Babel 1.9

[gaurav]

This PR makes some changes for Babel 1.9:

• Update some download versions
  • Updated Biolink Model version from 4.2.2 to 4.2.6-rc2
  • Updated UMLS version from 2024AA to 2024AB
  • Updated RxNorm from 09032024 to 01062025
  • Updated Drugbank version from 5-1-12 to 5-1-13
  • Updated the HGNC download URL from https://ftp.ebi.ac.uk/pub/databases/genenames/new/json/hgnc_complete_set.json to https://storage.googleapis.com/public-download-files/hgnc/json/json/hgnc_complete_set.json.
  • Updated HGNC family URL from ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/csv/genefamily_db_tables/family.csv to https://storage.googleapis.com/public-download-files/hgnc/csv/csv/genefamily_db_tables/family.csv.
• Fixed a bug in choosing the best label shorter than a particular size in src/babel_utils.py:write_compendium()
• Cleaned up src/createcompendia/chemicals.py:parse_smifile() so that includes the ChEMBL ID and calculates the column index by name, with ValueErrors thrown if the column name is missing.
• Filtered out .nfs* files from the file list tests, which appear sometimes on Sterling as a NFS file issues.
• Other minor fixes.

Stats:

Filename	babel-2024oct24	babel-2024jan23	Diff	% Diff
Count of CURIEs in all files	666,832,906	675,768,955	8,936,049	1.34%
Count of cliques in all files	479,151,771	481,727,857	2,576,086	0.54%
AnatomicalEntity	148,924	150,530	1,606	1.08%
BiologicalProcess	25,964	68,099	42,135	162.28%
Cell	12,752	12,908	156	1.22%
CellularComponent	14,201	14,677	476	3.35%
ChemicalEntity	14,547,571	657,747	-13,889,824	-95.48%
ChemicalMixture	523	529	6	1.15%
ComplexMolecularMixture	286	286	0	0.00%
Disease	608,588	628,350	19,762	3.25%
Drug	245,800	358,635	112,835	45.91%
Gene	70,776,817	73,531,407	2,754,590	3.89%
GeneFamily	27,954	27,970	16	0.06%
GrossAnatomicalStructure	15,650	15,639	-11	-0.07%
MacromolecularComplex	1,258	1,258	0	0.00%
MolecularActivity	174,709	202,568	27,859	15.95%
MolecularMixture	17,037,493	21,114,772	4,077,279	23.93%
OrganismTaxon	3,419,177	3,455,953	36,776	1.08%
Pathway	53,248	53,320	72	0.14%
PhenotypicFeature	466,802	481,172	14,370	3.08%
Polypeptide	191	191	0	0.00%
Protein	269,925,820	275,925,416	5,999,596	2.22%
Publication	76,423,391	77,347,207	923,816	1.21%
SmallMolecule	211,949,396	220,812,972	8,863,576	4.18%
umls	956,391	907,349	-49,042	-5.13%