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OORT_logs_2021-09-02_15:48:28.txt
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OORT_logs_2021-09-02_15:48:28.txt
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2021-09-02 15:48:29,218 INFO (OboOntologyReleaseRunner:21) Base directory path /Users/evan/github_repos/SO-Ontologies/Ontology_Files
2021-09-02 15:48:29,224 INFO (OboOntologyReleaseRunner:21) Using staging folder for release manager: /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging
2021-09-02 15:48:29,226 INFO (OboOntologyReleaseRunner:21) Using the following ontologies: [so-edit.obo]
2021-09-02 15:48:29,484 INFO (ParserWrapper:75) Start loading ontology: file:/Users/evan/github_repos/SO-Ontologies/so-edit.obo from: file:/Users/evan/github_repos/SO-Ontologies/so-edit.obo
2021-09-02 15:48:30,073 WARN (OBOFormatParser:1469) LINE: 21818 accepting bad xref with spaces:PMID: 19407924 LINE:
def: "The non-coding region of the mitochondrial genome that controls RNA and DNA synthesis." [PMID: 19407924, PMID:10968878]
2021-09-02 15:48:30,077 WARN (OBOFormatParser:1469) LINE: 22310 accepting bad xref with spaces:PMID: 118436 LINE:
def: "A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera." [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488]
2021-09-02 15:48:30,078 WARN (OBOFormatParser:1469) LINE: 22310 accepting bad xref with spaces:PMID: 29474379 LINE:
def: "A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera." [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488]
2021-09-02 15:48:30,078 WARN (OBOFormatParser:1469) LINE: 22310 accepting bad xref with spaces:PMID: 3136294 LINE:
def: "A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera." [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488]
2021-09-02 15:48:30,078 WARN (OBOFormatParser:1469) LINE: 22321 accepting bad xref with spaces:PMID: 118436 LINE:
def: "Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules." [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488]
2021-09-02 15:48:30,078 WARN (OBOFormatParser:1469) LINE: 22321 accepting bad xref with spaces:PMID: 29474379 LINE:
def: "Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules." [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488]
2021-09-02 15:48:30,078 WARN (OBOFormatParser:1469) LINE: 22321 accepting bad xref with spaces:PMID: 3136294 LINE:
def: "Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules." [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488]
2021-09-02 15:48:30,079 WARN (OBOFormatParser:1469) LINE: 22400 accepting bad xref with spaces:PMID: 24572720 LINE:
def: "Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes." [PMID: 24572720, PMID:3044395]
2021-09-02 15:48:30,080 WARN (OBOFormatParser:1469) LINE: 22412 accepting bad xref with spaces:PMID: 24572720 LINE:
def: "Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes." [PMID: 24572720, PMID:3044395]
2021-09-02 15:48:30,080 WARN (OBOFormatParser:1469) LINE: 22424 accepting bad xref with spaces:PMID: 24572720 LINE:
def: "Plastid rRNA is an RNA component of the small or large subunits of plastid (such as chloroplast) ribosomes." [PMID: 24572720, PMID:3044395]
2021-09-02 15:48:30,080 WARN (OBOFormatParser:1469) LINE: 22434 accepting bad xref with spaces:PMID: 24572720 LINE:
def: "Plastid SSU rRNA is an RNA component of the small subunit of plastid (such as chloroplast) ribosomes." [PMID: 24572720, PMID:3044395]
2021-09-02 15:48:30,080 WARN (OBOFormatParser:1469) LINE: 22445 accepting bad xref with spaces:PMID: 24572720 LINE:
def: "Plastid LSU rRNA is an RNA component of the large subunit of plastid (such as chloroplast) ribosomes." [PMID: 24572720, PMID:3044395]
2021-09-02 15:48:30,515 INFO (ParserWrapper:82) Finished loading ontology: http://purl.obolibrary.org/obo/so.owl from: file:/Users/evan/github_repos/SO-Ontologies/so-edit.obo
2021-09-02 15:48:30,523 INFO (OboOntologyReleaseRunner:21) The following prefixes will be used to determine which classes belong in source:[so]
2021-09-02 15:48:30,831 INFO (OboOntologyReleaseRunner:47) OntologyChecks for so:
Name Status Message
Self Reference In Definition Success
Name Redundancy Check Warning
Primary label 'NMD_transcript' <http://purl.obolibrary.org/obo/SO_0002114> re-used as EXACT synonym for IRIs: <http://purl.obolibrary.org/obo/SO_0001621> 'NMD_transcript_variant'
Obsolete Class in Signature Check Success
Dangling Reference Check Success
Summary (Total, Success, Warning, Error): (4, 3, 1, 0)
2021-09-02 15:48:30,834 INFO (OboOntologyReleaseRunner:21) Creating main ontology
2021-09-02 15:48:30,834 INFO (OboOntologyReleaseRunner:21) Using reasoner to add/retract links in main ontology
2021-09-02 15:48:30,835 INFO (OboOntologyReleaseRunner:21) Checking consistency
2021-09-02 15:48:30,835 INFO (OboOntologyReleaseRunner:21) Creating reasoner using: ReasonerFactory
2021-09-02 15:48:30,994 INFO (OboOntologyReleaseRunner:21) Created reasoner: Reasoner
2021-09-02 15:48:30,994 INFO (OboOntologyReleaseRunner:21) Consistency check started............
2021-09-02 15:48:30,995 INFO (OboOntologyReleaseRunner:21) Is the ontology consistent .....................true, 0
2021-09-02 15:48:31,210 INFO (OboOntologyReleaseRunner:21) unsat: http://www.w3.org/2002/07/owl#Nothing
2021-09-02 15:48:31,210 INFO (OboOntologyReleaseRunner:21) Checking consistency completed
2021-09-02 15:48:31,211 INFO (OboOntologyReleaseRunner:21) Creating inferences
2021-09-02 15:48:31,211 INFO (OboOntologyReleaseRunner:21) Finding asserted equivalencies...
2021-09-02 15:48:31,213 INFO (OboOntologyReleaseRunner:21) Finding inferred superclasses...
2021-09-02 15:48:31,257 INFO (OboOntologyReleaseRunner:21) Checking for redundant assertions caused by inferences
2021-09-02 15:48:31,334 INFO (OboOntologyReleaseRunner:21) Done building inferences
2021-09-02 15:48:31,334 INFO (OboOntologyReleaseRunner:21) Inferences creation completed
2021-09-02 15:48:31,334 INFO (OboOntologyReleaseRunner:21) Finding redundant axioms
2021-09-02 15:48:31,334 INFO (OboOntologyReleaseRunner:21) Redundant axioms removed
2021-09-02 15:48:31,334 INFO (OboOntologyReleaseRunner:21) Check for potential redundant subClass axioms
2021-09-02 15:48:31,341 INFO (OboOntologyReleaseRunner:47)
2021-09-02 15:48:31,344 INFO (OboOntologyReleaseRunner:21) Saving: so
2021-09-02 15:48:31,345 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so.owl
2021-09-02 15:48:32,213 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so.owx
2021-09-02 15:48:32,776 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0000019)' generated in frame: SO:0000313
2021-09-02 15:48:32,779 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00033)' generated in frame: SO:0000409
2021-09-02 15:48:32,779 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00012)' generated in frame: SO:0000417
2021-09-02 15:48:32,780 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00134)' generated in frame: SO:0000417
2021-09-02 15:48:32,780 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00159)' generated in frame: SO:0000418
2021-09-02 15:48:32,780 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00149)' generated in frame: SO:0000419
2021-09-02 15:48:32,785 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00067)' generated in frame: SO:0000691
2021-09-02 15:48:32,786 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00055)' generated in frame: SO:0000725
2021-09-02 15:48:32,788 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00124)' generated in frame: SO:0000839
2021-09-02 15:48:32,788 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00331)' generated in frame: SO:0000839
2021-09-02 15:48:32,788 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00203)' generated in frame: SO:0000912
2021-09-02 15:48:32,789 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0000974)' generated in frame: SO:0000980
2021-09-02 15:48:32,790 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00063)' generated in frame: SO:0001061
2021-09-02 15:48:32,790 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00077)' generated in frame: SO:0001062
2021-09-02 15:48:32,790 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00129)' generated in frame: SO:0001063
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00076)' generated in frame: SO:0001064
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00068)' generated in frame: SO:0001066
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00032)' generated in frame: SO:0001067
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00070)' generated in frame: SO:0001068
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00337)' generated in frame: SO:0001070
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00128)' generated in frame: SO:0001071
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00154)' generated in frame: SO:0001072
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00145)' generated in frame: SO:0001073
2021-09-02 15:48:32,791 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00144)' generated in frame: SO:0001074
2021-09-02 15:48:32,792 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00156)' generated in frame: SO:0001075
2021-09-02 15:48:32,792 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00155)' generated in frame: SO:0001076
2021-09-02 15:48:32,792 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00158)' generated in frame: SO:0001077
2021-09-02 15:48:32,792 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00003)' generated in frame: SO:0001078
2021-09-02 15:48:32,792 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:0000338)' generated in frame: SO:0001079
2021-09-02 15:48:32,792 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00041)' generated in frame: SO:0001080
2021-09-02 15:48:32,792 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00147)' generated in frame: SO:0001081
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00125)' generated in frame: SO:0001082
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00182)' generated in frame: SO:0001083
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00072)' generated in frame: SO:0001084
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00069)' generated in frame: SO:0001085
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00181)' generated in frame: SO:0001086
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00178)' generated in frame: SO:0001087
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00028)' generated in frame: SO:0001088
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00052)' generated in frame: SO:0001089
2021-09-02 15:48:32,793 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00246)' generated in frame: SO:0001090
2021-09-02 15:48:32,794 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00029)' generated in frame: SO:0001091
2021-09-02 15:48:32,794 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00027)' generated in frame: SO:0001092
2021-09-02 15:48:32,794 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00131)' generated in frame: SO:0001093
2021-09-02 15:48:32,794 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00186)' generated in frame: SO:0001094
2021-09-02 15:48:32,794 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00136)' generated in frame: SO:0001095
2021-09-02 15:48:32,794 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00146)' generated in frame: SO:0001096
2021-09-02 15:48:32,794 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00137)' generated in frame: SO:0001097
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00187)' generated in frame: SO:0001098
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00140)' generated in frame: SO:0001099
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00141)' generated in frame: SO:0001100
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00142)' generated in frame: SO:0001101
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00143)' generated in frame: SO:0001102
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00185)' generated in frame: SO:0001103
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00026)' generated in frame: SO:0001104
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00157)' generated in frame: SO:0001105
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00202)' generated in frame: SO:0001106
2021-09-02 15:48:32,795 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00208)' generated in frame: SO:0001107
2021-09-02 15:48:32,796 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00209)' generated in frame: SO:0001108
2021-09-02 15:48:32,796 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00210)' generated in frame: SO:0001109
2021-09-02 15:48:32,796 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00211)' generated in frame: SO:0001110
2021-09-02 15:48:32,796 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00042)' generated in frame: SO:0001111
2021-09-02 15:48:32,796 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:0000341)' generated in frame: SO:0001112
2021-09-02 15:48:32,796 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00151)' generated in frame: SO:0001113
2021-09-02 15:48:32,796 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00152)' generated in frame: SO:0001114
2021-09-02 15:48:32,796 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00222)' generated in frame: SO:0001115
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:0000339)' generated in frame: SO:0001116
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00040)' generated in frame: SO:0001117
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00153)' generated in frame: SO:0001118
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:0000340)' generated in frame: SO:0001119
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00223)' generated in frame: SO:0001120
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00224)' generated in frame: SO:0001121
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00225)' generated in frame: SO:0001122
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00226)' generated in frame: SO:0001123
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00228)' generated in frame: SO:0001124
2021-09-02 15:48:32,797 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00227)' generated in frame: SO:0001125
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00229)' generated in frame: SO:0001126
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00230)' generated in frame: SO:0001127
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00148)' generated in frame: SO:0001128
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00206)' generated in frame: SO:0001129
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00204)' generated in frame: SO:0001130
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00205)' generated in frame: SO:0001131
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00207)' generated in frame: SO:0001132
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00212)' generated in frame: SO:0001133
2021-09-02 15:48:32,798 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00215)' generated in frame: SO:0001134
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00213)' generated in frame: SO:0001135
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00216)' generated in frame: SO:0001136
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00214)' generated in frame: SO:0001137
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00219)' generated in frame: SO:0001138
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00220)' generated in frame: SO:0001139
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00221)' generated in frame: SO:0001140
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00231)' generated in frame: SO:0001141
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00234)' generated in frame: SO:0001142
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00232)' generated in frame: SO:0001143
2021-09-02 15:48:32,799 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00235)' generated in frame: SO:0001144
2021-09-02 15:48:32,800 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00233)' generated in frame: SO:0001145
2021-09-02 15:48:32,800 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00336)' generated in frame: SO:0001146
2021-09-02 15:48:32,800 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00071)' generated in frame: SO:0001147
2021-09-02 15:48:32,800 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00036)' generated in frame: SO:0001148
2021-09-02 15:48:32,800 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001065)' generated in frame: SO:0001149
2021-09-02 15:48:32,800 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( BS:00073)' generated in frame: SO:0001149
2021-09-02 15:48:32,810 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001588)' generated in frame: SO:0001819
2021-09-02 15:48:32,810 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001651)' generated in frame: SO:0001821
2021-09-02 15:48:32,811 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001652)' generated in frame: SO:0001822
2021-09-02 15:48:32,815 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0002000)' generated in frame: SO:0002024
2021-09-02 15:48:32,817 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001903)' generated in frame: SO:0002131
2021-09-02 15:48:32,878 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so.obo
2021-09-02 15:48:32,943 INFO (OboOntologyReleaseRunner:21) exporting json to so.json
2021-09-02 15:48:32,944 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so.json
2021-09-02 15:48:33,185 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so-metadata.txt
2021-09-02 15:48:33,302 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:33,302 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:33,302 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:33,303 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:33,303 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasAlternativeId; we will use an original iri as the identifier.
2021-09-02 15:48:33,303 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:33,303 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasDbXref; we will use an original iri as the identifier.
2021-09-02 15:48:33,304 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasExactSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:33,304 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:33,304 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasOBONamespace; we will use an original iri as the identifier.
2021-09-02 15:48:33,305 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:33,305 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:33,305 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:33,305 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#inSubset; we will use an original iri as the identifier.
2021-09-02 15:48:33,305 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:33,305 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:33,306 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:33,306 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:33,329 INFO (OboOntologyReleaseRunner:21) writing named subsets
2021-09-02 15:48:33,352 INFO (OboOntologyReleaseRunner:21) subset:SOFA #classes:251
2021-09-02 15:48:33,356 INFO (Mooncat:852) Testing 25249 axioms
2021-09-02 15:48:33,392 INFO (Mooncat:888) Base axioms to be added: 5562
2021-09-02 15:48:33,393 INFO (Mooncat:890) Checking closure for: 251
2021-09-02 15:48:33,596 INFO (Mooncat:934) # of gaps spanned = 314
2021-09-02 15:48:33,622 INFO (Mooncat:943) Removing 2612 dangling axioms from http://purl.obolibrary.org/obo/so/subsets/SOFA.owl
2021-09-02 15:48:33,631 INFO (Mooncat:662) Removing 0 dangling axioms
2021-09-02 15:48:33,631 INFO (Mooncat:664) FINISHED Removing 0 dangling axioms
2021-09-02 15:48:33,632 INFO (OboOntologyReleaseRunner:21) subOnt:Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/so/subsets/SOFA.owl>) VersionIRI(<null>))) [Axioms: 2985 Logical Axioms: 336] First 20 axioms: {AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/SO_0000650> "SO:0000650"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/SO_0000140> "INSDC_qualifier:attenuator"^^xsd:string) AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://www.rna.ucla.edu/index.html"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/SO_0000602> "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA."^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/SO_0000418> <http://purl.obolibrary.org/obo/so#SOFA>) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/SO_0000274> "INSDC_qualifier:snRNA"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/SO_0000276> "SO:0000276"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/SO_0000393> "U4 snRNA"^^xsd:string) AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "SO:ke"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/SO_0000730> "A gap in the sequence of known length. The unknown bases are filled in with N's."^^xsd:string) AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/SO_0000386> "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs."^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/so#started_by> "started_by"^^xsd:string) AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "SO:ke"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/SO_0000233> "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified."^^xsd:string) AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/SO_0000393> "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6."^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/so#part_of> "sequence"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/so#trans_spliced_to> "sequence"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/SO_0001214> "sequence"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/SO_0000717> "reading frame"^^xsd:string) AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/so#genome_of> "genome_of"^^xsd:string) AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/so#starts> "Example: start_codon starts CDS."^^xsd:string) AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/SO_0000777> "Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations."^^xsd:string) AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/SO_0000657> "repeat_region"^^xsd:string) } #axioms:2985
2021-09-02 15:48:33,632 INFO (OboOntologyReleaseRunner:21) Saving: subsets/SOFA
2021-09-02 15:48:33,632 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/SOFA.owl
2021-09-02 15:48:33,689 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/SOFA.owx
2021-09-02 15:48:33,747 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/SOFA.obo
2021-09-02 15:48:33,753 INFO (OboOntologyReleaseRunner:21) exporting json to subsets/SOFA.json
2021-09-02 15:48:33,754 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/SOFA.json
2021-09-02 15:48:33,778 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/SOFA-metadata.txt
2021-09-02 15:48:33,881 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:33,881 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:33,881 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:33,881 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:33,881 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasAlternativeId; we will use an original iri as the identifier.
2021-09-02 15:48:33,881 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:33,882 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasDbXref; we will use an original iri as the identifier.
2021-09-02 15:48:33,882 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasExactSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:33,882 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:33,882 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasOBONamespace; we will use an original iri as the identifier.
2021-09-02 15:48:33,882 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:33,882 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:33,882 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:33,883 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#inSubset; we will use an original iri as the identifier.
2021-09-02 15:48:33,883 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:33,883 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:33,883 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:33,883 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:33,926 INFO (OboOntologyReleaseRunner:21) subset:biosapiens #classes:122
2021-09-02 15:48:33,931 INFO (Mooncat:852) Testing 25249 axioms
2021-09-02 15:48:33,958 INFO (Mooncat:888) Base axioms to be added: 4311
2021-09-02 15:48:33,958 INFO (Mooncat:890) Checking closure for: 122
2021-09-02 15:48:34,045 INFO (Mooncat:934) # of gaps spanned = 130
2021-09-02 15:48:34,069 INFO (Mooncat:943) Removing 2594 dangling axioms from http://purl.obolibrary.org/obo/so/subsets/biosapiens.owl
2021-09-02 15:48:34,074 INFO (Mooncat:662) Removing 0 dangling axioms
2021-09-02 15:48:34,074 INFO (Mooncat:664) FINISHED Removing 0 dangling axioms
2021-09-02 15:48:34,074 INFO (OboOntologyReleaseRunner:21) subOnt:Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/so/subsets/biosapiens.owl>) VersionIRI(<null>))) [Axioms: 1723 Logical Axioms: 150] First 20 axioms: {Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001150>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001116>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001080>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#trans_spliced_from>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001134>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0100004>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#processed_into>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001107>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0100008>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001098>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#non_functional_homolog_of>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001132>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0100014>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#started_by>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001142>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#is_consecutive_sequence_of>)) Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001077>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#position_of>)) Declaration(AnnotationProperty(rdfs:comment)) } #axioms:1723
2021-09-02 15:48:34,075 INFO (OboOntologyReleaseRunner:21) Saving: subsets/biosapiens
2021-09-02 15:48:34,075 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/biosapiens.owl
2021-09-02 15:48:34,108 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/biosapiens.owx
2021-09-02 15:48:34,142 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/biosapiens.obo
2021-09-02 15:48:34,145 INFO (OboOntologyReleaseRunner:21) exporting json to subsets/biosapiens.json
2021-09-02 15:48:34,146 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/biosapiens.json
2021-09-02 15:48:34,163 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/biosapiens-metadata.txt
2021-09-02 15:48:34,260 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:34,260 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:34,260 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:34,260 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:34,260 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasAlternativeId; we will use an original iri as the identifier.
2021-09-02 15:48:34,261 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,261 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasDbXref; we will use an original iri as the identifier.
2021-09-02 15:48:34,261 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasExactSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,261 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,261 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasOBONamespace; we will use an original iri as the identifier.
2021-09-02 15:48:34,262 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,262 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:34,262 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:34,262 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#inSubset; we will use an original iri as the identifier.
2021-09-02 15:48:34,262 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:34,262 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:34,262 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:34,263 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:34,294 INFO (OboOntologyReleaseRunner:21) subset:DBVAR #classes:10
2021-09-02 15:48:34,299 INFO (Mooncat:852) Testing 25249 axioms
2021-09-02 15:48:34,322 INFO (Mooncat:888) Base axioms to be added: 3222
2021-09-02 15:48:34,322 INFO (Mooncat:890) Checking closure for: 10
2021-09-02 15:48:34,323 INFO (Mooncat:934) # of gaps spanned = 3
2021-09-02 15:48:34,340 INFO (Mooncat:943) Removing 2704 dangling axioms from http://purl.obolibrary.org/obo/so/subsets/DBVAR.owl
2021-09-02 15:48:34,342 INFO (Mooncat:662) Removing 0 dangling axioms
2021-09-02 15:48:34,343 INFO (Mooncat:664) FINISHED Removing 0 dangling axioms
2021-09-02 15:48:34,343 INFO (OboOntologyReleaseRunner:21) subOnt:Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/so/subsets/DBVAR.owl>) VersionIRI(<null>))) [Axioms: 519 Logical Axioms: 23] First 20 axioms: {SymmetricObjectProperty(<http://purl.obolibrary.org/obo/so#paralogous_to>) SymmetricObjectProperty(<http://purl.obolibrary.org/obo/so#similar_to>) SymmetricObjectProperty(<http://purl.obolibrary.org/obo/so#orthologous_to>) SymmetricObjectProperty(<http://purl.obolibrary.org/obo/so#homologous_to>) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/so#guides> "guides"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/so#is_consecutive_sequence_of> "kareneilbeck"^^xsd:string) AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/so#disconnected_from> "disconnected_from"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/so#non_functional_homolog_of> "non_functional_homolog_of"^^xsd:string) AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/so#DBVAR> "database of genomic structural variation"^^xsd:string) AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#inSubset> "in_subset"^^xsd:string) AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/so#gained> "gained"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/so#position_of> "sequence"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/SO_0000199> "sequence"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/so#recombined_from> "kareneilbeck"^^xsd:string) AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:20226267"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/so#starts> "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary."^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/so#finished_by> "finished_by"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/so#recombined_to> "kareneilbeck"^^xsd:string) AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/so#complete_evidence_for_feature> "If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222."^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/so#started_by> "2010-10-14T01:43:55Z"^^xsd:string) AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/so#derives_from> "derives_from"^^xsd:string) } #axioms:519
2021-09-02 15:48:34,343 INFO (OboOntologyReleaseRunner:21) Saving: subsets/DBVAR
2021-09-02 15:48:34,344 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/DBVAR.owl
2021-09-02 15:48:34,378 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/DBVAR.owx
2021-09-02 15:48:34,388 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/DBVAR.obo
2021-09-02 15:48:34,390 INFO (OboOntologyReleaseRunner:21) exporting json to subsets/DBVAR.json
2021-09-02 15:48:34,391 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/DBVAR.json
2021-09-02 15:48:34,424 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/DBVAR-metadata.txt
2021-09-02 15:48:34,520 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:34,520 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:34,520 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:34,520 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:34,520 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasAlternativeId; we will use an original iri as the identifier.
2021-09-02 15:48:34,521 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,521 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasDbXref; we will use an original iri as the identifier.
2021-09-02 15:48:34,521 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasExactSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,521 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,521 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasOBONamespace; we will use an original iri as the identifier.
2021-09-02 15:48:34,521 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,522 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:34,522 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:34,522 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#inSubset; we will use an original iri as the identifier.
2021-09-02 15:48:34,522 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:34,522 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:34,522 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:34,522 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:34,554 INFO (OboOntologyReleaseRunner:21) subset:Alliance_of_Genome_Resources #classes:3
2021-09-02 15:48:34,561 INFO (Mooncat:852) Testing 25249 axioms
2021-09-02 15:48:34,582 INFO (Mooncat:888) Base axioms to be added: 3153
2021-09-02 15:48:34,582 INFO (Mooncat:890) Checking closure for: 3
2021-09-02 15:48:34,582 INFO (Mooncat:934) # of gaps spanned = 0
2021-09-02 15:48:34,599 INFO (Mooncat:943) Removing 2710 dangling axioms from http://purl.obolibrary.org/obo/so/subsets/Alliance_of_Genome_Resources.owl
2021-09-02 15:48:34,601 INFO (Mooncat:662) Removing 0 dangling axioms
2021-09-02 15:48:34,601 INFO (Mooncat:664) FINISHED Removing 0 dangling axioms
2021-09-02 15:48:34,601 INFO (OboOntologyReleaseRunner:21) subOnt:Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/so/subsets/Alliance_of_Genome_Resources.owl>) VersionIRI(<null>))) [Axioms: 443 Logical Axioms: 20] First 20 axioms: {TransitiveObjectProperty(<http://purl.obolibrary.org/obo/so#evidence_for_feature>) TransitiveObjectProperty(<http://purl.obolibrary.org/obo/so#contains>) TransitiveObjectProperty(<http://purl.obolibrary.org/obo/so#contained_by>) TransitiveObjectProperty(<http://purl.obolibrary.org/obo/so#member_of>) TransitiveObjectProperty(<http://purl.obolibrary.org/obo/so#complete_evidence_for_feature>) TransitiveObjectProperty(<http://purl.obolibrary.org/obo/so#part_of>) TransitiveObjectProperty(<http://purl.obolibrary.org/obo/so#derives_from>) SymmetricObjectProperty(<http://purl.obolibrary.org/obo/so#homologous_to>) SymmetricObjectProperty(<http://purl.obolibrary.org/obo/so#paralogous_to>) SymmetricObjectProperty(<http://purl.obolibrary.org/obo/so#orthologous_to>) SymmetricObjectProperty(<http://purl.obolibrary.org/obo/so#similar_to>) Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#gained>)) Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001263>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#exemplar_of>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#recombined_from>)) Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>)) Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#auto-generated-by>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#translation_of>)) Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/so#overlaps>)) } #axioms:443
2021-09-02 15:48:34,601 INFO (OboOntologyReleaseRunner:21) Saving: subsets/Alliance_of_Genome_Resources
2021-09-02 15:48:34,602 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/Alliance_of_Genome_Resources.owl
2021-09-02 15:48:34,633 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/Alliance_of_Genome_Resources.owx
2021-09-02 15:48:34,644 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/Alliance_of_Genome_Resources.obo
2021-09-02 15:48:34,645 INFO (OboOntologyReleaseRunner:21) exporting json to subsets/Alliance_of_Genome_Resources.json
2021-09-02 15:48:34,647 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/Alliance_of_Genome_Resources.json
2021-09-02 15:48:34,655 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/subsets/Alliance_of_Genome_Resources-metadata.txt
2021-09-02 15:48:34,744 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:34,744 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:34,744 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:34,744 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:34,744 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasAlternativeId; we will use an original iri as the identifier.
2021-09-02 15:48:34,744 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,745 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasDbXref; we will use an original iri as the identifier.
2021-09-02 15:48:34,745 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasExactSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,745 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,745 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasOBONamespace; we will use an original iri as the identifier.
2021-09-02 15:48:34,745 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:34,745 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:34,745 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:34,746 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#inSubset; we will use an original iri as the identifier.
2021-09-02 15:48:34,746 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:34,746 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:34,746 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:34,746 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:34,768 INFO (OboOntologyReleaseRunner:21) Creating simple ontology
2021-09-02 15:48:34,768 INFO (OboOntologyReleaseRunner:21) Setting core ontology idspace: [so]
2021-09-02 15:48:34,778 INFO (OboOntologyReleaseRunner:21) Estimated core ontology number of classes: 2599
2021-09-02 15:48:34,779 INFO (Mooncat:713) Num of classes to be removed = 97
2021-09-02 15:48:34,792 INFO (Mooncat:662) Removing 97 dangling axioms
2021-09-02 15:48:34,793 INFO (Mooncat:664) FINISHED Removing 97 dangling axioms
2021-09-02 15:48:34,793 INFO (OboOntologyReleaseRunner:21) Removing 220 EquivalentClasses axioms from simple
2021-09-02 15:48:34,803 INFO (Mooncat:662) Removing 0 dangling axioms
2021-09-02 15:48:34,803 INFO (Mooncat:664) FINISHED Removing 0 dangling axioms
2021-09-02 15:48:34,803 INFO (OboOntologyReleaseRunner:21) Removing axiom annotations which are equivalent to trailing qualifiers
2021-09-02 15:48:34,817 INFO (OboOntologyReleaseRunner:21) Saving: so-simple
2021-09-02 15:48:34,818 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so-simple.owl
2021-09-02 15:48:35,309 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so-simple.owx
2021-09-02 15:48:35,647 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0000019)' generated in frame: SO:0000313
2021-09-02 15:48:35,658 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0000974)' generated in frame: SO:0000980
2021-09-02 15:48:35,660 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001065)' generated in frame: SO:0001149
2021-09-02 15:48:35,669 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001588)' generated in frame: SO:0001819
2021-09-02 15:48:35,669 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001651)' generated in frame: SO:0001821
2021-09-02 15:48:35,669 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001652)' generated in frame: SO:0001822
2021-09-02 15:48:35,672 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0002000)' generated in frame: SO:0002024
2021-09-02 15:48:35,673 ERROR (OWLAPIOwl2Obo:1064) Duplicate clause 'alt_id( SO:0001903)' generated in frame: SO:0002131
2021-09-02 15:48:35,714 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so-simple.obo
2021-09-02 15:48:35,774 INFO (OboOntologyReleaseRunner:21) exporting json to so-simple.json
2021-09-02 15:48:35,775 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so-simple.json
2021-09-02 15:48:35,877 INFO (OboOntologyReleaseRunner:21) saving to /Users/evan/github_repos/SO-Ontologies/Ontology_Files/staging/so-simple-metadata.txt
2021-09-02 15:48:35,955 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:35,955 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#created_by; we will use an original iri as the identifier.
2021-09-02 15:48:35,955 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:35,955 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#creation_date; we will use an original iri as the identifier.
2021-09-02 15:48:35,956 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasAlternativeId; we will use an original iri as the identifier.
2021-09-02 15:48:35,956 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:35,956 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasDbXref; we will use an original iri as the identifier.
2021-09-02 15:48:35,956 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasExactSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:35,956 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:35,956 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasOBONamespace; we will use an original iri as the identifier.
2021-09-02 15:48:35,956 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym; we will use an original iri as the identifier.
2021-09-02 15:48:35,957 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:35,957 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#id; we will use an original iri as the identifier.
2021-09-02 15:48:35,957 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.geneontology.org/formats/oboInOwl#inSubset; we will use an original iri as the identifier.
2021-09-02 15:48:35,957 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:35,957 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#comment; we will use an original iri as the identifier.
2021-09-02 15:48:35,957 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:35,957 WARN (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOwl#id as the identifier for http://www.w3.org/2000/01/rdf-schema#label; we will use an original iri as the identifier.
2021-09-02 15:48:35,973 INFO (OboOntologyReleaseRunner:21) Creating simple ontology completed
2021-09-02 15:48:36,060 INFO (OboOntologyReleaseRunner:21) Finished release manager process
2021-09-02 15:48:36,061 INFO (OboOntologyReleaseRunner:21) Done!
2021-09-02 15:48:36,061 INFO (OboOntologyReleaseRunner:21) deleting lock file