dominiquesydow commented 3 years ago

Description

The KLIFS maintainers added a few new features to the KLIFS Swagger API, many many thanks!

Changes available at https://dev.klifs.net/swagger_v2/ --- changes include:

Updated Information.kinase_names:
- Split "name" into "name" (Manning name or UniProt gene name) and "gene_name" (HGNC or MGI gene names)
- Added "accession" (UniProt accession ID)
- Renamed "kinase_class" to "subfamily"
Updated Ligands.bioactivity_list_pdb and Ligands.bioactivity_list_id:
- Added target and compound ChEMBL ID ("target_chembl_id" and "chembl_id")
Updated Information.kinase_information:
- Renamed "kinase_class" to "subfamily"
- Renamed "HGNC" to "gene_name"
- Updated Structures.structure_list and related methods
- Added "ligand_ID", "alloteric_ligand_ID", and "curation_flag"
Some ligand PDB IDs mapped to mulitple ligand KLIFS IDs (6VL to 3015/3065, 7KC to 65/2967) - this was fixed manually in KLIFS

In this PR, I would like to integrate the new definitions in our opencadd package.

Todos

[x] Update KLIFS Swagger URL to development version https://dev.klifs.net/swagger_v2/
[x] Move many globals in schema module that touch KLIFS field names/types to a new fields.Fields class (there was a bit too much redundancy here and the old setup was hard to maintain when new fields come in because we had to touch too many different globals in sync)
- [x] Cavet: Rename existing kinase.hgnc_name>kinase.gene_name
- [x] Cavet: Rename existing kinase.class > kinase.subfamily
- [x] Cavet: Change existing signature Kinases.all_kinase_families(group, species) to Kinases.all_kinase_families(groups, species)
- [x] Cavet: Change existing signature Kinases.all_kinases(group, family, species) to Kinases.all_kinases(groups, families, species) --- KLIFS allows for multiple inputs now
- [x] Update schema for kinases: Add kinase.klifs_name and kinase.uniprot
- [x] Update schema for bioactivities: Add kinase.chembl_id and ligand.chembl_id
- [x] Update schema for structures: Add ligand.klifs_id
[x] Rerun opencadd.databases.klifs tutorial notebook!
[x] Rerun notebook that saves all KLIFS IDs locally (after KLIFS fixed the "Some ligand PDB IDs mapped to mulitple ligand KLIFS IDs" problem)
[x] Escape HTML encoding for all output DataFrames: https://github.com/volkamerlab/opencadd/issues/67
[x] Add test that syncs the KLIFS fields (remote) with the opencadd fields (if new fields available in KLIFS, CI will fail)