Andrew Su

Annotate ChEMBL service for drug indications

1

Example query: https://www.ebi.ac.uk/chembl/api/data/drug_indication.json?molecule_chembl_id=CHEMBL25 ChEMBL API docs: https://www.ebi.ac.uk/chembl/api/data/docs Example output: ``` { "drug_indications": [ { "drugind_id": 22713, "efo_id": "EFO:0000275", "efo_term": "atrial fibrillation", "indication_refs": [ { "ref_id": "NCT00244426,NCT00496769,NCT00623779,NCT01830543,NCT02164864,NCT02387229,NCT02960126", "ref_type": "ClinicalTrials", "ref_url": "https://clinicaltrials.gov/search?id=%22NCT00244426%22OR%22NCT00496769%22OR%22NCT00623779%22OR%22NCT01830543%22OR%22NCT02164864%22OR%22NCT02387229%22OR%22NCT02960126%22"...

The clue.io API is documented here: https://clue.io/api * https://api.clue.io/api/perts?filter={%22where%22:{%22pert_iname%22:%22erlotinib%22}}&user_key=bf92d3cb1afa1d3d2135cb2848ef7a51 links compounds to cell lines, MOAs, and targets * https://api.clue.io/api/rep_drug_indications?filter={%22where%22:{%22pert_iname%22:%22afatinib%22}}&user_key=bf92d3cb1afa1d3d2135cb2848ef7a51 links compounds to indications * https://api.clue.io/api/rep_drug_targets/?filter={%22where%22:{%22pert_iname%22:%22erlotinib%22}}&user_key=bf92d3cb1afa1d3d2135cb2848ef7a51 links compounds to targets (with...

optimize deployment protocol

1

The original deployment protocol to https://sulab.github.io/DrugMechDB/ was based entirely on github actions. But then the data got so big that we overran the time limits for github actions in the...

We currently do not have any validation system in place to confirm that the node IDs used in each record use the correct names and labels. While our curators are...

automatically create HTML version

3

I think a human readable version of DrugMechDB could help new users. For example, consider the repo for `biolink-model`. Somehow [this YAML file](https://github.com/biolink/biolink-model/blob/master/biolink-model.yaml) gets automagically converted to [this documentation page](https://biolink.github.io/biolink-model/docs/)....

separate ABL1 gene/protein from BCR/ABL translocation

1

In the `imatinib` - `CML (ph+)` path, BCR/ABL is referenced as the intermediate node in [L20](https://github.com/SuLab/DrugMechDB/blob/b2beb63833dc85326e7075657b8ec37e654157d8/indication_paths.yaml#L20), with the edges `imatinib` `INHIBITS` `BCR/ABL`, and `BCR/ABL` `CAUSES` `CML (ph+)`. I think this...

I just renewed our improvmx subscription for another year, now good until 2025-02-09. But for simplicity's sake, it would be ideal to switch to AWS workmail to consolidate resources. @newgene...

The line charts under Epidemiology -> Cumulative (cases/deaths) shows the exact counts in a mouseover tooltip. Would love to see that in the bar charts under Epidemiology -> Daily new...