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update RegenerateConnectome.py to read data from OpenWorm database instead of a spreadsheet #140

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kneuron opened this Issue Sep 13, 2013 · 16 comments

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kneuron commented Sep 13, 2013

Issue

Currently, RegenerateConnectome.py reads synapse position data from a spreadsheet. (I think this one: Steven Cook Data ). See issue 136 for more info. This issue is effectively update "a)" from that issue.

In order to close the data->model loop, we should replace this step with one that reads the data from our currently in-development biological data database

motivation

This will serve as the first test case for closing the loop between the biological data repository we are aggregating from the scientific literature and the simulations we plan to run to explore and test this data.

steps

  1. make sure Cook's Data is in the database - upload it if not
  2. #143 - create script to query and present data from the semantic database as RDF
  3. appropriately represent RDF data to RegenerateConnectome.py (either by munging the RDF into the format that RegenerateConnectome.py is already expecting, or modifying RegenerateConnectome.py to work with RDF)
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kneuron Sep 25, 2013

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updated the "steps" section to reflect #143

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kneuron commented Sep 25, 2013

updated the "steps" section to reflect #143

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Interintel Sep 25, 2013

This is long overdue - explanation of our current semantic database.

Not sure where it should go on our repositories?

Tim

On Wed, Sep 25, 2013 at 8:35 AM, kneuron notifications@github.com wrote:

updated the "steps" section to reflect #143#143


Reply to this email directly or view it on GitHubhttps://github.com//issues/140#issuecomment-25097937
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Interintel commented Sep 25, 2013

This is long overdue - explanation of our current semantic database.

Not sure where it should go on our repositories?

Tim

On Wed, Sep 25, 2013 at 8:35 AM, kneuron notifications@github.com wrote:

updated the "steps" section to reflect #143#143


Reply to this email directly or view it on GitHubhttps://github.com//issues/140#issuecomment-25097937
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kneuron Sep 25, 2013

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Hi Tim, See #141, I think that provides a nice starting place.

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kneuron commented Sep 25, 2013

Hi Tim, See #141, I think that provides a nice starting place.

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Lambdanaut Dec 12, 2013

Does this still need to be done? I'd like to attempt to work on this if there hasn't been substantial headway.

Lambdanaut commented Dec 12, 2013

Does this still need to be done? I'd like to attempt to work on this if there hasn't been substantial headway.

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@Lambdanaut yes this still needs work. Your help would be appreciated. The description appears to do a good job of explaining the issue. Issue #143 has some notes in one of the comments from me that has example python code that can be used to query data out of the database via rdflib. A version of RegenerateConnectome.py that used these kinds of methods would be very helpful to making the connectome model more rapidly data driven. It provides a great impetus for us to continue populating the database.

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slarson commented Dec 12, 2013

@Lambdanaut yes this still needs work. Your help would be appreciated. The description appears to do a good job of explaining the issue. Issue #143 has some notes in one of the comments from me that has example python code that can be used to query data out of the database via rdflib. A version of RegenerateConnectome.py that used these kinds of methods would be very helpful to making the connectome model more rapidly data driven. It provides a great impetus for us to continue populating the database.

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Thanks for offering to help with this @Lambdanaut. Can you make a new RegenerateConnectomeDB.py though, so it's easier to compare the output from the spreadsheet & what's in the database, until we're sure they're completely synced?

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pgleeson commented Dec 12, 2013

Thanks for offering to help with this @Lambdanaut. Can you make a new RegenerateConnectomeDB.py though, so it's easier to compare the output from the spreadsheet & what's in the database, until we're sure they're completely synced?

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kneuron Dec 12, 2013

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@Lambdanaut, thanks so much for offering to help with this. As others have mentioned, it still needs to be done - I assigned it to myself and then disappeared... I'm still around to help, but I don't have a ton of time in the near future to devote to code (maybe over the holiday break). I hope I've made the necessary steps clear in the description above.

I think @pgleeson's suggestion of starting from a fresh copy of the python script is a smart one. (new: RegenerateConnectomeDB.py vs old: RegenerateConnectome.py)

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kneuron commented Dec 12, 2013

@Lambdanaut, thanks so much for offering to help with this. As others have mentioned, it still needs to be done - I assigned it to myself and then disappeared... I'm still around to help, but I don't have a ton of time in the near future to devote to code (maybe over the holiday break). I hope I've made the necessary steps clear in the description above.

I think @pgleeson's suggestion of starting from a fresh copy of the python script is a smart one. (new: RegenerateConnectomeDB.py vs old: RegenerateConnectome.py)

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slarson Jan 3, 2014

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@Lambdanaut any update on this? Can I be of any help?

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slarson commented Jan 3, 2014

@Lambdanaut any update on this? Can I be of any help?

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Lambdanaut Jan 3, 2014

My work schedule has recently changed dramatically and I'm going to have to
pass the torch on this one.

On Fri, Jan 3, 2014 at 1:03 AM, Stephen Larson notifications@github.comwrote:

@Lambdanaut https://github.com/Lambdanaut any update on this? Can I be
of any help?


Reply to this email directly or view it on GitHubhttps://github.com//issues/140#issuecomment-31511681
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Josh Thomas
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Lambdanaut commented Jan 3, 2014

My work schedule has recently changed dramatically and I'm going to have to
pass the torch on this one.

On Fri, Jan 3, 2014 at 1:03 AM, Stephen Larson notifications@github.comwrote:

@Lambdanaut https://github.com/Lambdanaut any update on this? Can I be
of any help?


Reply to this email directly or view it on GitHubhttps://github.com//issues/140#issuecomment-31511681
.

Josh Thomas
Software Developer
910-508-1977

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@Lambdanaut No problem!

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pgleeson commented Jan 3, 2014

@Lambdanaut No problem!

@slarson slarson added this to the Build data to model pipeline milestone Mar 5, 2014

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mwatts15 May 7, 2014

I can't assign myself to this issue, but I'll be working on it this week.

mwatts15 commented May 7, 2014

I can't assign myself to this issue, but I'll be working on it this week.

@tarelli tarelli assigned mwatts15 and unassigned kneuron May 7, 2014

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@mwatts15 just added you to the list of contributors!

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tarelli commented May 7, 2014

@mwatts15 just added you to the list of contributors!

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slarson May 7, 2014

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@mwatts15 terrific! -- This is a good one to hone in on.

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slarson commented May 7, 2014

@mwatts15 terrific! -- This is a good one to hone in on.

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@mwatts15 -- if you're happy with your latest changes on this, can you issue a pull request and we can start a discussion around them? Thanks!

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slarson commented May 29, 2014

@mwatts15 -- if you're happy with your latest changes on this, can you issue a pull request and we can start a discussion around them? Thanks!

@slarson slarson assigned rayner and unassigned mwatts15 and rayner Jun 19, 2014

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zachzundel Jan 3, 2015

Hi-- what's the latest status on this? I can work on this if you need someone.

zachzundel commented Jan 3, 2015

Hi-- what's the latest status on this? I can work on this if you need someone.

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slarson Jan 6, 2015

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@16zzundel5 this did get done in draft form in relation to the PyOpenWorm effort. If you'd like to help out with this, come join us over in the chat room. Thanks!

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slarson commented Jan 6, 2015

@16zzundel5 this did get done in draft form in relation to the PyOpenWorm effort. If you'd like to help out with this, come join us over in the chat room. Thanks!

@slarson slarson closed this Jan 6, 2015

@slarson slarson removed the in progress label Jan 6, 2015

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