26 PM, Daniel Quest <[hidden email]> wrote:
Thinking about this a bit more, I think the most direct approach from the clinical perspective is to identify a set of cohorts in the clinical space where there is poor/no therapeutic options and then curate/experiment in the model organism to better understand the fundamentals, assays (e.g. Sequencing) done in tandem in the clinical space and model organism.  Many such initiatives could be undertaken at the same time.  This way we don't try to populate all kinds of phenotypes with no clinical link, or populate phenotypes where there is a clinical link, but nothing can be done in the model/human (I.e. Aids does not infect mice or fly, but does infect Resus monkey and humans).  

Thoughts?

Dan

Sent from my iPad

On Dec 17, 2013, at 4:32 PM, David Emmert <[hidden email]> wrote:

Hi Daniel,

but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

I could not agree more.  

I'm particularly happy to have met you through this - I think you may have exactly the kind of understanding of human clinical data I've been worried our curators didn't have access to when they were developing their curation strategy.   If you'd be game, I'd love to bounce a few ideas off you from time to time as we go forward at FlyBase, to see whether what we're doing seems sensible from the human clinical data side.

Best,

-Dave


On Dec 14, 2013, at 9:57 PM, Daniel Quest <[hidden email]> wrote:

Hey Dave,

Sorry, I did not see the OMIM links.  That is good.  Our clinical systems have SNOMED/ICD9 codes, so if you can link to those, I think it would help adoption. I think scientific advisors are important, but I think driving usage  through to the practice also requires database people with a deep understanding of clinical data.

Best wishes
Daniel


On Fri, Dec 13, 2013 at 8:49 AM, David Emmert <[hidden email]> wrote:
Hi Dan,

If you have a look at the second document Scott sent around you'll get an idea of what FlyBase curators are currently planning to curate (obviously including links to external databases as appropriate).   The curators' plan is the result of extensive discussions within the group and review by scientific advisors and other interested parties, but as I told Scott, there are liable to be some changes as we move to implementation.

Of course, none of these details are going to be directly reflected in the chado tables, which are deliberately designed to be generic, to support the wide range of data and external links disparate MODs are likely to want to curate, and to support as much as possible new developments going forward in data to be curated and in linkable external databases.

Best,

-Dave




On Thu, Dec 12, 2013 at 8:17 PM, Daniel Quest <[hidden email]> wrote:
Forgive my ignorance... But doesn't it make sense to link this data you will be collecting to SNOWMED/ICD9 codes/OMIM/ect?  Drugs are also important.  I can't look at the schema on my iPad right now, but my feeling is if you really want to make stuff impact the clinic, you will want to start with a set of (human) cohorts that share genetic features (e.g. Variants) where there is a model in Fly/worm ect.  The link could go through any of the data sources mentioned (e.g. Drug, SNOWMED, ect)... Most valuable is a collection of literature verifying mechanism/treatment in the model organism that would be the basis for a clinical trial.  Prioritization of clinically significant mechanisms in model organisms could be based on the size of the human cohort group, the strength of the source evidence, ect.  If we (Mayo Clinic) tried to use such a thing we would need the ability to extract-transform+load the Chado database and link it to our clinical/research database systems.  

Hope this is helpful
Dan


Sent from my iPad

On Dec 12, 2013, at 10:49 AM, Scott Cain <[hidden email]> wrote:

Hello,

Next Tuesday at 12:30 Eastern, Dave Emmert from FlyBase will be talking about their suggested new module for Chado called "health".  I'm forwarding the email he sent me along with attachments.  If you'd like to be included in the call, please let me know and I will send you the call in info.

Thanks,
Scott


---------- Forwarded message ----------
From: David Emmert <[hidden email]>
Date: Fri, Dec 6, 2013 at 3:49 PM
Subject: Health module info for GMOD teleconf
To: Scott Cain <[hidden email]>
Cc: FlyBase - Harvard Developers <[hidden email]>


Hi Scott,

As I mentioned in my note the other day, FlyBase is starting to curate data on human diseases and health-related processes for which
there are models in the fly.  We've been looking at two options for managing this data in chado: either using the existing phenotype
module or implementing a new "health" module.   I think the consensus here is that we think it would be best to go forward with the new
"health" module, but we'd very much like to get input from GMOD before we go forward.

As you suggested, I'm including some documentation to illustrate what we have in mind, namely the DDL for the proposed "health" module
(attachment: health.sql), developed by Andy Schroeder here at FlyBase, and the document produced by the Harvard Curators that
describes field-by-field what data we're planning to capture (HHproformaspecs.pdf).   Note that these are both drafts, and its fairly
likely that there will be some changes once we start actual implementation and rubber meets road.

I'm not including any documents on the current chado phenotype module (its available on the gmod svn), but it looks like in order to
manage the health data we'll be collecting, we'd need to add around 10 tables, all fairly standard chado tables (e.g., a "relationship"
table, relationships to cv, pub & dbxref modules, attributes of these, and so forth.

What we're looking for from GMOD is input whether there are any objections in principle to implementing a new "health" module in chado,
especially considering that some might argue that the diseases and conditions we'd be collecting information on for humans (tho note
that the health module is organism-agnostic) are really just phenotypes.  I think the general opinion here (certainly mine, anyway) is
that the health data is distinct enough from the phenotype data we've been collecting for flies and storing in the phenotype module
that it makes sense to use a new module, especially if there's any indication from the GMOD community that such a "health" module might
be of general interest.

We expect that other MODs are, like FlyBase, liable to be managing data on disease models, since there's lots of pressure from funding
agencies to make MODs more relevant to human health research.  We know that WormBase is undertaking such curation, and our curators
have been in touch with theirs but I think they're just comparing notes at this point; I have no idea how WB is managing their disease
model data.

If you could let us know when you plan on putting this on the agenda for a GMOD teleconf, Andy and I will make sure to join...

Many thanks!

Best,

-Dave




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
<health.sql>
<HHproformaspecs.pdf>
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Re: Fwd: Health module info for GMOD teleconf

Karl O. Pinc
On 12/19/2013 09:40:59 PM, Daniel Quest wrote:

> Interesting... VCF has stated to dominate here (perhaps because of
> 1000genomes)... I don't like putting the data into these files as it
> is very limiting but the bioinformatics core has gotten very creative
> in shoving all kinds of data into VCF.  We have reacted with good
> tooling for annotating, manipulating and filtering these files.  BioR
> is one of these tools - you can get it here:
> http://bioinformaticstools.mayo.edu
>
> The filtering tool, VCF-Miner will probably be out in Spring.  Open
> source tooling like tabix and vcf tools are all starting to create an
> ecosystem around this silly-limited format.  How one does deeper
> things like orthalogs for the type of thing you are talking about is
> anyone's guess.   Can you provide some concrete examples of things
> you
> want to represent in a file that you can't put in VCF?  We have done
> crazy stuff such as drilling out fields from this deeply nested
> drugbank.xml file and placed them in the VCF info field.  Flags for
> phenotype conditions can even be placed in the sample columns (as
> long
> as they are described in the Format field).
>
> Thoughts?

Postgres foreign data wrappers?  There's one for XML already
I believe.

Probably best used as a way to import/export rather than
analyze directly, but that's a guess.


Karl <[hidden email]>
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