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load and export methods added #40

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@nacharov nacharov commented May 24, 2020

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Aleksei Nacharov and others added 28 commits May 24, 2020 21:25
load and export methods added
32550e9
csv added
f21245e
graph overview and format description
173d259
graph pre-proccessed by Charlie Hoyt
c093cee
pre-processed graph and snipnet for dealing with INDRA added
49030be
csv updated
952029d
pre-processed graph and snipnet for dealing with INDRA added
46dd828
@dnsosa
Merge branch 'master' into immunology_kg
67a3de5
@IlanaL1
added skeleton code
3357437
@kaleidoescape
initial commit; frauenhofer sentence extraction and cord19 article te…
0d50a48 
…xt content object
@IlanaL1
updated steps for snorkel heuristic labelling
e369463
@IlanaL1
processed covid19-annovated.csv to training data
d428db5
@kaleidoescape
feat(frauenhofer,-spacey): add initial spacy nlp pipeline with RE
21d8ce1
@kaleidoescape
feat(spacy): store the char start/end of entities as well
b32a460
@kaleidoescape
feat(requirements): add my environment requirements
30c3a3b
@kaleidoescape
fix(spacy): correctly add start_char/end_char and change start/end to…
169ce33 
… start_token/end_token to avoid ambiguity
@IlanaL1
updated with new pybel
0f7e282
@IlanaL1
updated with new pybel
e7813a6
@kaleidoescape
feat(frauenhofer): add all sentences (not just 0th), convert pmcid to…
a59b140 
… string
@kaleidoescape
Merge remote-tracking branch 'origin/immunology_kg' into kaleidoescap…
d4187c0 
…e_kg
@kaleidoescape
feat(frauenhofer): extract seemingly matching entities
ad9994d
@kaleidoescape
feat(frauenhofer): update matched entities format; add more comments …
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…in code
@kaleidoescape
feat(frauenhofer): calculate entries where source AND target were mat…
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…ched
@IlanaL1
added file
53d6f20
@kaleidoescape
feat(frauenhofer,spacify): add Entity.namespace; convert sent tokens …
d9494a4 
…to str; add doccano integration
@kaleidoescape
fix(spacify): fix dict output key
b410259
@kaleidoescape
feat(spacify): only include scientific entities
f9c5c15
@IlanaL1
addded thesuarus and EDA notebokks
3f42df4
@cthoyt
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cthoyt commented Jun 29, 2020

Is there any chance you can add some of the code in these notebooks as python modules that are imported in the notebooks? This has several benefits:

  1. allows for code quality checks
  2. Allows for code review in this PR
  3. Makes notebooks more reproducible
  4. Removes clutter from notebook so the notebooks can be focused on the scientific story rather than the code that accomplishes it

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6 participants

@nacharov @cthoyt @dnsosa @IlanaL1 @kaleidoescape