CElegans MySQL Database

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InterIntelligence Research

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Aug 11, 2013, 7:35:50 PM8/11/13
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As promised in the Data meeting, the semantic data base is now in a MySQL form:
 
 
Database Name: mysql_31129_celegans
Database Server: my01.winhost.com
Database User: openworm
Database Password: openworm
 
I have not changed on the application to look at this data base yet but will over the next couple of days.
 
Thanks
 
Tim Busbice
                                                                                                                                                               
                                                                                                                                                               
                                                                                                                                                               
                                                   

 

Dan Knudsen

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Aug 12, 2013, 1:51:07 PM8/12/13
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Thanks, Tim!

I look forward to getting my connection set up and taking a look.

-Dan Knudsen

Stephen Larson

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Sep 24, 2013, 8:01:10 PM9/24/13
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Hi all,

   I just created a super simple example of reading this via Python over here:


   I'm thinking it would be pretty straightforward to be able to start querying this via semantic graph queries if some Python code were written to munge this into an RDF graph.  Here's some ideas on how that could be done:


Thanks,
  Stephen


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InterIntelligence Research

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Sep 24, 2013, 8:53:10 PM9/24/13
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Very cool - I know what I'll be doing tomorrow :-)
 
Tim


Stephen Larson

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Sep 29, 2013, 4:03:28 PM9/29/13
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Hi all,

There's some new activity on the issue tracking this over here: 


We have the beginnings of a script that opens the OpenWorm semantic database, generates RDF, and does a graph query (SPARQL) to pull information out a single neuron.  There's an iPython notebook that successively walks through examples posted online.

If folks like this, we may be coming close to finally finding the ideal integrated format for the information we have long held in spreadsheets, then google spreadsheets, and then this database.  The final example script in the notebook above could now rapidly be adapted to be the input to RegenerateConnectome.py (issue 140).

Thoughts are welcome.

Best,
  Stephen


Padraig Gleeson

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Sep 30, 2013, 8:43:32 AM9/30/13
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Hi,

Great work Stephen! This will indeed be very useful for feeding data to and validating the NeuroML model.

Sorry to keep banging on about this though... Almost as important as what the data is that's going in to the model is where it's come from... It's very tempting for us as hackers to get structured data and put it into our models, but if you can't link those numbers back to the original experimental data it will be hard to convince people further down the line that it's a physiologically detailed model. For any query that returns info that there are N connections between cell A and cell B, I should be able to do queries like "Who added this to the database?" "Which lab produced the data?" "Where is a description of the experimental preparation?" "Has data been used/described in a publication?".

As a first step it may require adding a top level entity to the database "Data Source" with a free text field (and URL to ext resource) and maybe a field "Data submitter" (then all relationships can point to one or both), but the longer we take to address these questions, the more difficult it will be to add these features in future.

Padraig

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Jim Hokanson

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Sep 30, 2013, 12:19:10 PM9/30/13
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Agreed!!!

It also seems like it would be worth breaking up data source a bit further to into the other things that Padraig mentioned (instead of just leaving a text description).

Perhaps:
Data Source Type:
- publication
   - identifiers????
- derived calculation or inference
   - other data source type entries that were involved
   - a description of the derivation
   - gist link?
- experimental data
   - source <- ??? not sure how to define this in a "nice" way - public DB, lab, ?
   - published? <- note, the data values might not be explicitly published but the data set itself might be, it would be good to decide which goes 
   - publication source <- reference to above data type if published is true

These could also be an array:

neuron x resting membrane potential:
1) -80 mV - publication 1
               - publication 4
2) -85 mV - publication 2
3) -83 mV - publication 3

This of course gets more complicated if instead you have:

neuron x resting membrane potential at temp 2 (where temp 2 is not "normal")

Anyways, I'm getting a bit carried away but I very much agree with Padraig's sentiments.

Jim

InterIntelligence Research

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Sep 30, 2013, 1:25:31 PM9/30/13
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Can we get a data meeting setup and discuss what and how RDF can help us, how we can use going forward, what if anything we need to do differently than what we are doing now?
 
This is very interesting - I just want to make sure I (we) understand what it is and make some decisions on how we can move forward.
 
Thanks
 
Tim


Mike Vella

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Oct 2, 2013, 10:37:25 AM10/2/13
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Padraig does make a very good point, data is less valuable without easy access to the relevant metadata. However, Tim and Stephen's contributions here are certainly the first steps towards this.


Stephen Larson

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Oct 21, 2013, 1:04:10 PM10/21/13
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Hi Padraig -- yes this is a very good point.  Couple things on this:

  1. Tim started putting provenance information like what you ask into the OpenWorm semantic database already.  There are relationships that have citations already.  We talked a little bit about how to expand this in the last data meeting
  2. The mechanism in RDF to do this looks like it should be using named graphs.  Here's an example of how that works.  I'm working up an example that combines the example I started with this model of provenance.
Best,
  Stephen


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