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Omnipath processor #1158

Merged
merged 100 commits into from
Aug 24, 2020
Merged

Omnipath processor #1158

merged 100 commits into from
Aug 24, 2020

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kkaris
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@kkaris kkaris commented Aug 18, 2020

This PR adds the Omnipath processor that queries the omnipath web api. Currently two datasets are handled, the ptms dataset containing enzyme-substrate interactions and the ligand-receptor interactions dataset.

@kkaris kkaris requested review from johnbachman and bgyori August 18, 2020 20:27
bgyori
bgyori requested changes Aug 19, 2020
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Thanks @kkaris! I added some comments.

doc/modules/sources/index.rst Show resolved Hide resolved
indra/databases/hgnc_client.py Outdated Show resolved Hide resolved
indra/sources/omnipath/__init__.py Show resolved Hide resolved
indra/sources/omnipath/api.py Outdated Show resolved Hide resolved
indra/sources/omnipath/processor.py Outdated Show resolved Hide resolved
indra/sources/omnipath/processor.py Outdated Show resolved Hide resolved
indra/statements/statements.py Outdated Show resolved Hide resolved
indra/tests/test_omnipath.py Outdated Show resolved Hide resolved
models/paper2/stmts_vs_pmids.py Outdated Show resolved Hide resolved
setup.py Show resolved Hide resolved
@kkaris kkaris force-pushed the omnipath_processor branch 2 times, most recently from 09bf58d to a068c37 Compare August 19, 2020 21:43
@kkaris kkaris requested a review from bgyori August 19, 2020 21:50
johnbachman and others added 24 commits August 20, 2020 00:24
@johnbachman @bgyori
Initial commit of Omnipath PTM query
c3eaa06
@johnbachman @bgyori
Add func to hgnc_client to get db_refs from hgnc name
c4bb529
@johnbachman @bgyori
Get mod statements from omnipath
2dc97c7
@johnbachman @bgyori
Add docs to funcs
f1ea514
@johnbachman @bgyori
Build statements for other mod types
91395c3
@johnbachman @bgyori
Move omnipath_client to sources
a21bb52
@kkaris @bgyori
Add function to get receptor-ligand interactions
fdd3897
@kkaris @bgyori
WIP Add prototype generator of rec-lig statements
e2492f2
@kkaris @bgyori
Formatting
3935b28
@kkaris @bgyori
Better docstring
f248842
@kkaris @bgyori
Get agents contained in op complex string
39cf353
@kkaris @bgyori
Handle more cases of up_id_strings
8298e4c
@kkaris @bgyori
Add helper for making text refs
e83667f
@kkaris @bgyori
Use PyPath instead of web client
13c7e56
@kkaris @bgyori
Manually rebase api.py
65a7263
@kkaris @bgyori
Manually rebase omnipath_processor
705046d
@kkaris @bgyori
Re-rename omnipath_client -> processor
59aba06
@kkaris @bgyori
Update init
4a34e24
@kkaris @bgyori
Update with new classes
b2ef37a
@kkaris @bgyori
Clean up imports, global scope variables
d60b554
@kkaris @bgyori
Fix docstring, add function to delete cache
7aae009
@kkaris @bgyori
Improve hidden method description
29077a8
@kkaris @bgyori
Add more annotations
2c328ae
@kkaris @bgyori
Only add cellphonedb info for cellphonedb stmts
80891ae
kkaris and others added 24 commits August 20, 2020 00:24
@kkaris @bgyori
Remove unused imports in omnipath processor
080f47b
@kkaris @bgyori
Remove pypath and dependencies from setup.py
4821636
@kkaris @bgyori
Remove docstring overflow
a6d80a3
@kkaris @bgyori
Rename helper method
5c58d36
@kkaris @bgyori
Log count of bad pmids (len>8)
409c371
@kkaris @bgyori
Add bound condition regulations
5e150ce
@kkaris @bgyori
Add docstring for process_from_web
0ceca9e
@kkaris @bgyori
Add omnipath to docs
85528bb
@kkaris @bgyori
Remove pypath dependencies in travis config
b56702c
@kkaris @bgyori
Add sources/omnipath/index.rst
8c3d2ef
@kkaris @bgyori
Reverse removed newline
b08c3a5
@kkaris @bgyori
Fix grammar
0a58335
@kkaris @bgyori
Write short blurb about module and its usage
4b10355
@kkaris @bgyori
Standardize logger name
5dacf51
@kkaris @bgyori
Directly use name standardization
61f9260
@kkaris @bgyori
Do not initialize the processing from init
59266c7
@kkaris @bgyori
Initialize agent name with up_id as safeguard
6464daa
@kkaris @bgyori
Switch to ontology standardizing in tests
8ece227
@kkaris @bgyori
Add omnipath to list of sources in README
45fa569
@kkaris @bgyori
Add skips for already known sources
8f9713c
@kkaris @bgyori
Remove logger warning
82a13df
@bgyori
Add omnipath to belief json
74acab5
@bgyori
Add omnipath to HTML assembler
943b66d
@bgyori
Remove print
59e3a0a
@bgyori bgyori force-pushed the omnipath_processor branch from b2daeb2 to 59e3a0a Compare August 20, 2020 04:25
@bgyori bgyori merged commit f3f2341 into sorgerlab:master Aug 24, 2020
@kkaris kkaris deleted the omnipath_processor branch August 25, 2020 13:07
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@bgyori bgyori bgyori approved these changes

@johnbachman johnbachman Awaiting requested review from johnbachman

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@kkaris @bgyori @johnbachman