QB1.4_Post_Trans_Mod notebook status

NCATS-Tangerine / cq-notebooks

Notebooks for answering competency questions

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QB1.4_Post_Trans_Mod notebook status #23

Open mbrush opened 7 years ago

mbrush commented 7 years ago

Notebook Folder Link:

https://github.com/NCATS-Tangerine/cq-notebooks/blob/master/Orange_QB1_Benchmark_CQs/QB1.4_Post_Trans_Mod/README.md

Implementors:

@stuppie *
. . .

(* = notebook lead)

Status:

[x] Staged (described in a readme)
[x] Notebook started
[x] Notebook finished (at least one)
[x] Outcomes documented (in this ticket)

Primary Knowledge Sources Used:

Uniprot

APIs Used:

Uniprot Proteins endpoint: http://www.ebi.ac.uk/proteins/api/doc/

Notes: See Readme

kevinxin90 commented 6 years ago

Outcomes documented at https://github.com/NCATS-Tangerine/cq-notebooks/blob/master/Orange_QB1_Benchmark_CQs/QB1.4_Post_Trans_Mod/ptm_final_results.csv

kevinxin90 commented 6 years ago

Notebook links: https://github.com/NCATS-Tangerine/cq-notebooks/blob/master/Orange_QB1_Benchmark_CQs/QB1.4_Post_Trans_Mod/Workflow%20for%20CQ1.4%20using%20BioThings%20Explorer.ipynb. Final output: https://github.com/NCATS-Tangerine/cq-notebooks/blob/master/Orange_QB1_Benchmark_CQs/QB1.4_Post_Trans_Mod/final_results/ptm_final_results.csv

kevinxin90 commented 6 years ago

Updated link for the notebook: https://github.com/NCATS-Tangerine/cq-notebooks/blob/master/Orange_QB1_Benchmark_CQs/QB1.4_Post_Trans_Mod/BTExplorer-QB1.4.ipynb

andrewsu commented 6 years ago

Just a note that Cathy Wu is very willing to share the flat files for iPTMnet, which itself is an aggregate of many other resources. I may hack on this at the hackathon -- trying to prioritize human PTMs based on evolutionary conservation.