DrugMechDB
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SuLab
A database of paths that represent the mechanism of action from a drug to a disease in an indication.
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...
Simple script to confirm that the node identifiers used in each indication record use the correct name. Issue opened here: [link](https://github.com/SuLab/DrugMechDB/issues/480)
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...
Some paths are not displayed in https://sulab.github.io/DrugMechDB/. Here are some examples: - Graphs for Nadolol: DB01203_MESH_D006973_1 DB01203_MESH_D000787_1  - Graphs for Famotidine: DB00927_MESH_D013276_1 DB00927_MESH_D004415_1 -Other graphs: DB00672_MESH_D003924_1 DB00926_MESH_D011565_1 DB00375_MESH_D006937_1 Not...
The deprecated_ids.txt file has this Graph ID added:DB00792_MESH_D065631_2 and this graph is not present in the indication_paths.yaml, but it is displayed on the web page: https://sulab.github.io/DrugMechDB/db00792-mesh-d065631-2.html. I don’t think this...
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/)....
Currently, .json and .yaml implementations of DrugMechDB are built from the excel spreadsheet available on Zenodo. However, to more easily incorporate new drug mechanisms, the YAML file will be used...
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...
added utility to normalize all curies in the nodes and links of an indication_paths.json document using translator nodenorm, updated indication_paths.json file included in PR Total unique normalized IDs: 4857 Total...
