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rsoscia / BAMS-to-NeuroLex

Some scripts to adapt the content from brain architecture management system (BAMS) into a form that can be shared on NeuroLex.org
MIT License
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Test CSV output via a Hello World example #7

Closed slarson closed 10 years ago

slarson commented 10 years ago

Use the simple example in the Python docs for the CSV writer to create a hello world that exposes some CSV

slarson commented 10 years ago

How did we do with this this week?

rsoscia commented 10 years ago

@slarson I'll be in within the hour.

rsoscia commented 10 years ago

Notes From The BAMS Meeting (Tuesday Oct. 14th 2013) For Stephen:

  1. The multiple definition problem has already been decided (by and large) according to Maryann. Mihail thought a good, modern definition of Basal Ganglia can be constructed from annotation #1 and #3 from this link ( http://brancusi.usc.edu/connections/view-citation.php?stru=1807&idr=1361 ) because it was a cross-species definition.
  2. I fixed some of the queries so we are able to extract 4 unique definitions for Basal Ganglia, 2 unique definitions of Basal Nuclei, and 1unique definition for Basal Ganglia of Telencephalon. There are 3 separate queries i used to get this information.. I wasn't sure if it was crucial for me to just use one query.
  3. I am currently working on generating the CSV output form the BAMS queries. After this is complete i'm going to look into generating XLS output too.
  4. I met with Zaid yesterday (Wednesday) and we discussed a little bit about the bulk uploader (he says it is being reformatted to accept XLS documents (either in addition to or instead of CSV)). He made it seem like i may need some guidance from you (Stephen) in terms of getting the bulk uploader to work properly.. when the time comes (hopefully i'll be at that step today or tomorrow).
  5. Mihail was pretty certain that the additional BAMS content was not "broken" (aka smothered in anchor tags that block the definitions from being queried) like that BAMS Thesaurus data prior to being fixed. I downloaded the most recent version of the BAMS data (from http://brancusi1.usc.edu/ontology/ ) and ran the same queries on it as we did on the fixed BAMS Thesaurus data -- the results were the exact same, so i think Mihail was right.
  6. As for the smaller RDF ontology you suggested i request, i'm not really sure where we stand on that. Most of the discussion focused on whether the additional BAMS data needed to be reformatted without anchor tags. I think i need clarification as to what i should ask Mihail for exactly, assuming we still need a smaller RDF ontology.