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renaud / neuroNER

named entity recognizer for neuronal cells, based on UIMA Ruta rules
GNU Lesser General Public License v3.0
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comparing neurolex to bbp and quantifying complete and partial overlap #27

Closed stripathy closed 9 years ago

stripathy commented 9 years ago
  1. come up with two examples, something like a bipartite graph illustrating correspondence between neurolex and BBP, choose examples well.
  2. statistics: how many terms in bbp exactly match a neurolex term, match but missing a term (like nest), etc.
  3. literature comparison: neocortex nest basket cell : term frequency nest basket cell basket cell nest cell neocortex basket cell ...
stripathy commented 9 years ago

Schematic of correspondence between neurolex and BBP (A and B). C is an example showing that even BBP cell types are insufficient to fully describe some of the things in the literature, illustrating the need for a compositional feature approach.

normalization_schematic_v2

Below is a histogram contrasting the number of missing terms per BBP entity when compared to neurolex neuron types. See this ipython notebook for code: https://www.dropbox.com/s/eyok1abbup4rfbd/neurolex_bbp_ontology_compare.ipynb?dl=0

neurolex_bbp_histo

@renaud Can you do the literature comparison for a few terms?

renaud commented 9 years ago

Excellent, thanks a lot!

Yes, I will do the literature comparison if you don't have time.