https://github.com/openms/updatehmdb
Script to update OpenMS' internal HMDB database
https://github.com/openms/updatehmdb
Last synced: 3 months ago
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Script to update OpenMS' internal HMDB database
- Host: GitHub
- URL: https://github.com/openms/updatehmdb
- Owner: OpenMS
- Created: 2021-11-02T13:03:58.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2021-11-02T13:09:36.000Z (over 3 years ago)
- Last Synced: 2024-04-14T16:15:05.416Z (about 1 year ago)
- Language: Python
- Size: 37.1 KB
- Stars: 0
- Watchers: 7
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.MD
Awesome Lists containing this project
README
This script updates the Human Metabolites Database (HMDB) files for OpenMS
It generates a HMDBMappingFile.tsv and a HMDB2StructMapping.tsv that is used by the AccurateMassSearch tool
Steps to do:
============
1. `git clone` this repo
2. Download "**All Metabolites**" files as XML from http://www.hmdb.ca/downloads
3. extract into any folder, e.g, default: /your/path/hmdb_metabolites
4. delete hmdb_metabolites.xml unless it is the only file
5. execute python script:
```
python generateHMDBFilesForOpenMS.py /your/path/hmdb_metabolites/
```
6. double-check
7. create a pull request to the OpenMS/OpenMS repository
Requires:
=========
- python 3.6+
- lxml