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Merge pull request #116 from SciCrunch/uri-switch

merge changes for 2.13
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tgbugs committed Sep 10, 2017
2 parents 992c2de + 29c62a5 commit 6de411683b2bec8ed96c03a9eded32cc0dbe226b
Showing with 14,301 additions and 15,225 deletions.
  1. +93 −19 dev-reasoner.patch
  2. +51 −32 scigraph/nifstd_curie_map.yaml
  3. +10 −61 ttl/BIRNLex-OBI-proxy.ttl
  4. +11 −271 ttl/BIRNLex-OBO-UBO.ttl
  5. +120 −47 ttl/BIRNLex_annotation_properties.ttl
  6. +2 −1 ttl/NIF-Annotation-Standard.ttl
  7. +110 −156 ttl/NIF-Cell.ttl
  8. +41 −79 ttl/NIF-Chemical.ttl
  9. +2 −1 ttl/NIF-DOID-Bridge.ttl
  10. +5 −59 ttl/NIF-Dysfunction.ttl
  11. +2 −63 ttl/NIF-Function.ttl
  12. +160 −213 ttl/NIF-Government-Granting-Agency.ttl
  13. +160 −206 ttl/NIF-GrossAnatomy.ttl
  14. +2 −1 ttl/NIF-Investigation-OBI-Bridge.ttl
  15. +169 −192 ttl/NIF-Investigation.ttl
  16. +2 −1 ttl/NIF-Molecule-Role-Bridge.ttl
  17. +41 −39 ttl/NIF-Molecule-Role-Inferred.ttl
  18. +30 −69 ttl/NIF-Molecule.ttl
  19. +3 −2 ttl/NIF-Neuron-BR-Inferred.ttl
  20. +3 −2 ttl/NIF-Neuron-BrainRegion-Bridge.ttl
  21. +2 −1 ttl/NIF-Neuron-Circuit-Role-Bridge.ttl
  22. +2 −1 ttl/NIF-Neuron-Circuit-Role-Inferred.ttl
  23. +7 −6 ttl/{NIF_Neuron_MolecularConstituent_Bridge.ttl → NIF-Neuron-MolecularConstituent-Bridge.ttl}
  24. +21 −20 ttl/NIF-Neuron-MolecularConstituent-Inferred.ttl
  25. +2 −1 ttl/NIF-Neuron-Morphology-Bridge.ttl
  26. +2 −1 ttl/NIF-Neuron-Morphology-Inferred.ttl
  27. +2 −1 ttl/NIF-Neuron-NT-Bridge-Inferred.ttl
  28. +8 −7 ttl/NIF-Neuron-NT-Bridge.ttl
  29. +605 −635 ttl/NIF-Organism.ttl
  30. +2 −2 ttl/NIF-PRO-Bridge.ttl
  31. +125 −172 ttl/NIF-Quality.ttl
  32. +23 −231 ttl/NIF-Resource.ttl
  33. +38 −53 ttl/NIF-Scientific-Discipline.ttl
  34. +312 −336 ttl/NIF-Subcellular.ttl
  35. +9 −15 ttl/NIF-Unclassified.ttl
  36. +36 −28 ttl/OBO_annotation_properties.ttl
  37. +2 −1 ttl/bridge/aba-bridge.ttl
  38. +17 −0 ttl/bridge/anatomy-bridge.ttl
  39. +29 −16 ttl/bridge/chebi-bridge.ttl
  40. +2 −1 ttl/bridge/doid-bridge.ttl
  41. +11 −0 ttl/bridge/ero-bridge.ttl
  42. +26 −0 ttl/bridge/go-bridge.ttl
  43. +11 −0 ttl/bridge/pr-bridge.ttl
  44. +13 −0 ttl/bridge/tax-bridge.ttl
  45. +25 −39 ttl/bridge/uberon-bridge.ttl
  46. +23 −16 ttl/catalog-v001.xml
  47. +1 −1 ttl/external/CogPO.owl
  48. +1,721 −1,721 ttl/external/cogat_v0.3.owl
  49. +313 −0 ttl/external/ro_bfo1-1_bridge.owl
  50. +3 −1 ttl/external/uberon.owl
  51. +2 −1 ttl/generated/NIF-Neuron-HBP-cell-import.ttl
  52. +2 −1 ttl/generated/chebi-dead.ttl
  53. +2 −1 ttl/generated/chebislim.ttl
  54. +2 −1 ttl/generated/ksdesc-defs.ttl
  55. +2 −1 ttl/generated/ncbigeneslim.ttl
  56. +3 −2 ttl/generated/parcellation.ttl
  57. +34 −32 ttl/generated/parcellation/Cerebellum_MNIflirt.ttl
  58. +34 −32 ttl/generated/parcellation/Cerebellum_MNIfnirt.ttl
  59. +54 −52 ttl/generated/parcellation/HarvardOxford-Cortical.ttl
  60. +27 −25 ttl/generated/parcellation/HarvardOxford-Subcortical.ttl
  61. +55 −53 ttl/generated/parcellation/JHU-labels.ttl
  62. +26 −24 ttl/generated/parcellation/JHU-tracts.ttl
  63. +127 −125 ttl/generated/parcellation/Juelich.ttl
  64. +15 −13 ttl/generated/parcellation/MNI.ttl
  65. +16 −14 ttl/generated/parcellation/MarsParietalParcellation.ttl
  66. +8 −6 ttl/generated/parcellation/MarsTPJParcellation.ttl
  67. +18 −16 ttl/generated/parcellation/NeubertVentralFrontalParcellation.ttl
  68. +8 −6 ttl/generated/parcellation/STN.ttl
  69. +16 −14 ttl/generated/parcellation/SalletDorsalFrontalParcellation.ttl
  70. +9 −7 ttl/generated/parcellation/Striatum-Connectivity-3sub.ttl
  71. +13 −11 ttl/generated/parcellation/Striatum-Connectivity-7sub.ttl
  72. +10 −8 ttl/generated/parcellation/Striatum-Structural.ttl
  73. +1,112 −1,110 ttl/generated/parcellation/Talairach.ttl
  74. +13 −11 ttl/generated/parcellation/Thalamus.ttl
  75. +5 −3 ttl/generated/parcellation/cocomacslim.ttl
  76. +4 −3 ttl/generated/parcellation/hbaslim.ttl
  77. +185 −184 ttl/generated/parcellation/hcp_parcellation.ttl
  78. +109 −9 ttl/generated/parcellation/mbaslim.ttl
  79. +1,640 −1,639 ttl/generated/parcellation/paxinos_r_s_6.ttl
  80. +98 −96 ttl/generated/parcellation/whs_sd_2.ttl
  81. +1,398 −1,397 ttl/generated/swanson_hierarchies.ttl
  82. +13 −7 ttl/generated/uberon-parcellation-mappings.ttl
  83. +11 −19 ttl/nif.ttl
  84. +19 −48 ttl/nif_backend.ttl
  85. +3 −105 ttl/quality_bfo_bridge.ttl
  86. +599 −595 ttl/resources.ttl
  87. +0 −149 ttl/ro_bfo1-1_bridge.ttl
  88. +12 −19 ttl/{ → unused}/NIF-Eagle-I-Bridge.ttl
  89. +3 −2 ttl/{ → unused}/NIF-GO-CC-Bridge.ttl
  90. +3,768 −3,932 ttl/unused/NIF-GrossAnatomy-Inferred.ttl
  91. +2 −1 ttl/unused/NIF-Molecule-PRO-Bridge.ttl
  92. +2 −5 ttl/unused/NIF-NCBITax-Bridge.ttl
  93. +2 −1 ttl/unused/NIF-NCBITax-Slim-Inferred.ttl
  94. +2 −1 ttl/unused/NIF-NCBITaxonomy-EnglishNames.ttl
  95. +2 −1 ttl/unused/NIF-NCBITaxonomy-Slim-EnglishNames.ttl
  96. +4 −207 ttl/unused/NIF-NCBITaxonomy-Slim.ttl
  97. +4 −3 ttl/unused/NIF-Neuron-Bridge.ttl
  98. +2 −1 ttl/unused/NIF-Neuron-Inferred.ttl
  99. +2 −1 ttl/unused/NIF-Neuron-Quality-Bridge.ttl
  100. +2 −1 ttl/unused/NIF-Neuron-SomaLocation-Bridge.ttl
  101. +135 −202 ttl/unused/NIF-Retired.ttl
  102. +2 −1 ttl/unused/NIF-Subcell-GO-CC-Equiv-Bridge.ttl
  103. +2 −1 ttl/unused/NIF_Resource_Inferred.ttl
  104. +222 −185 ttl/{ → unused}/SAO-CORE_properties.ttl
  105. +2 −1 ttl/unused/ro_bfo_bridge.ttl
  106. +12 −10 ttl/unused/sequence_slim.ttl
  107. +5 −4 ttl/{ → unused}/uberon-bridge-to-nifstd.ttl
  108. +2 −1 ttl/utility/NIF-Anatomy-view.ttl
  109. +2 −1 ttl/utility/NIF-Cell-view.ttl
  110. +2 −1 ttl/utility/NIF-Dysfunction-view.ttl
  111. +2 −1 ttl/utility/NIF-Investigation-view.ttl
  112. +2 −1 ttl/utility/NIF-Resource-view.ttl
  113. +2 −1 ttl/utility/NIF-Subcellular-view.ttl
View
@@ -1,19 +1,93 @@
diff --git a/ttl/nif.ttl b/ttl/nif.ttl
index f8792cc..c2b7ad4 100644
--- a/ttl/nif.ttl
+++ b/ttl/nif.ttl
@@ -11,10 +11,10 @@
owl:imports <http://ontology.neuinfo.org/NIF/ttl/bridge/chebi-bridge.ttl>,
<http://ontology.neuinfo.org/NIF/ttl/bridge/doid-bridge.ttl>,
<http://ontology.neuinfo.org/NIF/ttl/bridge/uberon-bridge.ttl>,
- <http://ontology.neuinfo.org/NIF/ttl/external/ero.owl>,
- <http://ontology.neuinfo.org/NIF/ttl/external/go.owl>,
- <http://ontology.neuinfo.org/NIF/ttl/external/pr.owl>,
- <http://ontology.neuinfo.org/NIF/ttl/external/uberon.owl>,
+ <http://purl.obolibrary.org/obo/ero.owl>,
+ <http://purl.obolibrary.org/obo/go.owl>,
+ <http://purl.obolibrary.org/obo/pr.owl>,
+ <http://purl.obolibrary.org/obo/uberon.owl>,
<http://ontology.neuinfo.org/NIF/ttl/generated/ksdesc-defs.ttl>,
<http://ontology.neuinfo.org/NIF/ttl/generated/ncbigeneslim.ttl>,
<http://ontology.neuinfo.org/NIF/ttl/generated/NIF-Neuron-HBP-cell-import.ttl>,
diff --git a/ttl/NIF-Investigation.ttl b/ttl/NIF-Investigation.ttl
index 3e3a27d..93cedfc 100644
--- a/ttl/NIF-Investigation.ttl
+++ b/ttl/NIF-Investigation.ttl
@@ -22,8 +22,8 @@
<http://ontology.neuinfo.org/NIF/ttl/NIF-Investigation.ttl> a owl:Ontology ;
owl:imports <http://ontology.neuinfo.org/NIF/ttl/BIRNLex-OBI-proxy.ttl>,
- <http://ontology.neuinfo.org/NIF/ttl/external/cogat_v0.3.owl>,
- <http://ontology.neuinfo.org/NIF/ttl/external/CogPO.owl>,
+ <http://www.cognitiveatlas.org/ontology/cogat.owl>,
+ <http://www.cogpo.org/ontologies/CogPOver2010.owl>,
<http://ontology.neuinfo.org/NIF/ttl/NIF-Government-Granting-Agency.ttl>,
<http://ontology.neuinfo.org/NIF/ttl/NIF-Resource.ttl>,
<http://ontology.neuinfo.org/NIF/ttl/NIF-Scientific-Discipline.ttl>,
diff --git a/ttl/bridge/doid-bridge.ttl b/ttl/bridge/doid-bridge.ttl
index fb925b9..062efbb 100644
--- a/ttl/bridge/doid-bridge.ttl
+++ b/ttl/bridge/doid-bridge.ttl
@@ -8,7 +8,7 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://ontology.neuinfo.org/NIF/ttl/bridge/doid-bridge.ttl> a owl:Ontology ;
- owl:imports <http://ontology.neuinfo.org/NIF/ttl/external/doid.owl>,
+ owl:imports <http://purl.obolibrary.org/obo/doid.owl>,
<http://ontology.neuinfo.org/NIF/ttl/nif_backend.ttl> .
### Annotations
diff --git a/ttl/bridge/ero-bridge.ttl b/ttl/bridge/ero-bridge.ttl
index 7aed46c..f79b55c 100644
--- a/ttl/bridge/ero-bridge.ttl
+++ b/ttl/bridge/ero-bridge.ttl
@@ -6,6 +6,6 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://ontology.neuinfo.org/NIF/ttl/bridge/ero-bridge.ttl> a owl:Ontology ;
- owl:imports <http://ontology.neuinfo.org/NIF/ttl/external/ero.owl> .
+ owl:imports <http://purl.obolibrary.org/obo/ero.owl> .
### Serialized using the nifstd custom serializer v1.0.7
diff --git a/ttl/bridge/go-bridge.ttl b/ttl/bridge/go-bridge.ttl
index 1cb24a9..e98785f 100644
--- a/ttl/bridge/go-bridge.ttl
+++ b/ttl/bridge/go-bridge.ttl
@@ -9,7 +9,7 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://ontology.neuinfo.org/NIF/ttl/bridge/go-bridge.ttl> a owl:Ontology ;
- owl:imports <http://ontology.neuinfo.org/NIF/ttl/external/go.owl>,
+ owl:imports <http://purl.obolibrary.org/obo/go.owl>,
<http://ontology.neuinfo.org/NIF/ttl/nif_backend.ttl> .
### Classes
diff --git a/ttl/bridge/pr-bridge.ttl b/ttl/bridge/pr-bridge.ttl
index c34e372..55b8ec2 100644
--- a/ttl/bridge/pr-bridge.ttl
+++ b/ttl/bridge/pr-bridge.ttl
@@ -6,6 +6,6 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://ontology.neuinfo.org/NIF/ttl/bridge/pr-bridge.ttl> a owl:Ontology ;
- owl:imports <http://ontology.neuinfo.org/NIF/ttl/external/pr.owl> .
+ owl:imports <http://purl.obolibrary.org/obo/pr.owl> .
### Serialized using the nifstd custom serializer v1.0.7
diff --git a/ttl/bridge/uberon-bridge.ttl b/ttl/bridge/uberon-bridge.ttl
index 17c21a9..891cad4 100644
--- a/ttl/bridge/uberon-bridge.ttl
+++ b/ttl/bridge/uberon-bridge.ttl
@@ -10,7 +10,7 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://ontology.neuinfo.org/NIF/ttl/bridge/uberon-bridge.ttl> a owl:Ontology ;
- owl:imports <http://ontology.neuinfo.org/NIF/ttl/external/uberon.owl> ;
+ owl:imports <http://purl.obolibrary.org/obo/uberon.owl> ;
rdfs:label "NIFSTD Uberon Bridge" ;
rdfs:comment "This is the bridge file that holds local NIFSTD additions to uberon. This is also staging for any changes that we want to push upstream." ;
owl:versionInfo "2016-11-03" ;
diff --git a/ttl/nif_backend.ttl b/ttl/nif_backend.ttl
index 1e95a9e..c8147b7 100644
--- a/ttl/nif_backend.ttl
+++ b/ttl/nif_backend.ttl
@@ -11,8 +11,8 @@
<http://ontology.neuinfo.org/NIF/ttl/nif_backend.ttl> a owl:Ontology ;
owl:imports <http://ontology.neuinfo.org/NIF/ttl/BIRNLex-OBO-UBO.ttl>,
<http://ontology.neuinfo.org/NIF/ttl/BIRNLex_annotation_properties.ttl>,
- <http://ontology.neuinfo.org/NIF/ttl/external/pato.owl>,
- <http://ontology.neuinfo.org/NIF/ttl/external/ro_bfo1-1_bridge.owl>,
+ <http://purl.obolibrary.org/obo/pato.owl>,
+ <http://purl.org/obo/owl/ro_bfo1-1_bridge>,
<http://ontology.neuinfo.org/NIF/ttl/quality_bfo_bridge.ttl>,
<http://purl.obolibrary.org/obo/iao.owl>,
<http://purl.obolibrary.org/obo/ro.owl>,
@@ -1,5 +1,28 @@
# NO EMPTY
'': 'file:///ERROR/EMPTY/PREFIX/BANNED/'
# base
'': 'http://uri.neuinfo.org/nif/nifstd/'
'NIFSTD': 'http://uri.neuinfo.org/nif/nifstd/'
# NIFSTD namespaces
'BIRNLEX': 'http://uri.neuinfo.org/nif/nifstd/birnlex_'
'NIFEXT': 'http://uri.neuinfo.org/nif/nifstd/nifext_'
'NLX': 'http://uri.neuinfo.org/nif/nifstd/nlx_'
'NLXANAT': 'http://uri.neuinfo.org/nif/nifstd/nlx_anat_'
'NLXCELL': 'http://uri.neuinfo.org/nif/nifstd/nlx_cell_'
'NLXCHEM': 'http://uri.neuinfo.org/nif/nifstd/nlx_chem_'
'NLXDYS': 'http://uri.neuinfo.org/nif/nifstd/nlx_dys_'
'NLXFUNC': 'http://uri.neuinfo.org/nif/nifstd/nlx_func_'
'NLXINV': 'http://uri.neuinfo.org/nif/nifstd/nlx_inv_'
'NLXMOL': 'http://uri.neuinfo.org/nif/nifstd/nlx_mol_'
'NLXNEURNT': 'http://uri.neuinfo.org/nif/nifstd/nlx_neuron_nt_'
'NLXORG': 'http://uri.neuinfo.org/nif/nifstd/nlx_organ_'
'NLXQUAL': 'http://uri.neuinfo.org/nif/nifstd/nlx_qual_'
'NLXRES': 'http://uri.neuinfo.org/nif/nifstd/nlx_res_'
'NLXSUB': 'http://uri.neuinfo.org/nif/nifstd/nlx_subcell_'
'NLXUBO': 'http://uri.neuinfo.org/nif/nifstd/nlx_ubo_'
'NLXUNCL': 'http://uri.neuinfo.org/nif/nifstd/nlx_uncl_'
'SAO': 'http://uri.neuinfo.org/nif/nifstd/sao'
# interlex
'ILX': 'http://uri.interlex.org/base/ilx_'
@@ -9,42 +32,45 @@
'SCR': 'http://scicrunch.org/resolver/SCR_'
# ontologies
'obo': 'http://purl.obolibrary.org/obo/'
'HP': 'http://purl.obolibrary.org/obo/HP_'
'RO': 'http://purl.obolibrary.org/obo/RO_'
'OBO': 'http://purl.obolibrary.org/obo/'
'OBI': 'http://purl.obolibrary.org/obo/OBI_'
'OIO': 'http://www.geneontology.org/formats/oboInOwl#'
'oboInOwl': 'http://www.geneontology.org/formats/oboInOwl#'
'IAO': 'http://purl.obolibrary.org/obo/IAO_'
'SO' : 'http://purl.obolibrary.org/obo/SO_'
'SO': 'http://purl.obolibrary.org/obo/SO_'
'BFO': 'http://purl.obolibrary.org/obo/BFO_'
'DOID': 'http://purl.obolibrary.org/obo/DOID_'
'DOID2': 'http://purl.obolibrary.org/obo/DOID#DOID_'
'PATO': 'http://purl.obolibrary.org/obo/PATO_'
'PATO2': 'http://purl.obolibrary.org/obo/PATO#PATO_' #AAAAAAAAAAA
'PATO3': 'http://purl.org/obo/owl/PATO#PATO_' #AAAAAAAAAAAAAAAAAA
'PR': 'http://purl.obolibrary.org/obo/PR_'
'PW' : 'http://purl.obolibrary.org/obo/PW_'
'CL' : 'http://purl.obolibrary.org/obo/CL_'
'CLO' : 'http://purl.obolibrary.org/obo/CLO_'
'GO' : 'http://purl.obolibrary.org/obo/GO_'
'SIO' : 'http://semanticscience.org/resource/SIO_'
'EFO' : 'http://www.ebi.ac.uk/efo/EFO_'
'UBERON' : 'http://purl.obolibrary.org/obo/UBERON_'
'ERO' : 'http://purl.obolibrary.org/obo/ERO_'
'NCBIGene' : 'http://www.ncbi.nlm.nih.gov/gene/'
'NCBITaxon' : 'http://purl.obolibrary.org/obo/NCBITaxon_'
'NCBITaxon2' : 'http://purl.org/obo/owl/NCBITaxon#NCBITaxon_'
'PW': 'http://purl.obolibrary.org/obo/PW_'
'CL': 'http://purl.obolibrary.org/obo/CL_'
'CLO': 'http://purl.obolibrary.org/obo/CLO_'
'GO': 'http://purl.obolibrary.org/obo/GO_'
'SIO': 'http://semanticscience.org/resource/SIO_'
'EFO': 'http://www.ebi.ac.uk/efo/EFO_'
'SWO': 'http://www.ebi.ac.uk/efo/swo/SWO_'
'UBERON': 'http://purl.obolibrary.org/obo/UBERON_'
'ERO': 'http://purl.obolibrary.org/obo/ERO_'
'NCBIGene': 'http://www.ncbi.nlm.nih.gov/gene/'
'NCBITaxon': 'http://purl.obolibrary.org/obo/NCBITaxon_'
'UO': 'http://purl.obolibrary.org/obo/UO_'
'CHEBI': 'http://purl.obolibrary.org/obo/CHEBI_'
'OLD_CHEBI': 'http://purl.obolibrary.org/obo/chebi.owl#CHEBI_'
'FMA': 'http://purl.org/sig/ont/fma/fma'
'MBA': 'http://api.brain-map.org/api/v2/data/Structure/'
#'NEMOANN': 'http://purl.bioontology.org/NEMO/ontology/NEMO_annotation_properties.owl'
#'NEMO': 'http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_'
'BFO1': 'http://www.ifomis.org/bfo/1.1#'
'BFO1SNAP': 'http://www.ifomis.org/bfo/1.1/snap#'
'BFO1SPAN': 'http://www.ifomis.org/bfo/1.1/span#'
'COGAT': 'http://www.cognitiveatlas.org/ontology/cogat.owl#'
'COGPO': 'http://www.cogpo.org/ontologies/COGPO_' # doesn't resolve
# NIF Import closure
'BIRNANN': 'http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#'
'BIRNOBI': 'http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#'
'BIRNOBO': 'http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#'
'NIFBE': 'http://ontology.neuinfo.org/NIF/Backend/nif_backend.owl#'
#'NIFBE': 'http://ontology.neuinfo.org/NIF/Backend/nif_backend.owl#'
'NIFQUAL': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Quality.owl#'
'OBOANN': 'http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#'
'NIFANN': 'http://ontology.neuinfo.org/NIF/NIF-Annotation-Standard.owl#'
@@ -62,27 +88,20 @@
'NIFSCID': 'http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Scientific-Discipline.owl#'
'NIFDYS': 'http://ontology.neuinfo.org/NIF/Dysfunction/NIF-Dysfunction.owl#'
'NIFFUN': 'http://ontology.neuinfo.org/NIF/Function/NIF-Function.owl#'
'NEMOANN': 'http://purl.bioontology.org/NEMO/ontology/NEMO_annotation_properties.owl'
'NEMO': 'http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_'
'BFO1': 'http://www.ifomis.org/bfo/1.1#'
'BFO1SNAP': 'http://www.ifomis.org/bfo/1.1/snap#'
'BFO1SPAN': 'http://www.ifomis.org/bfo/1.1/span#'
'COGAT': 'http://www.cognitiveatlas.org/ontology/cogat.owl#'
'COGPO': 'http://www.cogpo.org/ontologies/COGPO_' # doesn't resolve
# Inferred or Slim
'NIFMOLINF': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule-Role-Inferred.owl#'
'NIFNCBISLIM': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-NCBITaxonomy-Slim.owl#'
# Bridge
'QUALBB': 'http://ontology.neuinfo.org/NIF/Backend/quality_bfo_bridge.owl#'
'NIFNEURON': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF_Neuron_MolecularConstituent_Bridge.owl#'
'NIFERO': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Eagle-I-Bridge.owl#'
'NIFGOCC': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GO-CC-Bridge.owl#'
#'QUALBB': 'http://ontology.neuinfo.org/NIF/Backend/quality_bfo_bridge.owl#'
#'NIFERO': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Eagle-I-Bridge.owl#'
#'NIFGOCC': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GO-CC-Bridge.owl#'
'NIFMOLROLE': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule-Role-Bridge#' #AAAAAAA
'NIFNCBI': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-NCBITax-Bridge.owl#'
'NIFNEURMC': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF_Neuron_MolecularConstituent_Bridge.owl#'
'NIFNEURBR': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-BrainRegion-Bridge.owl#'
'NIFNEURBR2': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-Brain-Bridge.owl#' #AAAAAAAA FIXME
'NIFNEURBR2': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-Brain-Bridge.owl#' #AAAAAAAA
'NIFNEURCIR': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-Circuit-Role-Bridge.owl#'
'NIFNEURMOR': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-Morphology-Bridge.owl#'
'NIFNEURNT': 'http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Neuron-NT-Bridge.owl#'
View
@@ -1,10 +1,11 @@
@prefix : <file:///ERROR/EMPTY/PREFIX/BANNED/> .
@prefix BFO1SNAP: <http://www.ifomis.org/bfo/1.1/snap#> .
@prefix BFO1SPAN: <http://www.ifomis.org/bfo/1.1/span#> .
@prefix BIRNANN: <http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#> .
@prefix BIRNOBI: <http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBI-proxy.owl#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> .
@prefix NIFGA: <http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#> .
@prefix NIFMOL: <http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#> .
@prefix OBOANN: <http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix PROTEGE: <http://protege.stanford.edu/plugins/owl/protege#> .
@@ -15,6 +16,7 @@
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://ontology.neuinfo.org/NIF/ttl/BIRNLex-OBI-proxy.ttl> a owl:Ontology ;
owl:imports <http://ontology.neuinfo.org/NIF/ttl/nif_backend.ttl> ;
dc:title "BIRNLex-OBI-proxy"^^xsd:string ;
skos:definition "The BIRN Project lexicon uses this file as a temporary proxy for classes from the Ontology of Biomedical Investigation (OBI). These classes will be replaced by their OBI equivalents, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
skos:editorialNote "ID use: 11000 - 11048"^^xsd:string,
@@ -36,58 +38,8 @@
dc:creator "The BIRN Ontology Task Force"^^xsd:string ;
dc:subject "The BIRN project lexicon"^^xsd:string .
### Annotation Properties
BIRNANN:birnlexDefinition a owl:AnnotationProperty .
BIRNANN:hasBirnlexCurator a owl:AnnotationProperty .
BIRNANN:hasCurationStatus a owl:AnnotationProperty .
BIRNANN:hasFormerParentClass a owl:AnnotationProperty .
BIRNANN:isReplacedByClass a owl:AnnotationProperty .
OBOANN:abbrev a owl:AnnotationProperty .
OBOANN:createdDate a owl:AnnotationProperty .
OBOANN:externalSourceURI a owl:AnnotationProperty .
OBOANN:hasDefinitionSource a owl:AnnotationProperty .
OBOANN:modifiedDate a owl:AnnotationProperty .
OBOANN:nifID a owl:AnnotationProperty .
OBOANN:synonym a owl:AnnotationProperty .
skos:altLabel a owl:AnnotationProperty .
skos:changeNote a owl:AnnotationProperty .
skos:definition a owl:AnnotationProperty .
skos:editorialNote a owl:AnnotationProperty .
skos:prefLabel a owl:AnnotationProperty .
### Classes
BFO1SNAP:Disposition a owl:Class .
BFO1SNAP:GenericallyDependentContinuant a owl:Class .
BFO1SNAP:MaterialEntity a owl:Class .
BFO1SNAP:ObjectAggregate a owl:Class .
BFO1SNAP:Role a owl:Class .
BFO1SPAN:Process a owl:Class .
BIRNANN:_birnlex_retired_class a owl:Class .
BIRNOBI:birnlex_11000 a owl:Class ;
rdfs:label "Non-realizable information entity"^^xsd:string ;
skos:prefLabel "Non-realizable information entity"^^xsd:string ;
@@ -100,6 +52,7 @@ BIRNOBI:birnlex_11000 a owl:Class ;
OBOANN:externalSourceURI <http://obi.sourceforge.net/ontology/OBI.owl#OBI_295> .
BIRNOBI:birnlex_11001 a owl:Class ;
owl:equivalentClass IAO:0000030 ;
rdfs:label "Information content entity"^^xsd:string ;
skos:prefLabel "Information content entity"^^xsd:string ;
rdfs:subClassOf BIRNOBI:birnlex_11000 ;
@@ -200,7 +153,7 @@ BIRNOBI:birnlex_11009 a owl:Class ;
BIRNANN:hasBirnlexCurator BIRNANN:Bill_Bug ;
BIRNANN:hasCurationStatus BIRNANN:graph_position_temporary ;
OBOANN:externalSourceURI <http://obi.sourceforge.net/ontology/OBI.owl#OBI_270> ;
OBOANN:hasDefinitionSource "OBI"^^xsd:string .
OBOANN:hasDefinitionSource OBOANN:OBI_defSource .
BIRNOBI:birnlex_11010 a owl:Class ;
rdfs:label "Protocol"^^xsd:string ;
@@ -677,15 +630,11 @@ BIRNOBI:nlx_inv_20081201 a owl:Class ;
rdfs:comment "We need to have this in there somewhere, but it looks like OBI has something equivalent \"source code module\"; they have it classified as an information content entity, so I placed it here. (Maryann Martone)"^^xsd:string ;
OBOANN:createdDate "December 15, 2008"^^xsd:string ;
OBOANN:externalSourceId "OBI_0000039"^^xsd:string ;
OBOANN:hasDefinitionSource "OBI"^^xsd:string .
OBOANN:hasDefinitionSource OBOANN:OBI_defSource .
NIFGA:birnlex_6 a owl:Class .
IAO:0000030 a owl:Class ;
rdfs:subClassOf BIRNOBI:birnlex_11000 .
### Annotations
NIFMOL:CHEBI_15765 OBOANN:abbrev "L-Dopa"^^xsd:string ;
skos:definition """An amino acid precursor of dopamine with antiparkinsonian properties. L-DOPA is a prodrug that is converted to dopamine by DOPA decarboxylase and can cross the blood-brain barrier. When in the brain, L-DOPA is decarboxylated to dopamine and stimulates the dopaminergic receptors. (Adapted from NCI Thesaurus)
Levodopa is naturally occurring form of dihydroxyphenylalanine and the immediate precursor of dopamine. Unlike dopamine itself, it can be taken orally and crosses the blood-brain barrier. It is rapidly taken up by dopaminergic neurons and converted to dopamine. It is used for the treatment of parkinsonian disorders and is usually given with agents that inhibit its conversion to dopamine outside of the central nervous system. (PubChem) Pharmacology: Levodopa (L-dopa) is used to replace dopamine lost in Parkinson's disease because dopamine itself cannot cross the blood-brain barrier where its precursor can. However, L-DOPA is converted to dopamine in the periphery as well as in the CNS, so it is administered with a peripheral DDC (dopamine decarboxylase) inhibitor such as carbidopa, without which 90% is metabolised in the gut wall, and with a COMT inhibitor if possible; this prevents about a 5% loss. The form given therapeutically is therefore a prodrug which avoids decarboxylation in the stomach and periphery, can cross the blood-brain barrier, and once in the brain is converted to the neurotransmitter dopamine by the enzyme aromatic-L-amino-acid decarboxylase. Mechanism of action: Striatal dopamine levels in symptomatic Parkinson's disease are decreased by 60 to 80%, striatal dopaminergic neurotransmission may be enhanced by exogenous supplementation of dopamine through administration of dopamine's precursor, levodopa. A small percentage of each levodopa dose crosses the blood-brain barrier and is decarboxylated to dopamine. This newly formed dopamine then is available to stimulate dopaminergic receptors, thus compensating for the depleted supply of endogenous dopamine. Drug type: Approved. Small Molecule. Drug category: Antidyskinetics. Antiparkinson Agents. Dopamine Agents"""^^xsd:string .
NIFGA:birnlex_6 a owl:Class .
### Serialized using the nifstd custom serializer v1.0.5
### Serialized using the nifstd custom serializer v1.0.7
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