import chain doid.owl imported from canonical iri

Following a review of doid.owl we now import it via its canonical iri.
Removed local copy of doid.owl.
Added symp-dead and trans-dead that are imported via doid, they are
imported via doid-bridge (deads from parts of the import chain we do not
control should be imported at the first point we can).
Assoc updates to catalog-extras, catalog-v001.xml, and dev-reasoner.path.

catalog-extras

@@ -1,3 +1,4 @@
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/doid.owl" uri="external/doid.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go.owl" uri="external/go.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/iao.owl" uri="external/iao.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl" uri="external/taxslim.owl"/>

dev-reasoner.patch

@@ -11,19 +11,6 @@ index 8b9ced0..1311ef4 100644
          <http://ontology.neuinfo.org/NIF/ttl/external/CogPO.ttl>,
          <http://ontology.neuinfo.org/NIF/ttl/NIF-Government-Granting-Agency.ttl>,
          <http://ontology.neuinfo.org/NIF/ttl/NIF-Resource.ttl>,
-diff --git a/ttl/bridge/doid-bridge.ttl b/ttl/bridge/doid-bridge.ttl
-index 2b1542f..cc5dd6a 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/generated/doid-dead.ttl>,
-         <http://ontology.neuinfo.org/NIF/ttl/nif_backend.ttl> .
-
 diff --git a/ttl/bridge/pr-bridge.ttl b/ttl/bridge/pr-bridge.ttl
 index 983a3b3..41deaef 100644
 --- a/ttl/bridge/pr-bridge.ttl

ttl/bridge/doid-bridge.ttl

@@ -8,9 +8,11 @@
 @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>,
-        <http://ontology.neuinfo.org/NIF/ttl/generated/doid-dead.ttl>,
-        <http://ontology.neuinfo.org/NIF/ttl/nif_backend.ttl> .
+    owl:imports <http://ontology.neuinfo.org/NIF/ttl/generated/doid-dead.ttl>,
+        <http://ontology.neuinfo.org/NIF/ttl/generated/symp-dead.ttl>,
+        <http://ontology.neuinfo.org/NIF/ttl/generated/trans-dead.ttl>,
+        <http://ontology.neuinfo.org/NIF/ttl/nif_backend.ttl>,
+        <http://purl.obolibrary.org/obo/doid.owl> .
 
 ### Annotations
 

ttl/catalog-v001.xml

@@ -47,7 +47,6 @@
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/bridge/uberon-bridge.ttl" uri="bridge/uberon-bridge.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/external/CogPO.ttl" uri="external/CogPO.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/external/cogat_v0.3.owl" uri="external/cogat_v0.3.owl"/>
-    <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/external/doid.owl" uri="external/doid.owl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/external/pr.owl" uri="external/pr.owl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/NIF-NIFSTD-mapping.ttl" uri="generated/NIF-NIFSTD-mapping.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/NIF-Neuron-HBP-cell-import.ttl" uri="generated/NIF-Neuron-HBP-cell-import.ttl"/>
@@ -85,6 +84,8 @@
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/pato-dead.ttl" uri="generated/pato-dead.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/pr-dead.ttl" uri="generated/pr-dead.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/so-dead.ttl" uri="generated/so-dead.ttl"/>
+    <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/symp-dead.ttl" uri="generated/symp-dead.ttl"/>
+    <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/trans-dead.ttl" uri="generated/trans-dead.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/swanson_hierarchies.ttl" uri="generated/swanson_hierarchies.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/tax-dead.ttl" uri="generated/tax-dead.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/generated/uberon-dead.ttl" uri="generated/uberon-dead.ttl"/>
@@ -118,7 +119,6 @@
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/utility/NIF-Investigation-view.ttl" uri="utility/NIF-Investigation-view.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/utility/NIF-Resource-view.ttl" uri="utility/NIF-Resource-view.ttl"/>
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/ttl/utility/NIF-Subcellular-view.ttl" uri="utility/NIF-Subcellular-view.ttl"/>
-    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/doid.owl" uri="external/doid.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pr.owl" uri="external/pr.owl"/>
     <uri id="User Entered Import Resolution" name="http://www.cognitiveatlas.org/ontology/cogat.owl" uri="external/cogat_v0.3.owl"/>
 </catalog>