/
parameters_test.yml
50 lines (37 loc) · 1.32 KB
/
parameters_test.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
# 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 : 2
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 : 5
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 : 1
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"