# Build information. Currently unstructured -- you can use this to write down any notes on what is going on with
# this specific build of Babel.
build:
  branch: babel-1.14

# Versions that need to be updated on every release.
biolink_version: "4.3.3"
umls_version: "2025AB"
rxnorm_version: "10062025"
drugbank_version: "5-1-13"

# Overall inputs and outputs.
input_directory: input_data
download_directory: babel_downloads
intermediate_directory: babel_outputs/intermediate
output_directory: babel_outputs
tmp_directory: babel_downloads/tmp

#
# SHARED
#

# DuckDB settings for use in all DuckDB connections:
duckdb_config: {}

#
# UMLS
#
umls:
  subset: "level-0"
  # Replace with "level-0" to get only the level 0 subset (https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html).
  # subset: "level-0"

#
# PROTEINS
#

# Chris Bizon prepared a list of UMLS/UniProtKB mappings which we download and use.
UMLS_UniProtKB_download_raw_url: "https://raw.githubusercontent.com/cbizon/UMLS_UniProtKB/refs/heads/main/outputs/UMLS_UniProtKB.tsv"

#
# The rest of these configs need to be cleaned up.
#

ncbi_files:
  - gene2ensembl.gz
  - gene_info.gz
  - gene_orthologs.gz
  - gene_refseq_uniprotkb_collab.gz
  - mim2gene_medgen

generate_dirs_for_labels_and_synonyms_prefixes:
  - GO
  - CL
  - NCIT
  - UBERON
  - CHEBI
  - HP
  - MONDO
  - PR

ubergraph_ontologies:
  - UBERON
  - CL
  - GO
  - NCIT
  - ECO
  - ECTO
  - ENVO
  - HP
  - UPHENO
  - BFO
  - BSPO
  - CARO
  - CHEBI
  - CP
  - GOREL
  - IAO
  - MAXO
  - MONDO
  - PATO
  - PR
  - RO
  - UBPROP

mods:
  - WormBase
  - FB
  - MGI
  - ZFIN
  - RGD
  - SGD

common:
  labels:
    - ubergraph/labels
  synonyms:
    - ubergraph/synonyms.jsonl
  descriptions:
    - ubergraph/descriptions.jsonl

anatomy_prefixes:
  - UBERON
  - GO
  - CL
  - UMLS
  - MESH
  - NCIT
  - SNOMEDCT

anatomy_ids:
  - UBERON
  - GO
  - CL
  - UMLS
  - MESH
  - NCIT

anatomy_concords:
  - UBERON
  - GO
  - CL
  - UMLS
  - WIKIDATA

anatomy_outputs:
  - AnatomicalEntity.txt
  - Cell.txt
  - CellularComponent.txt
  - GrossAnatomicalStructure.txt

gene_labels:
  - HGNC
  - NCBIGene
  - UMLS

gene_ids:
  - ENSEMBL
  - HGNC
  - NCBIGene
  - UMLS
  - OMIM
  - ZFIN
  - WormBase
  - FB
  - MGI
  - RGD
  - SGD

gene_concords:
  - NCBIGene
  - NCBIGeneENSEMBL
  - medgen
  - UMLS
  - UMLS_NCBIGene

gene_outputs:
  - Gene.txt

protein_labels:
  - UniProtKB
  - PR
  - UMLS

protein_synonyms:
  - PR
  - UMLS

protein_ids:
  - ENSEMBL
  - UniProtKB
  - PR
  - UMLS

protein_concords:
  - UniProtKB
  - PR
  - NCIT_UniProtKB
  - NCIT_UMLS
  - UMLS
  - UMLS_UniProtKB

protein_outputs:
  - Protein.txt

disease_labelsandsynonyms:
  - MONDO
  - DOID
  - Orphanet
  - HP
  - MESH
  - NCIT
  - UMLS
  - SNOMEDCT
  - EFO

disease_ids:
  - MONDO
  - DOID
  - Orphanet
  - HP
  - MESH
  - NCIT
  - UMLS
  - OMIM
  - EFO

disease_concords:
  - HP
  - MONDO
  - UMLS
  - DOID
  - EFO
  - Manual

disease_outputs:
  - Disease.txt
  - PhenotypicFeature.txt

process_labels:
  - GO
  - REACT
  - RHEA
  - EC
  - SMPDB
  - PANTHER.PATHWAY
  - UMLS

process_ids:
  - GO
  - REACT
  - RHEA
  - EC
  - SMPDB
  - PANTHER.PATHWAY
  - UMLS

process_concords:
  - GO
  - RHEA
  - UMLS

process_outputs:
  - Pathway.txt
  - BiologicalProcess.txt
  - MolecularActivity.txt

unichem_datasources:
  - CHEMBL.COMPOUND
  - DRUGBANK
  - GTOPDB
  - KEGG.COMPOUND
  - CHEBI
  - UNII
  - HMDB
  - PUBCHEM.COMPOUND
  - DrugCentral

chemical_labels:
  - CHEMBL.COMPOUND
  - GTOPDB
  - KEGG.COMPOUND
  - CHEBI
  - UNII
  - HMDB
  - PUBCHEM.COMPOUND
  - DrugCentral
  - UMLS
  - DRUGBANK

chemical_synonyms:
  - GTOPDB
  - CHEBI
  - UNII
  - HMDB
  - PUBCHEM.COMPOUND
  - UMLS
  - DRUGBANK

chemical_concords:
  - wikipedia_mesh_chebi
  - PUBCHEM_MESH
  - mesh_cas
  - mesh_unii
  - PUBCHEM_CAS
  - GTOPDB
  - CHEBI
  - UMLS
  - DrugCentral
  - RXNORM

chemical_ids:
  - CHEMBL.COMPOUND
  - GTOPDB
  - KEGG.COMPOUND
  - CHEBI
  - UNII
  - HMDB
  - PUBCHEM.COMPOUND
  - DrugCentral
  - DRUGBANK
  - MESH
  - UMLS
  - RXNORM

chemical_outputs:
  - MolecularMixture.txt
  - SmallMolecule.txt
  - Polypeptide.txt
  - ComplexMolecularMixture.txt
  - ChemicalEntity.txt
  - ChemicalMixture.txt
  - Drug.txt

drugchemicalconflated_synonym_outputs:
  - DrugChemicalConflated.txt

geneproteinconflated_synonym_outputs:
  - GeneProteinConflated.txt

taxon_labels:
  - NCBITaxon
  - MESH
  - UMLS

taxon_synonyms:
  - NCBITaxon
  - UMLS

taxon_ids:
  - NCBITaxon
  - MESH
  - UMLS

taxon_concords:
  - NCBI_MESH
  - UMLS

taxon_outputs:
  - OrganismTaxon.txt

cell_line_outputs:
  - CellLine.txt

genefamily_labels:
  - PANTHER.FAMILY
  - HGNC.FAMILY

genefamily_ids:
  - PANTHER.FAMILY
  - HGNC.FAMILY

genefamily_outputs:
  - GeneFamily.txt

umls_outputs:
  - umls.txt

macromolecularcomplex_outputs:
  - MacromolecularComplex.txt

ubergraph_iri_stem_to_prefix_map:
  "https://identifiers.org/ncbigene/": NCBIGene
  "http://www.ncbi.nlm.nih.gov/gene/": NCBIGene
  "http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=": HGNC
  "http://www.informatics.jax.org/marker/MGI:": MGI
  "http://www.pombase.org/spombe/result/": PomBase
  "http://www.wormbase.org/species/c_elegans/gene/": WormBase
  "http://flybase.org/reports/": FB
  "http://www.ecogene.org/gene/": ecogene
  "http://zfin.org/action/marker/view/": ZFIN
  "http://birdgenenames.org/cgnc/GeneReport?id=": cgnc
  "http://www.ensemblgenomes.org/id/": ENSEMBL
  "http://www.ensembl.org/id/": ENSEMBL
  "http://purl.obolibrary.org/obo/AISM_": AISM
  "http://purl.obolibrary.org/obo/BCO_": BCO
  "http://purl.obolibrary.org/obo/CDNO_": CDNO
  "http://purl.obolibrary.org/obo/CLAO_": CLAO
  "http://purl.obolibrary.org/obo/GNO_": GNO
  "http://purl.obolibrary.org/obo/HAO_": HAO
  "http://purl.obolibrary.org/obo/LEPAO_": LEPAO
  "http://purl.obolibrary.org/obo/MMO_": MMO
  "http://purl.obolibrary.org/obo/MRO_": MRO
  "http://purl.obolibrary.org/obo/MmusDv_": MmusDv
  "http://purl.obolibrary.org/obo/OARCS_": OARCS
  "http://purl.obolibrary.org/obo/OBA_": OBA
  "http://purl.obolibrary.org/obo/PCL_": PCL
  "http://purl.obolibrary.org/obo/PECO_": PECO
  "http://purl.obolibrary.org/obo/PPO_": PPO
  "http://purl.obolibrary.org/obo/TS_": TS
  "http://purl.obolibrary.org/obo/UO_": UO
  "http://purl.obolibrary.org/obo/PCO_": PCO
  "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=": RGD

publication_outputs:
  - Publication.txt

geneprotein_outputs:
  - GeneProtein.txt

drugchemical_outputs:
  - DrugChemical.txt

preferred_name_boost_prefixes:
  biolink:ChemicalEntity:
    - DRUGBANK
    - DrugCentral
    - CHEBI
    - MESH
    - CHEMBL.COMPOUND
    - GTOPDB
    - HMDB
    - RXCUI
    - PUBCHEM.COMPOUND

ensembl_datasets_to_skip:
  - elucius_gene_ensembl
  - hgfemale_gene_ensembl
  - charengus_gene_ensembl
  - otshawytscha_gene_ensembl
  - aocellaris_gene_ensembl

demote_labels_longer_than: 25

