Notebook experimenting with boomer runs

.gitignore

@@ -3,4 +3,16 @@
 boomer_input/symbiont-merged-all.owl
 omim-ordo/tmp/*
 omim-ordo/boomer_input/symbiont-merged-all.owl
-omim-ordo-do/boomer_input/symbiont-merged-all.owl
+omim-ordo-do/boomer_input/*.owl
+notebooks/output/*.json
+omim-ordo-do/boomer_output/*/*.json
+omim-ordo-do/boomer_output/*/*.dot
+omim-ordo-do/boomer_output/mondo_omim_ordo_do/comparison/diff.sssom.tsv
+omim-ordo-do/boomer_input/symbiont-merged-all.db
+omim-ordo-do/.template.db
+omim-ordo-do/boomer_input/mondo.db
+omim-ordo-do/boomer_input/mondo-relation-graph.tsv.gz
+omim-ordo-do/boomer_output/mondo_omim_ordo_do/comparison/report.html
+omim-ordo-do/boomer_input/merged.db
+omim-ordo-do/boomer_input/mondo_with_merged_labels-relation-graph.tsv.gz
+omim-ordo-do/boomer_input/mondo_with_merged_labels.db

boomer_input/combined.sssom.tsv

@@ -35,7 +35,7 @@
 #   NCIT: http://purl.obolibrary.org/obo/NCIT_
 #   OBI: http://purl.obolibrary.org/obo/OBI_
 #   OGMS: http://purl.obolibrary.org/obo/OGMS_
-#   OMIM: http://omim.org/entry/
+#   OMIM: https://omim.org/entry/
 #   OMIMPS: https://omim.org/phenotypicSeries/
 #   Orphanet: http://www.orpha.net/ORDO/Orphanet_
 #   PATO: http://purl.obolibrary.org/obo/PATO_

boomer_input/prefix.yaml

@@ -34,7 +34,7 @@ NCI: http://purl.obolibrary.org/obo/NCIT_
 NCIT: http://purl.obolibrary.org/obo/NCIT_
 OBI: http://purl.obolibrary.org/obo/OBI_
 OGMS: http://purl.obolibrary.org/obo/OGMS_
-OMIM: http://omim.org/entry/
+OMIM: https://omim.org/entry/
 OMIMPS: https://omim.org/phenotypicSeries/
 Orphanet: http://www.orpha.net/ORDO/Orphanet_
 PATO: http://purl.obolibrary.org/obo/PATO_

config/boomer-style.json

@@ -0,0 +1,92 @@
+{
+    "styles": ["filled",
+               "rounded"],
+    "fillcolor": "white",
+    "includeIdInLabel": true,
+
+
+
+    "excludeSingletons": "true",
+    "relationProperties": {
+        "rdfs:subClassOf": {
+            "color": "black",
+            "penwidth": 1,
+            "arrowhead": "open",
+            "label": ""
+        },
+        "is_a": {
+            "color": "black",
+            "penwidth": 1,
+            "arrowhead": "open",
+            "label": ""
+        },
+        "owl:equivalentClass": {
+            "color": "red",
+            "penwidth": 1,
+            "arrowhead": "box",
+            "arrowtail": "box",
+            "dir": "both",
+            "label": ""
+        },
+        "http://www.w3.org/2004/02/skos/core#exactMatch": {
+            "style": "dashed",
+            "arrowhead": "open",
+            "arrowtail": "open",
+            "dir": "both",
+            "label": ""
+        },
+        "rdf:type": {
+            "color": "blue",
+            "arrowhead": "open",
+            "label": "type"
+        },
+        "RO:0002220": {
+            "color": "green",
+            "label": "DF"
+        },
+        "BFO:0000050": {
+            "arrowhead": "tee",
+            "color": "blue",
+            "penwidth": 3,            
+            "label": ""
+        },
+        "part_of": {
+            "arrowhead": "tee",
+            "color": "blue",
+            "penwidth": 3,            
+            "label": ""
+        }
+    },
+    "displayAnnotations": [
+        "definition", "definition_xref"
+    ],
+    "prefixProperties": {
+        "%CLIQUE": {
+            "fillcolor": "white"
+        },
+        "http://purl.obolibrary.org/obo/GO_": {
+            "fillcolor": "yellow"
+        },
+        "MONDO": {
+            "fillcolor": "yellow"
+        },
+        "ICD10CM": {
+            "fillcolor": "hotpink"
+        },
+        "ICD10": {
+            "fillcolor": "hotpink"
+        },
+        "NCIT": {
+            "fillcolor": "magenta"
+        },
+        "ORDO": {
+            "fillcolor": "magenta"
+        },
+        "DOID": {
+            "fillcolor": "cyan"
+        }
+    },
+    "cliqueRelations": [
+        "equivalent_to", "same_as"
+    ]
+}

data/empty.sssom.tsv

@@ -4,5 +4,5 @@
 # mapping_date: '2022-03-24'
 # mapping_provider: https://github.com/mapping-commons/mapping-commons.github.io
 # mapping_set_id: http://w3id.org/sssom/commons/general/empty.sssom.tsv
-subject_id	predicate_id	object_id	match_type
-owl:Thing	owl:equivalentClass	owl:Thing	HumanCurated
+subject_id	predicate_id	object_id	match_type	mapping_justification	confidence
+owl:Thing	owl:equivalentClass	owl:Thing	HumanCurated	semapv:HumanCurated	0.5