semmed_biolink_environment.py

import os
from dotenv import load_dotenv, find_dotenv
load_dotenv(find_dotenv(), verbose=True)

# DATA points to the location of all (meta-)data files used in the data processing pipeline
DATA = os.getenv("DATA")

# See project README for more details about UMLS metadata file download and preparation
UMLS_VERSION = os.getenv("UMLS_VERSION")

# just taking the 'active' vocabularies; TODO: should the UMLS_PATH be further parameterized?
UMLS_PATH = DATA + UMLS_VERSION + "_Active/"
MRSAT_ARCHIVE = UMLS_PATH + "MRSAT.RRF.gz"
MRCONSO_ENG_ARCHIVE = UMLS_PATH + "MRCONSO_ENG.RRF.gz"
MRSTY_ARCHIVE = UMLS_PATH + "MRSTY.RRF.gz"

# The MetaMap semantic encodings
METAMAP_VERSION = os.getenv("METAMAP_VERSION")

SEMGROUPS = "https://metamap.nlm.nih.gov/Docs/SemGroups_"+METAMAP_VERSION+".txt"
SEMTYPES = "https://metamap.nlm.nih.gov/Docs/SemanticTypes_"+METAMAP_VERSION+"AA.txt"

# Original source data of Semantic Medline Database
# Generated by the script 'semmed_sql_to_csv.sh' script from SemMedDb SQL dumps
SEMEDDB_VERSION = os.getenv("SEMEDDB_VERSION")
SEMEDDB_PUBMED_RELEASE = os.getenv("SEMEDDB_PUBMED_RELEASE")

SEMMEDB_FILE_PREFIX = "semmedVER"+SEMEDDB_VERSION

# Name file format as of Release 4.0(?)
SEMMEDDB_PREDICATION_FILE = SEMMEDB_FILE_PREFIX+"_"+SEMEDDB_PUBMED_RELEASE+"_R_PREDICATION"
SEMMEDDB_PREDICATION_CSV = DATA+SEMMEDDB_PREDICATION_FILE+".csv"

# Pipeline of data files, don't really need to change between updates
EDGES1_TSV = DATA + "edges1.tsv"
EDGES2_TSV = DATA + "edges2.tsv"
EDGES3_TSV = DATA + "edges3.tsv"
EDGES4_TSV = DATA + "edges4.tsv"

NODES1_TSV = DATA + "nodes1.tsv"
NODES_BLM_TSV = DATA + "nodes_blm.tsv"

EDGES_FILTERED_TSV = DATA + "edges_filtered.tsv"
NODES_FILTERED_TSV = DATA + "nodes_filtered.tsv"

EDGES_BIOLINK_TSV = DATA + "edges_biolink.tsv"
NODES_BIOLINK_TSV = DATA + "nodes_biolink.tsv"

UNII_VERSION = os.getenv("UNII_VERSION")
UNII_RECORDS = DATA+"UNII_Records_"+UNII_VERSION+".txt"

XREFS_SHELVE = DATA+"xrefs.shelve"
UBERON_CSV = DATA+"uberon.csv"
DOID_CSV = DATA+"doid.csv"

MESH_XREFS_TSV = DATA+"mesh_xrefs.tsv"

NODES_XREF_TSV = DATA + "nodes_xref.tsv"

NODES_KGX_TSV = DATA+"nodes_kgx.tsv"
EDGES_KGX_TSV = DATA+"edges_kgx.tsv"