Merge pull request #36 from monarch-initiative/slurpdraft

Slurp pipeline: Initial design

.gitignore

@@ -7,6 +7,7 @@ semantic.cache/
 *.tmp.obo
 *.tmp.owl
 *.tmp.json
+*.db
 
 .DS_Store
 
@@ -29,7 +30,7 @@ src/ontology/reports/*
 !src/ontology/reports/README.md
 !src/ontology/reports/*excluded_terms_in_mondo_xrefs.tsv
 !src/ontology/reports/*exclusion_reasons.robot.template.tsv
-!src/ontology/reports/*term_exclusions.txt
+!src/ontology/reports/*excluded_terms.txt
 src/ontology/mondo-ingest.owl
 src/ontology/mondo-ingest.obo
 src/ontology/mondo-ingest.json
@@ -59,9 +60,7 @@ src/ontology/imports/*.owl
 src/ontology/imports/*.json
 src/ontology/imports/*_terms_combined.txt
 
-src/ontology/components/*.owl
-src/ontology/components/*.json
-src/ontology/components/*_terms_combined.txt
+src/ontology/components/*
 
 src/patterns/data/**/*.ofn
 src/patterns/data/**/*.txt

requirements.txt

@@ -62,7 +62,8 @@ myst-parser==0.18.0
 networkx==2.8
 numpy==1.22.3
 nxontology==0.4.1
-oaklib==0.1.34
+oaklib==0.1.36
+ontoportal-client==0.0.3
 openpyxl==3.0.10
 packaging==21.3
 pandas==1.4.3
@@ -101,7 +102,7 @@ ruamel.yaml==0.17.21
 ruamel.yaml.clib==0.2.6
 scikit-learn==1.0.2
 scipy==1.8.0
-semsql==0.2.0
+semsql==0.1.7
 ShExJSG==0.8.2
 six==1.16.0
 snowballstemmer==2.2.0