Adding FMA ontology

bioresources/ner_kb.config

@@ -32,6 +32,12 @@ atcc	CellLine
 tissue-type	TissueType
 CellOntology	CellType
 Uberon	Organ
+FMA-organ	Organ
+FMA-anatomical-relation	AnatomicalRelation
+FMA-anatomical-transformation-entity	AnatomicalTransformationEntity
+FMA-organizational-pattern	OrganizationalPattern
+FMA-segmental-innervation	SegmentalInnervation
+
 
 # KBs auto-generated from Big Mechanism BioPax models:
 biopax-cellular_component	Cellular_component

bioresources/src/main/resources/application.conf

@@ -201,12 +201,62 @@ KnowledgeBases
             labels = [Disease]
         }
 
+        StaticOrgan {
+            path = ${KnowledgeBasesPath}/fma_indra_Material anatomical entity.tsv
+
+            namespace = fma
+            baseURI = "http://identifiers.org/fma/"
+            resourceId = "MIR:00000067"
+            priority = 19
+            labels = [Organ]
+        }
+
+        StaticAnatomicalRelation {
+            path = ${KnowledgeBasesPath}/fma_indra_anatomical_relation.tsv
+
+            namespace = fma
+            baseURI = "http://identifiers.org/fma/"
+            resourceId = "MIR:00000067"
+            priority = 20
+            labels = [AnatomicalRelation]
+        }
+
+        StaticAnatomicalTransformationEntity {
+            path = ${KnowledgeBasesPath}/fma_indra_anatomical_transformation_entity.tsv
+
+            namespace = fma
+            baseURI = "http://identifiers.org/fma/"
+            resourceId = "MIR:00000067"
+            priority = 21
+            labels = [AnatomicalTransformationEntity]
+        }
+
+        StaticOrganizationalPattern {
+            path = ${KnowledgeBasesPath}/fma_indra_organizational_pattern.tsv
+
+            namespace = fma
+            baseURI = "http://identifiers.org/fma/"
+            resourceId = "MIR:00000067"
+            priority = 22
+            labels = [OrganizationalPattern]
+        }
+
+        StaticSegmentalInnervation {
+            path = ${KnowledgeBasesPath}/fma_indra_segmental_innervation.tsv
+
+            namespace = fma
+            baseURI = "http://identifiers.org/fma/"
+            resourceId = "MIR:00000067"
+            priority = 23
+            labels = [SegmentalInnervation]
+        }
+
         ContextCellLine{
             path = ${KnowledgeBasesPath}/Cellosaurus.tsv
 
             namespace = cellosaurus
             hasSpeciesInfo = true
-            priority = 19
+            priority = 24
             species = [Human, Homo sapiens]
             labels = [CellLine]
         }
@@ -215,7 +265,7 @@ KnowledgeBases
             path = ${KnowledgeBasesPath}/atcc.tsv
 
             namespace = atcc
-            priority = 20
+            priority = 25
             labels = [CellLine]
         }
 
@@ -225,7 +275,7 @@ KnowledgeBases
             namespace = cl
             baseURI = "http://identifiers.org/cl/"
             resourceId = "MIR:00000110"
-            priority = 21
+            priority = 26
             labels = [CellType]
         }
 
@@ -235,7 +285,7 @@ KnowledgeBases
             namespace = uberon
             baseURI = "http://identifiers.org/uberon/"
             resourceId = "MIR:00000446"
-            priority = 22
+            priority = 27
             labels = [Organ]
             keyTransforms = [DefaultKeyTransforms, OrganAuxKeyTransforms, DefaultKeyTransforms]
         }
@@ -246,7 +296,7 @@ KnowledgeBases
             namespace = taxonomy
             baseURI = "http://identifiers.org/taxonomy/"
             resourceId = "MIR:00000006"
-            priority = 23
+            priority = 28
             labels = [Species]
         }
 
@@ -256,7 +306,7 @@ KnowledgeBases
             namespace = tissuelist
             baseURI = "http://identifiers.org/tissuelist/"
             resourceId = "MIR:00000360"
-            priority = 24
+            priority = 29
             labels = [TissueType]
         }