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carrineblank / MicrO

A Microbial Ontology of Phenotypic and Metabolic Characters, Assays, and Culture Media Found in Prokaryotic Taxonomic Descriptions
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Punning are preventing from importing terms from MicrO #21

Closed citmejia closed 6 years ago

citmejia commented 6 years ago

Hi,

There are a number of Illegal redeclarations of entities in MicrO. This is preventing me from using robot to extract and merge terms from MicrO.

carrineblank commented 6 years ago

Hello citmejia,

Can you give me some suggestions (is there any information as to which classes are leading to the violations in any error messages) as to whahttps://messaging.umt.edu/owa/?ae=Item&t=IPM.Note&id=RgAAAAD4RdV%2fyzI9TYnFZFnQVrOLBwAUvKOMtIvpQKuYPZUAYfp6AAAARngxAAByfrDFM%2bH5RoYtnK6Vgz23AAHPTk6aAAAJ&a=Reply&cb=0&pspid=_1528831151006_321333201#t might be causing the errors to help point me towards fixing the problem?

Thanks,

-Carrine

Carrine E. Blank, PhD Research Assistant Professor 109A Clapp Science Building Department of Geosciences University of Montana 32 Campus Drive Missoula, MT 59812-1296 406-880-3402 (cell); carrine.blank (Skype); carrine.blank@umontana.edu (email) http://hs.umt.edu/geosciences/people/research.php?s=Blank1937

From: citmejia [notifications@github.com] Sent: Tuesday, June 12, 2018 12:19 PM To: carrineblank/MicrO Cc: Subscribed Subject: [carrineblank/MicrO] Punning are preventing from importing terms from MicrO (#21)

Hi,

There are a number of Illegal redeclarations of entities in MicrO. This is preventing me from using robot to extract and merge terms from MicrO.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/carrineblank/MicrO/issues/21, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AK-iaQEIgq4YgtVYCb90kycskx9OjCzTks5t8AYjgaJpZM4Uk62T.

citmejia commented 6 years ago

Hi Carrine,

I copy and paste the errors thrown by the robot. Basically, MicrO is currently using the same IRI either for an annotation property and an object property, or for a data property and an annotation property.

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>)), Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI>)), Declaration(DataProperty(<http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000293 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/OBI_0000293)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000293))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000299 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000299)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OBI_0000299

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000054 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_0000054)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000054))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002526 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002526)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002526

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002303 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002303)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002303))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000055 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_0000055)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000055))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002576 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002576)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002576))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002220 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002220)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002220

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002509 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002509)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002509

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002526 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002526)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002526

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002303 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002303)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002303))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002509 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002509)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002509

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000293 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/OBI_0000293)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000293))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001199 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001199)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_0001199

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000299 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000299)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OBI_0000299

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001218 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001218)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_0001218

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000054 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_0000054)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000054))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>)), Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000055 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_0000055)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000055))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002576 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002576)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002576))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI>)), Declaration(DataProperty(<http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001462 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001462)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_0001462

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001463 in punning not allowed [Declaration(AnnotationProperty(< http://purl.obolibrary.org/obo/MICRO_0001463>)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001463))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001205 in punning not allowed [Declaration(AnnotationProperty(< http://purl.obolibrary.org/obo/MICRO_0001205>)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001205))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002220 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002220)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002220

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>))]

Best,

Citlalli

2018-06-12 14:20 GMT-05:00 Carrine Blank notifications@github.com:

Hello citmejia,

Can you give me some suggestions (is there any information as to which classes are leading to the violations in any error messages) as to wha< https://messaging.umt.edu/owa/?ae=Item&t=IPM.Note&id=RgAAAAD4RdV% 2fyzI9TYnFZFnQVrOLBwAUvKOMtIvpQKuYPZUAYfp6AAAARngxAAByfrDFM% 2bH5RoYtnK6Vgz23AAHPTk6aAAAJ&a=Reply&cb=0&pspid=_1528831151006_321333201#>t might be causing the errors to help point me towards fixing the problem?

Thanks,

-Carrine

Carrine E. Blank, PhD Research Assistant Professor 109A Clapp Science Building Department of Geosciences University of Montana 32 Campus Drive https://maps.google.com/?q=32+Campus+Drive+%0D%0AMissoula,+MT+59812&entry=gmail&source=g Missoula, MT 59812-1296 406-880-3402 (cell); carrine.blank (Skype); carrine.blank@umontana.edu (email) http://hs.umt.edu/geosciences/people/research.php?s=Blank1937

From: citmejia [notifications@github.com] Sent: Tuesday, June 12, 2018 12:19 PM To: carrineblank/MicrO Cc: Subscribed Subject: [carrineblank/MicrO] Punning are preventing from importing terms from MicrO (#21)

Hi,

There are a number of Illegal redeclarations of entities in MicrO. This is preventing me from using robot to extract and merge terms from MicrO.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ carrineblank/MicrO/issues/21, or mute the threadhttps://github.com/ notifications/unsubscribe-auth/AK-iaQEIgq4YgtVYCb90kycskx9OjCzTk s5t8AYjgaJpZM4Uk62T.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/carrineblank/MicrO/issues/21#issuecomment-396703802, or mute the thread https://github.com/notifications/unsubscribe-auth/AfyIG_phWMge-s1dL5hTTeZWAMNucx-Qks5t8BSZgaJpZM4Uk62T .

carrineblank commented 6 years ago

ΟΚ, thanks for the information Citlalli,

I'll try to identify what the problem is in the next day or so.

-Carrine

Carrine E. Blank, PhD Research Assistant Professor 109A Clapp Science Building Department of Geosciences University of Montana 32 Campus Drive Missoula, MT 59812-1296 406-880-3402 (cell); carrine.blank (Skype); carrine.blank@umontana.edu (email) http://hs.umt.edu/geosciences/people/research.php?s=Blank1937

From: citmejia [notifications@github.com] Sent: Tuesday, June 12, 2018 2:28 PM To: carrineblank/MicrO Cc: Carrine Blank; Comment Subject: Re: [carrineblank/MicrO] Punning are preventing from importing terms from MicrO (#21)

Hi Carrine,

I copy and paste the errors thrown by the robot. Basically, MicrO is currently using the same IRI either for an annotation property and an object property, or for a data property and an annotation property.

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>)), Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI>)), Declaration(DataProperty(<http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000293 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/OBI_0000293)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000293))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000299 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000299)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OBI_0000299

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000054 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_0000054)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000054))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002526 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002526)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002526

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002303 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002303)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002303))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000055 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_0000055)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000055))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002576 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002576)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002576))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002220 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002220)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002220

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002509 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002509)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002509

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002526 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002526)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002526

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002303 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002303)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002303))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002509 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002509)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002509

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000293 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/OBI_0000293)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000293))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001199 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001199)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_0001199

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000299 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000299)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OBI_0000299

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001218 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001218)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_0001218

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000054 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_0000054)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000054))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>)), Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000055 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_0000055)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000055))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002576 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/RO_0002576)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002576))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI>)), Declaration(DataProperty(<http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001462 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001462)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_0001462

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001463 in punning not allowed [Declaration(AnnotationProperty(< http://purl.obolibrary.org/obo/MICRO_0001463>)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001463))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001205 in punning not allowed [Declaration(AnnotationProperty(< http://purl.obolibrary.org/obo/MICRO_0001205>)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/MICRO_0001205))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002220 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002220)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002220

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>))]

Best,

Citlalli

2018-06-12 14:20 GMT-05:00 Carrine Blank notifications@github.com:

Hello citmejia,

Can you give me some suggestions (is there any information as to which classes are leading to the violations in any error messages) as to wha< https://messaging.umt.edu/owa/?ae=Item&t=IPM.Note&id=RgAAAAD4RdV% 2fyzI9TYnFZFnQVrOLBwAUvKOMtIvpQKuYPZUAYfp6AAAARngxAAByfrDFM% 2bH5RoYtnK6Vgz23AAHPTk6aAAAJ&a=Reply&cb=0&pspid=_1528831151006_321333201#>t might be causing the errors to help point me towards fixing the problem?

Thanks,

-Carrine

Carrine E. Blank, PhD Research Assistant Professor 109A Clapp Science Building Department of Geosciences University of Montana 32 Campus Drive https://maps.google.com/?q=32+Campus+Drive+%0D%0AMissoula,+MT+59812&entry=gmail&source=g Missoula, MT 59812-1296 406-880-3402 (cell); carrine.blank (Skype); carrine.blank@umontana.edu (email) http://hs.umt.edu/geosciences/people/research.php?s=Blank1937

From: citmejia [notifications@github.com] Sent: Tuesday, June 12, 2018 12:19 PM To: carrineblank/MicrO Cc: Subscribed Subject: [carrineblank/MicrO] Punning are preventing from importing terms from MicrO (#21)

Hi,

There are a number of Illegal redeclarations of entities in MicrO. This is preventing me from using robot to extract and merge terms from MicrO.

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carrineblank commented 6 years ago

Hi Citlalli,

I found 6 duplicate classes (not sure how that happened - they were in the same location of the owl file so some bug must have appeared at some point; five duplicates were MicrO classes and one was an RO class). The duplicate classes were removed and I've uploaded what is now the current version of MicrO (should be version 1.5.1). I can't push to github at present due to the dreaded tlsv1 alert protocol version error, and I've spent two days trying to work around that error. Luckily, I managed to upload the new files onto GitHub manually so you should be good-to-go.

Let me know if you have any additional issues.....

Thanks for alerting me to the errors!

-Carrine

citmejia commented 6 years ago

Hello Carrine,

I forked and cloned your repo, and I managed to fix MicrO. I had to change some imports declarations, since most "illegal reuse of entities" happened in properties imported from RO, OBI, and NDF-RT. What I did was:

1) Conflictual imports from RO and OBI were some object properties that used the same IRI as some annotation properties. I deleted annotation properties to preserve relations between classes using those object properties. As result, all metadata of the object properties (label, definition, etc.) was lost. Thus, I extracted corresponding terms from original ontologies and merged them with MicrO. Almost everything was restored except for metadata of BFO_0000055 and BFO_0000054.

2) Conflictual imports from NDF-RT were some data properties that used the same IRI as some annotation properties. I deleted data properties to preserve metadata of classes that used corresponding annotation properties. However, in NDF-RT, these were actually data properties. So I don't know if there is going to be a problem.

3) There were a few MicrO object properties that were also annotation properties. I deleted annotation properties and fixed by hand the metadata of corresponding object properties.

You can take a look at the result in my forked repo and see if it helps.

I'm going to try your new version too.

Best, Citlalli

2018-06-12 15:38 GMT-05:00 Carrine Blank notifications@github.com:

ΟΚ, thanks for the information Citlalli,

I'll try to identify what the problem is in the next day or so.

-Carrine

Carrine E. Blank, PhD Research Assistant Professor 109A Clapp Science Building Department of Geosciences University of Montana 32 Campus Drive https://maps.google.com/?q=32+Campus+Drive+%0D%0AMissoula,+MT+59812&entry=gmail&source=g Missoula, MT 59812-1296 406-880-3402 (cell); carrine.blank (Skype); carrine.blank@umontana.edu (email) http://hs.umt.edu/geosciences/people/research.php?s=Blank1937

From: citmejia [notifications@github.com] Sent: Tuesday, June 12, 2018 2:28 PM To: carrineblank/MicrO Cc: Carrine Blank; Comment Subject: Re: [carrineblank/MicrO] Punning are preventing from importing terms from MicrO (#21)

Hi Carrine,

I copy and paste the errors thrown by the robot. Basically, MicrO is currently using the same IRI either for an annotation property and an object property, or for a data property and an annotation property.

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>)), Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI>)), Declaration(DataProperty(<http://evs.nci.nih.gov/ftp1/NDF- RT/NDF-RT.owl#NUI

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000293 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/OBI_ 0000293)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000293))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000299 in punning not allowed [Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/OBI_0000299

)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OBI_0000299 ))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000054 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_ 0000054)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000054))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002526 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002526)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002526

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002303 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002303

)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002303))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000055 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_ 0000055)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000055))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002576 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002576

)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002576))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002220 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002220)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002220

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002509 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002509)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002509

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002526 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002526)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002526

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002303 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002303

)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002303))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_DUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002509 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002509)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002509

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000293 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/OBI_ 0000293)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/OBI_0000293))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#RxNorm_CUI>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001199 in punning not allowed [Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/MICRO_0001199

)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_ 0001199 ))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/OBI_0000299 in punning not allowed [Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/OBI_0000299

)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OBI_0000299 ))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Definition>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001218 in punning not allowed [Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/MICRO_0001218

)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_ 0001218 ))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000054 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_ 0000054)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000054))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>)), Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Display_Name>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000055 in punning not allowed [Declaration(AnnotationProperty(http://purl.obolibrary.org/obo/BFO_ 0000055)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/BFO_0000055))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002576 in punning not allowed [Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002576

)), Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002576))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI in punning not allowed [Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#NUI>)), Declaration(DataProperty(<http://evs.nci.nih.gov/ftp1/NDF- RT/NDF-RT.owl#NUI

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#Synonym>))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001462 in punning not allowed [Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/MICRO_0001462

)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/MICRO_ 0001462 ))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001463 in punning not allowed [Declaration(AnnotationProperty(< http://purl.obolibrary.org/obo/MICRO_0001463>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/MICRO_0001463

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/MICRO_0001205 in punning not allowed [Declaration(AnnotationProperty(< http://purl.obolibrary.org/obo/MICRO_0001205>)), Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/MICRO_0001205

))]

ERROR Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002220 in punning not allowed [Declaration(ObjectProperty(http://purl.obolibrary.org/obo/RO_0002220)), Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/RO_0002220

))]

ERROR Illegal redeclarations of entities: reuse of entity http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name in punning not allowed [Declaration(DataProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>)), Declaration(AnnotationProperty(< http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MeSH_Name>))]

Best,

Citlalli

2018-06-12 14:20 GMT-05:00 Carrine Blank notifications@github.com:

Hello citmejia,

Can you give me some suggestions (is there any information as to which classes are leading to the violations in any error messages) as to wha< https://messaging.umt.edu/owa/?ae=Item&t=IPM.Note&id=RgAAAAD4RdV% 2fyzI9TYnFZFnQVrOLBwAUvKOMtIvpQKuYPZUAYfp6AAAARngxAAByfrDFM% 2bH5RoYtnK6Vgz23AAHPTk6aAAAJ&a=Reply&cb=0&pspid=_ 1528831151006_321333201#>t might be causing the errors to help point me towards fixing the problem?

Thanks,

-Carrine

Carrine E. Blank, PhD Research Assistant Professor 109A Clapp Science Building Department of Geosciences University of Montana 32 Campus Drive https://maps.google.com/?q=32+Campus+Drive&entry=gmail&source=g https://maps.google.com/?q=32+Campus+Drive+%0D% 0AMissoula,+MT+59812&entry=gmail&source=g Missoula, MT 59812-1296 406-880-3402 (cell); carrine.blank (Skype); carrine.blank@umontana.edu (email) http://hs.umt.edu/geosciences/people/research.php?s=Blank1937

From: citmejia [notifications@github.com] Sent: Tuesday, June 12, 2018 12:19 PM To: carrineblank/MicrO Cc: Subscribed Subject: [carrineblank/MicrO] Punning are preventing from importing terms from MicrO (#21)

Hi,

There are a number of Illegal redeclarations of entities in MicrO. This is preventing me from using robot to extract and merge terms from MicrO.

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carrineblank commented 6 years ago

Hi Citlalli,

Thanks so much for your message; I haven't updated any of the ontology imports in over 6 months and if they have undergone major changes (which they often do) then I haven't been able to keep up with those. Hopefully we can get some funding in the future to further develop and build up MicrO and then these can be fixed; in the meantime all I am able to manage are some quick fixes here and there.

Best wishes on your project! If there is anything else I can do for you let me know.....

-Carrine