Merge pull request #1736 from FlyBase/release_2023-12-07

Release 2023-12-07
FlyBase · Dec 7, 2023 · 2cf2c63 · 2cf2c63
2 parents ed756fc + 693d62d
commit 2cf2c63
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Showing 20 changed files with 8,536 additions and 24,826 deletions.
diff --git a/fbbt.obo b/fbbt.obo
diff --git a/fly_anatomy.obo b/fly_anatomy.obo
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for fbbt
 # Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.4.3
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use fbbt.Makefile instead
 
@@ -43,14 +43,14 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.4
+ODK_VERSION_MAKEFILE =      v1.4.3
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/fbbt_ext.owl $(COMPONENTSDIR)/exact_mappings.owl $(COMPONENTSDIR)/neuron_symbols.owl $(COMPONENTSDIR)/larvalbrain_compartments.owl $(COMPONENTSDIR)/larvalbrain_fascicles.owl $(COMPONENTSDIR)/hemibrain_new_cells.owl $(COMPONENTSDIR)/hemibrain_new_ALLNs.owl $(COMPONENTSDIR)/Feng_neurons.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/fbbt_ext.owl $(COMPONENTSDIR)/exact_mappings.owl $(COMPONENTSDIR)/neuron_symbols.owl $(COMPONENTSDIR)/larvalbrain_compartments.owl $(COMPONENTSDIR)/larvalbrain_fascicles.owl $(COMPONENTSDIR)/hemibrain_new_cells.owl $(COMPONENTSDIR)/hemibrain_new_ALLNs.owl $(COMPONENTSDIR)/Feng_neurons.owl $(COMPONENTSDIR)/flybase_import.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -397,6 +397,7 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 
 
 
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

diff --git a/src/ontology/components/flybase_import.owl b/src/ontology/components/flybase_import.owl
@@ -585,6 +585,7 @@
         <oboInOwl:hasExactSynonym>imaginal morphogenesis protein-late 2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>imp-L2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>impL2</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>impl2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>neural and ectodermal development factor</oboInOwl:hasExactSynonym>
         <rdfs:label>ImpL2</rdfs:label>
     </owl:Class>
@@ -1987,6 +1988,7 @@
         <oboInOwl:hasExactSynonym>Pickpocket</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Pickpocket1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Ppk</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>Ppk1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>dfr</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>dmdNaC1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>dmdNaCl</oboInOwl:hasExactSynonym>
@@ -2155,6 +2157,7 @@
         <oboInOwl:hasExactSynonym>DOR62</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Dor62</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>EG:30B8.7</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR2a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 2a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 62</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Olfactory receptor 2F.1</oboInOwl:hasExactSynonym>
@@ -2455,6 +2458,7 @@
         <oboInOwl:hasExactSynonym>CG5006</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR33B.3</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR71</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR33c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 33c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Olfactory receptor 33B.3</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or33B.3</oboInOwl:hasExactSynonym>
@@ -2475,6 +2479,7 @@
         <oboInOwl:hasExactSynonym>CG16961</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR33B.2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR72</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR33b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 33b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Olfactory receptor 33B.2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or33B.2</oboInOwl:hasExactSynonym>
@@ -2495,6 +2500,7 @@
         <oboInOwl:hasExactSynonym>CG16960</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR33B.1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR73</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR33a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 33a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Olfactory receptor 33B.1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or33B.1</oboInOwl:hasExactSynonym>
@@ -2533,6 +2539,7 @@
         <oboInOwl:hasExactSynonym>CG11767</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR24D.1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR48</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR24a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 24a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Olfactory receptor 24D.1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or24D.1</oboInOwl:hasExactSynonym>
@@ -2553,6 +2560,7 @@
         <oboInOwl:hasExactSynonym>DOR64</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR64, AN5</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Dor64</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR23a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 23a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 64</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Olfactory receptor 23A.1</oboInOwl:hasExactSynonym>
@@ -2574,6 +2582,7 @@
         <oboInOwl:hasExactSynonym>CG15377</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR16</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR22C.1</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR22c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 22c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Olfactory receptor 22C.1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or22C.1</oboInOwl:hasExactSynonym>
@@ -3329,6 +3338,7 @@
         <oboInOwl:hasExactSynonym>PO45</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>PPO</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Phenoloxidase A3</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>Ppo2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>ProPO45</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Prophenoloxidase 2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>phenoloxidase subunit A3</oboInOwl:hasExactSynonym>
@@ -3350,6 +3360,7 @@
         <oboInOwl:hasExactSynonym>45a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG1978</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR58</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR45a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 45a</oboInOwl:hasExactSynonym>
         <rdfs:label>Or45a</rdfs:label>
     </owl:Class>
@@ -3364,6 +3375,7 @@
         <oboInOwl:hasExactSynonym>45b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG12931</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR107</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR45b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 45b</oboInOwl:hasExactSynonym>
         <rdfs:label>Or45b</rdfs:label>
     </owl:Class>
@@ -3478,6 +3490,7 @@
         <oboInOwl:hasExactSynonym>59c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG17226</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR120</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR59c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 59c</oboInOwl:hasExactSynonym>
         <rdfs:label>Or59c</rdfs:label>
     </owl:Class>
@@ -3724,6 +3737,7 @@
         <oboInOwl:hasExactSynonym>DmOR67a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DmOr67a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DmelOr67a.P</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR67a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 67a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>odorant receptor 67a</oboInOwl:hasExactSynonym>
         <rdfs:label>Or67a</rdfs:label>
@@ -4027,6 +4041,7 @@
         <oboInOwl:hasExactSynonym>83a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG10612</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR44</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR83a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 83a</oboInOwl:hasExactSynonym>
         <rdfs:label>Or83a</rdfs:label>
     </owl:Class>
@@ -4041,6 +4056,8 @@
         <oboInOwl:hasExactSynonym>83c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG15581</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR116</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR83C</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR83c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 83c</oboInOwl:hasExactSynonym>
         <rdfs:label>Or83c</rdfs:label>
     </owl:Class>
@@ -4123,6 +4140,7 @@
         <oboInOwl:hasExactSynonym>85d</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG11742</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR114</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR85d</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 85d</oboInOwl:hasExactSynonym>
         <rdfs:label>Or85d</rdfs:label>
     </owl:Class>
@@ -4220,6 +4238,7 @@
         <oboInOwl:hasExactSynonym>CCM</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CCha2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG14375</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>Ccha2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Dm-CCHa2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Drm-CCHamide-2</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>ccha2</oboInOwl:hasExactSynonym>
@@ -4329,6 +4348,7 @@
         <oboInOwl:hasExactSynonym>CG17916</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR111</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>OR 92a</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR92a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 92a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or92A</oboInOwl:hasExactSynonym>
         <rdfs:label>Or92a</rdfs:label>
@@ -4393,6 +4413,7 @@
         <oboInOwl:hasExactSynonym>94a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG17241</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR108</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR94a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 94a</oboInOwl:hasExactSynonym>
         <rdfs:label>Or94a</rdfs:label>
     </owl:Class>
@@ -4457,6 +4478,7 @@
         <oboInOwl:hasExactSynonym>98b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG1867</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR121</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR98b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 98b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or98bP</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>or98b</oboInOwl:hasExactSynonym>
@@ -4667,6 +4689,7 @@
         <oboInOwl:hasExactSynonym>DOR82</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR83</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DmOr69a</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR69a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 69a</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 69b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or69A</oboInOwl:hasExactSynonym>
@@ -4688,6 +4711,7 @@
         <oboInOwl:hasExactSynonym>CG32403</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR65</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>LU27.3</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR65c</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 65c</oboInOwl:hasExactSynonym>
         <rdfs:label>Or65c</rdfs:label>
     </owl:Class>
@@ -4702,6 +4726,7 @@
         <oboInOwl:hasExactSynonym>CG32402</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DOR63</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>LU27.1</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR65b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 65b</oboInOwl:hasExactSynonym>
         <rdfs:label>Or65b</rdfs:label>
     </owl:Class>
@@ -5052,6 +5077,7 @@
     <owl:Class rdf:about="http://flybase.org/reports/FBgn0062565">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
         <oboInOwl:hasExactSynonym>CG32825</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>OR19b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor 19b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Odorant receptor-19b</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Or-19b</oboInOwl:hasExactSynonym>
@@ -5529,6 +5555,7 @@
         <oboInOwl:hasExactSynonym>CG42639</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG5779</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Diphenol oxidase A1 subunit</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>DmPPO1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DmePPOA1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Dox-A1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>DoxA1</oboInOwl:hasExactSynonym>
@@ -5543,6 +5570,7 @@
         <oboInOwl:hasExactSynonym>PPO-A1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>PROPO-A1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Phox</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>Ppo1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Pro-phenol oxidase A1</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>ProPO</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>ProPO A1</oboInOwl:hasExactSynonym>
@@ -5718,6 +5746,7 @@
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000704"/>
         <oboInOwl:hasExactSynonym>BcDNA:GH07466</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>CG5518</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>Slamdance</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>sda</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>slamdance</oboInOwl:hasExactSynonym>
         <rdfs:label>CG46339</rdfs:label>