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Fixed errors where the ‘comment’ annotation property was used in plac…

…e of database_cross_reference, 8 errors in all.
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1 parent 01b79c8 commit 1ca0ff63dc35d193c64587514c7b0ec86efd982d Alexander Diehl committed Jan 27, 2017
Showing with 39 additions and 38 deletions.
  1. +33 −33 catalog-v001.xml
  2. +6 −5 src/ontology/cl-edit.owl
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@@ -1,38 +1,38 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl-bridge-to-uberon.owl" uri="src/ontology/bridge/cl-bridge-to-uberon.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl.owl" uri="cl.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/cl-basic.owl" uri="cl-basic.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/cl-plus-nif.owl" uri="src/ontology/cl-plus-nif.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/imports/clo_import.owl" uri="imports/clo_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/imports/go_import.owl" uri="imports/go_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/imports/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="duplicate:http://purl.obolibrary.org/obo/cl/imports/imports/go_import.owl" uri="imports/go_seed.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="duplicate:http://purl.obolibrary.org/obo/cl/imports/imports/go_import.owl" uri="imports/uberon_seed.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/imports/imports/pato_import.owl" uri="imports/pato_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/imports/imports/pr_import.owl" uri="imports/pr_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/imports/ro_import.owl" uri="imports/ro_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://purl.obolibrary.org/obo/cl/multispecies.owl" uri="src/ontology/multispecies.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="duplicate:http://www.gong.manchester.ac.uk/cto_norm.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/cto_norm.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="duplicate:http://www.gong.manchester.ac.uk/cto_norm.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/cto_norm_changes.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://www.gong.manchester.ac.uk/fma.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/fma.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://www.gong.manchester.ac.uk/go.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/go.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://www.gong.manchester.ac.uk/pato.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/pato.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="http://www.gong.manchester.ac.uk/ro.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/ro.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl.owl" uri="src/ontology/cl-edit_neg_exp.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/cl-basic.owl" uri="src/ontology/cl-basic.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/clo_import.owl" uri="src/ontology/imports/clo_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/go_import.owl" uri="src/ontology/imports/go_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/imports/chebi_import.owl" uri="src/ontology/imports/chebi_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/imports/go_import.owl" uri="src/ontology/imports/go_seed.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/imports/go_import.owl" uri="src/ontology/imports/uberon_seed.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/imports/pato_import.owl" uri="src/ontology/imports/pato_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/imports/pr_import.owl" uri="src/ontology/imports/pr_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/ncbitaxon_import.owl" uri="src/ontology/imports/ncbitaxon_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/ro_import.owl" uri="src/ontology/imports/ro_import.owl"/>
- <uri id="Automatically generated entry, Timestamp=1444349401386" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/uberon_import.owl" uri="src/ontology/imports/uberon_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl-bridge-to-uberon.owl" uri="src/ontology/bridge/cl-bridge-to-uberon.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl.owl" uri="cl.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/cl-basic.owl" uri="cl-basic.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/cl-plus-nif.owl" uri="src/ontology/cl-plus-nif.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/imports/chebi_import.owl" uri="src/ontology/imports/chebi_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/imports/clo_import.owl" uri="src/ontology/imports/clo_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/imports/go_import.owl" uri="src/ontology/imports/go_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="duplicate:http://purl.obolibrary.org/obo/cl/imports/imports/go_import.owl" uri="src/ontology/imports/go_seed.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="duplicate:http://purl.obolibrary.org/obo/cl/imports/imports/go_import.owl" uri="src/ontology/imports/uberon_seed.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/imports/ncbitaxon_import.owl" uri="src/ontology/imports/ncbitaxon_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/imports/pato_import.owl" uri="src/ontology/imports/pato_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/imports/pr_import.owl" uri="src/ontology/imports/pr_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/imports/ro_import.owl" uri="src/ontology/imports/ro_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/imports/uberon_import.owl" uri="src/ontology/imports/uberon_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://purl.obolibrary.org/obo/cl/multispecies.owl" uri="src/ontology/multispecies.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="duplicate:http://www.gong.manchester.ac.uk/cto_norm.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/cto_norm.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="duplicate:http://www.gong.manchester.ac.uk/cto_norm.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/cto_norm_changes.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://www.gong.manchester.ac.uk/fma.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/fma.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://www.gong.manchester.ac.uk/go.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/go.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://www.gong.manchester.ac.uk/pato.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/pato.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="http://www.gong.manchester.ac.uk/ro.owl" uri="for_reference/Manchester_CL_normalisation_expt/owl/ro.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl.owl" uri="src/ontology/cl-edit_neg_exp.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/cl-basic.owl" uri="src/ontology/cl-basic.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/clo_import.owl" uri="imports/clo_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/go_import.owl" uri="imports/go_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/imports/go_import.owl" uri="imports/go_seed.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/imports/go_import.owl" uri="imports/uberon_seed.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/pato_import.owl" uri="imports/pato_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/pr_import.owl" uri="imports/pr_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/ro_import.owl" uri="imports/ro_import.owl"/>
+ <uri id="Automatically generated entry, Timestamp=1469044058614" name="shadowed:http://purl.obolibrary.org/obo/cl/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
</group>
</catalog>
@@ -1,4 +1,4 @@
-Prefix(:=<http://purl.obolibrary.org/obo/cl.owl#>)
+Prefix(:=<http://purl.obolibrary.org/obo/cl.owl/>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
@@ -3848,7 +3848,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/CL_0000118> <http://purl.obolibrary.o
# Class: <http://purl.obolibrary.org/obo/CL_0000119> (cerebellar Golgi cell)
-AnnotationAssertion(Annotation(rdfs:comment "NIFSTD:sao1415726815") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0000119> "Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell enters ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004.")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "NIFSTD:sao1415726815") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0000119> "Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell enters ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_0000119> "Golgi cell")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_0000119> "Golgi neuron")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_0000119> "cerebellar Golgi neuron")
@@ -10623,7 +10623,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/CL_0000840> ObjectSomeValuesFrom(<htt
# Class: <http://purl.obolibrary.org/obo/CL_0000841> (mature conventional dendritic cell)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:add"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:tfm"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:9521319"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0000841> "A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node."^^xsd:string)
-AnnotationAssertion(Annotation(rdfs:comment "GOC:add") <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/CL_0000841> "mature dendritic cell")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:add") <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/CL_0000841> "mature dendritic cell")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CL_0000841> "FMA:83038"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/CL_0000841> "mature myeloid dendritic cell"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CL_0000841> "cell"^^xsd:string)
@@ -13121,7 +13121,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/CL_0001066> <http://purl.obolibrary.o
# Class: <http://purl.obolibrary.org/obo/CL_0001070> (beige adipocyte)
-AnnotationAssertion(Annotation(rdfs:comment "GOC:add"^^xsd:string) Annotation(rdfs:comment "GOC:cvs"^^xsd:string) Annotation(rdfs:comment "GOC:ymb"^^xsd:string) Annotation(rdfs:comment "PMID:22796012"^^xsd:string) Annotation(rdfs:comment "PMID:25851693"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0001070> "A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor.")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:add"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:cvs"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:ymb"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:22796012"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:25851693"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0001070> "A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_0001070> "beige brown adipocyte")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_0001070> "beige fat cell")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_0001070> "beige/brite adipocyte")
@@ -21612,7 +21612,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/CL_0010015> <http://purl.obolibrary.o
# Class: <http://purl.obolibrary.org/obo/CL_0010016> (collar cell)
-AnnotationAssertion(Annotation(rdfs:comment <http://dx.doi.org/10.1016/j.tree.2015.03.003>) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0010016> "a cell with a flagellum surrounded by a collar of microvilli. The motion of the flagellum draws water past the microvilli, serving either a feeding or sensory function. Collar cells are found in multiple animals, including sponges, echinoderms, and cnidarians. They are also found outside animals in the choanoflagellates. Although collar cells are superficially similar, their cytoskeletal structure and functional biology are different in different groups of organisms.")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:25840473") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0010016> "A cell with a flagellum surrounded by a collar of microvilli. The motion of the flagellum draws water past the microvilli, serving either a feeding or sensory function. Collar cells are found in multiple animals, including sponges, echinoderms, and cnidarians. They are also found outside animals in the choanoflagellates. Although collar cells are superficially similar, their cytoskeletal structure and functional biology are different in different groups of organisms.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CL_0010016> "cell")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0010016> "collar cell")
SubClassOf(<http://purl.obolibrary.org/obo/CL_0010016> <http://purl.obolibrary.org/obo/CL_0000548>)
SubClassOf(<http://purl.obolibrary.org/obo/CL_0010016> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/GO_0005929>))

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