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##### 1. Build and load KG2:
- [x] Clear the instance using `bash -x clear-instance.sh`
- [x] Clone the RTX repo from Github `git clone https://github.com/RTXteam/RTX-KG2.git`
- [x] Setup the KG2 b…
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Previously:
```python
FTP_HOST = 'ftp.ebi.ac.uk'
CWD_DIR = '/pub/databases/chembl/UniChem/data/oracleDumps'
```
Now:
```python
FTP_HOST = 'ftp.ebi.ac.uk'
CWD_DIR = '/pub/databases/chembl…
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We are currently using (and have been using for a while) version 30 of ChEMBL. ChEMBL is currently on version 33. Is it time to update which ChEMBL we use? In theory, this should be an easy change. (T…
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This might help with memory issues with KG2. This will not be ready in time for `KG2.8.4` at all.
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**Describe the bug**
I'm aware that parsing InChI is a risky business but RDKit is crashing when parsing some of them.
**To Reproduce**
Steps to reproduce the behavior, feel free to paste a bit o…
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The GSRS links on the compound record cards aren't working (also see Helpdesk tickets).
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This epic collects the different pieces of work that @MarineGirardey will touch during her internship at Open Targets.
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Check and update all relevant upstream sources:
- [x] SemMedDB: 43 (2021) - No change needed
- [x] UMLS: 2020AA to UMLS: 2022AA
- [x] ChEMBL: 27 to ChEMBL: 30
- [x] DrugBank: 5.1 to Drugbank: 5…
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Error with NCBI Gene Conversion
```
Traceback (most recent call last):
File "/home/ubuntu/kg2-code/drugcentral_json_to_kg_json.py", line 277, in
json_data = json.load(input_file)
File "/…
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As far as I can tell, this is because there are now two PubChem entries for water:
- https://pubchem.ncbi.nlm.nih.gov/compound/962 (type biolink:SmallMolecule)
- https://pubchem.ncbi.nlm.nih.gov/com…