parameters_sample.yml

# PYTHON NOTEBOOK PARAMETERS ----
# Register at https://utslogin.nlm.nih.gov/cas/login for MTI credentials
mti:
  email_id : "example@example.com"
  username : "username"
  password : "password"

pmid_threshold : 20
indra_db_rest_url : "SET_INDRA_DB_URL"

reactome_failed_terms_link : "https://gist.githubusercontent.com/PritiShaw/03ce10747835390ec8a755fed9ea813d/raw/cc72cb5479f09b574e03ed22c8d4e3147e09aa0c/Reactome.csv"
failed_query_threshold : null # null Indicates all terms will be processed
failed_query_hits_threshold : 10

reactome_pmid_url : "https://reactome.org/download/current/ReactionPMIDS.txt"

failed_query_output_file_path : "failed_query_analysis_output.tsv"

pmid_chunk_limit : 0
pmid_metadata_output_path : "reactome_pmid_metadata.tsv"

# R NOTEBOOK (Rmd) PARAMETERS ----

# Notebook
max_dt_table_display : 100

# Python environment
python_virtualenv : "/srv/venv"

# General
min_failed_search_hits : 10

# Rank Terms
top_n_reactome_journals : 10
min_indra_query_term_count : 0
min_indra_statement_count : 0
min_pmc_citation_count : 0
min_oc_citation_count : 0

# Reactome Parameters
reactome_organism: "Homo sapiens"

# User Query
query: "MATN2"

# Output
all_mesh_by_top_level_pathways_file : "all_mesh_by_top_level_pathways_full.txt"
top_level_pathways_file : "top_level_pathways.txt"
indra_stmt_html_file : "indra_output.html"
indra_stmt_json_file : "indra_output.json"