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get ancillary info #43

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4 tasks done
alexvpickering opened this issue May 4, 2019 · 2 comments
Closed
4 tasks done

get ancillary info #43

alexvpickering opened this issue May 4, 2019 · 2 comments

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@alexvpickering
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alexvpickering commented May 4, 2019 •
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Go ahead with:

  • GRAS
  • SIDER links
  • Drugbank links
  • Wikipedia links

Also see #4 for further discussion
@alexvpickering alexvpickering changed the title get GRAS data get ancillary info May 4, 2019
alexvpickering added a commit that referenced this issue May 7, 2019
@alexvpickering
init script to download Pug-Views for #43, #4
c34f95b
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alexvpickering commented May 7, 2019 •
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GRAS, SIDER, and Drugbank all use their own identifiers and I couldn't find a readily available mapping from Pubchem cids (what I currently have).

SIDER does use Pubchem cids in their hyperlinks so I just need to check that a url exists. I can't seem to figure out where I first encountered SIDER (I though it was on the Pubchem record for metformin but it doesn't seem to be there).

The most straightforward way that I found to get these data sources/links is from Pubchem. I've gone ahead and created a script to pull the JSON for the Pubchem records.

alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
simplify get_views for #43
b9ed777
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
init check_gras for #43
c9f6cb4
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
init getting DrugBank URL for #43
28063cb
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
init script to check for existence of SIDER links for #43
810beec
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
parse PUG-Views to get DrugBank links and GRAS notices for #43
2e83344 
Were 1230 unique cids with DrugBank links and 7 with GRAS notices
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
finish checking for SIDER for #43
ebe40e4 
Have 465 unique cids with SIDER link
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
just extract DrugBank ID, not URL. #43
f40b686
@alexvpickering
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alexvpickering commented May 8, 2019 •
edited
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There are only 7 compounds from CMAP02/L1000 identified as GRAS. All of them have a BRH clinical_phase of either 'Launched' or 'Phase 2'. Will append to clinical_phase so that they can be identified.

alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
just extract DrugBank ID, not URL. #43
8f700f7
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
add GRAS, DrugBank, and SIDER to annot for #43
6e18811
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
add DrugBank and SIDER links to explore_search for #43
afaa8b4 
Factored add_linkout out of add_table_html to generalize adding link HTML
alexvpickering added a commit that referenced this issue May 8, 2019
@alexvpickering
add DrugBank and SIDER links to explore_results for #43
9de631b 
Factored add_linkout out of add_table_html to generalize adding link HTML
alexvpickering added a commit that referenced this issue May 9, 2019
@alexvpickering
move DrugBank and SIDER columns closer; rename columns
fc21b47 
For #43
@alexvpickering alexvpickering mentioned this issue May 9, 2019
Closed
alexvpickering added a commit that referenced this issue May 9, 2019
@alexvpickering
test linkouts for #43 and #46
c1f51a1
alexvpickering added a commit that referenced this issue May 9, 2019
@alexvpickering
test linkouts for #43 and #46
c65e385
alexvpickering added a commit that referenced this issue May 22, 2019
@alexvpickering
get wikipedia page names for #43
e4f6ea1
alexvpickering added a commit that referenced this issue May 22, 2019
@alexvpickering
refactor L1000/CMAP02 annotation setup
6eebdc3 
Several changes:

1) BRH and Pug-View annotations are merged on CID, then on pert_iname, then grouped/filled by both.
This fixes issues where the same pert_iname has multiple CIDs and only one has BRH/Pug-View annotations.

2) Created a common setup_annot function to process both CMAP/L1000. This makes things easier to maintain.

3) Incorated Wikipedia into annotation for #43
alexvpickering added a commit that referenced this issue May 22, 2019
@alexvpickering
incorporate wikipedia links into explore_results for #43
b1a01a8
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
init script to download Pug-Views for #43, #4
65d2b5c 
Former-commit-id: c34f95b
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
simplify get_views for #43
2cc9a5f 
Former-commit-id: b9ed777
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
init check_gras for #43
4e09bc8 
Former-commit-id: c9f6cb4
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
init getting DrugBank URL for #43
3b9643f 
Former-commit-id: 28063cb
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
init script to check for existence of SIDER links for #43
695a8c8 
Former-commit-id: 810beec
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
parse PUG-Views to get DrugBank links and GRAS notices for #43
c187f65 
Were 1230 unique cids with DrugBank links and 7 with GRAS notices


Former-commit-id: 2e83344
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
finish checking for SIDER for #43
77461b0 
Have 465 unique cids with SIDER link


Former-commit-id: ebe40e4
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
just extract DrugBank ID, not URL. #43
b324f16 
Former-commit-id: 8f700f7
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
add GRAS, DrugBank, and SIDER to annot for #43
8d538e1 
Former-commit-id: 6e18811
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
add DrugBank and SIDER links to explore_results for #43
148ee33 
Factored add_linkout out of add_table_html to generalize adding link HTML


Former-commit-id: 9de631b
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
move DrugBank and SIDER columns closer; rename columns
15a806d 
For #43


Former-commit-id: fc21b47
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
test linkouts for #43 and #46
0502b80 
Former-commit-id: c65e385
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
get wikipedia page names for #43
545e83e 
Former-commit-id: e4f6ea1
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
refactor L1000/CMAP02 annotation setup
3db3ac8 
Several changes:

1) BRH and Pug-View annotations are merged on CID, then on pert_iname, then grouped/filled by both.
This fixes issues where the same pert_iname has multiple CIDs and only one has BRH/Pug-View annotations.

2) Created a common setup_annot function to process both CMAP/L1000. This makes things easier to maintain.

3) Incorated Wikipedia into annotation for #43


Former-commit-id: 6eebdc3
alexvpickering added a commit that referenced this issue Oct 22, 2019
@alexvpickering
incorporate wikipedia links into explore_results for #43
0ac0218 
Former-commit-id: b1a01a8
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
init script to download Pug-Views for #43, #4
b81f758 
Former-commit-id: c34f95b
Former-commit-id: 65d2b5c
Former-commit-id: 9a85cfc
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
simplify get_views for #43
fe31091 
Former-commit-id: b9ed777
Former-commit-id: 2cc9a5f
Former-commit-id: d640d6e
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
init check_gras for #43
274a78c 
Former-commit-id: c9f6cb4
Former-commit-id: 4e09bc8
Former-commit-id: d61d2e7
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
init getting DrugBank URL for #43
d1c0f14 
Former-commit-id: 28063cb
Former-commit-id: 3b9643f
Former-commit-id: bebda8a
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
init script to check for existence of SIDER links for #43
e020ce8 
Former-commit-id: 810beec
Former-commit-id: 695a8c8
Former-commit-id: 91c179a
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
parse PUG-Views to get DrugBank links and GRAS notices for #43
9b84383 
Were 1230 unique cids with DrugBank links and 7 with GRAS notices


Former-commit-id: 2e83344
Former-commit-id: c187f65
Former-commit-id: b9e0716
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
finish checking for SIDER for #43
620a04d 
Have 465 unique cids with SIDER link


Former-commit-id: ebe40e4
Former-commit-id: 77461b0
Former-commit-id: 5d27364
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
just extract DrugBank ID, not URL. #43
a3f2049 
Former-commit-id: 8f700f7
Former-commit-id: b324f16
Former-commit-id: bd86a72
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
add GRAS, DrugBank, and SIDER to annot for #43
1badf01 
Former-commit-id: 6e18811
Former-commit-id: 8d538e1
Former-commit-id: 41ede63
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
add DrugBank and SIDER links to explore_results for #43
ca260a4 
Factored add_linkout out of add_table_html to generalize adding link HTML


Former-commit-id: 9de631b
Former-commit-id: 148ee33
Former-commit-id: 1f6a10f
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
move DrugBank and SIDER columns closer; rename columns
a9415e5 
For #43


Former-commit-id: fc21b47
Former-commit-id: 15a806d
Former-commit-id: 50c575d
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
test linkouts for #43 and #46
a66d11d 
Former-commit-id: c65e385
Former-commit-id: 0502b80
Former-commit-id: 1700509
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
get wikipedia page names for #43
12ae3ae 
Former-commit-id: e4f6ea1
Former-commit-id: 545e83e
Former-commit-id: f1b6d41
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
refactor L1000/CMAP02 annotation setup
7ff23a1 
Several changes:

1) BRH and Pug-View annotations are merged on CID, then on pert_iname, then grouped/filled by both.
This fixes issues where the same pert_iname has multiple CIDs and only one has BRH/Pug-View annotations.

2) Created a common setup_annot function to process both CMAP/L1000. This makes things easier to maintain.

3) Incorated Wikipedia into annotation for #43


Former-commit-id: 6eebdc3
Former-commit-id: 3db3ac8
Former-commit-id: 40effdb
alexvpickering added a commit that referenced this issue Jan 12, 2021
@alexvpickering
incorporate wikipedia links into explore_results for #43
dd3a487 
Former-commit-id: b1a01a8
Former-commit-id: 0ac0218
Former-commit-id: 02332c3
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