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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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Format CSV output from BAMS queries for Bulk Uploader #9

Open rsoscia opened 10 years ago

rsoscia commented 10 years ago
rsoscia commented 10 years ago
  1. There was an error I overlooked when I switched over to the additional BAMS content from the (fixed) BAMS Thesaurus content. This link shows the BAMS Persist, Query, CSV Output all in one -- I only run sections of it at a time: https://github.com/rsoscia/BAMS-to-NeuroLex/blob/master/src/All_Encompassing.py . Essentially, the query results from the (fixed) BAMS Thesaurus are not identical to the query results from the additional BAMS content--which I previously noted.
  2. I noticed that the additional BAMS content is formatted in a very different manner than the (fixed) BAMS Thesaurus content. This link will show you the results of the second to last query from the All_Encompassing.py file: https://github.com/rsoscia/BAMS-to-NeuroLex/blob/master/src/tempVTest.csv .
  3. @slarson I'm working on formatting the CSV output, but i'm also wondering if my queries are retrieving all that they must retrieve. The tempVTest.csv file is a good representation of how the data is formatted for each "name", or rather "term"(as is declared in the (fixed) BAMS Thesaurus RDF), but I don't believe this is all of the Basal Ganglia information in the additional BAMS content RDF. Any thoughts?
slarson commented 10 years ago

@rsoscia have you made progress on this? If not, let's schedule a time to chat

rsoscia commented 10 years ago

@slarson I've made some progress, and am able to get a CSV formatted result from the BAMS Thesaurus data and the additional BAMS content. I was told to stick with the BAMS Thesaurus data for now. I'm getting a little bit hung-up on formatting the CSV file in a way that is consistent with the bulk uploader's requirements. This is primarily in regard to getting rid of the URI's attached to the the various triples. I think i'm on the right track to developing a solution, but i have been a little short on time with midterms and have been putting the bulk of my time and effort into the NeuroLex application, which i'm trying to finish by the end of this week. Furthermore, I think setting up a time to meet would be very beneficial for the completion of this task. Please just let me know when you're available.

slarson commented 10 years ago

Hi Ryan -- this week is coming into focus finally. Can you just set up a time for Wednesday - Friday here: http://meetme.so/stephenlarson