From f6a9a2b7412055875ece795b31f2c3752a903d4a Mon Sep 17 00:00:00 2001
From: Sarath Menon <sarathmenon@mailbox.org>
Date: Wed, 6 Dec 2023 15:26:06 +0100
Subject: [PATCH] add potential aso mappings

---
 pyscal_rdf/data/msmo.owl       | 56 ----------------------------------
 pyscal_rdf/network/ontology.py | 16 +++++-----
 2 files changed, 8 insertions(+), 64 deletions(-)
 delete mode 100644 pyscal_rdf/data/msmo.owl

diff --git a/pyscal_rdf/data/msmo.owl b/pyscal_rdf/data/msmo.owl
deleted file mode 100644
index ec9843f..0000000
--- a/pyscal_rdf/data/msmo.owl
+++ /dev/null
@@ -1,56 +0,0 @@
-<?xml version="1.0"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-         xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-         xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-         xmlns:owl="http://www.w3.org/2002/07/owl#"
-         xml:base="http://purls.helmholtz-metadaten.de/msmo/"
-         xmlns="http://purls.helmholtz-metadaten.de/msmo/">
-
-<owl:Ontology rdf:about="http://purls.helmholtz-metadaten.de/msmo"/>
-
-<owl:Class rdf:about="ComputationalMethod">
-  <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
-</owl:Class>
-
-<owl:Class rdf:about="AtomisticMethod">
-  <rdfs:subClassOf rdf:resource="ComputationalMethod"/>
-</owl:Class>
-
-<owl:Class rdf:about="Calculation">
-  <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
-</owl:Class>
-
-<owl:Class rdf:about="DensityFunctionalTheory">
-  <rdfs:subClassOf rdf:resource="AtomisticMethod"/>
-</owl:Class>
-
-<owl:Class rdf:about="MolecularDynamics">
-  <rdfs:subClassOf rdf:resource="AtomisticMethod"/>
-</owl:Class>
-
-<owl:Class rdf:about="AbinitioMolecularDynamics">
-  <rdfs:subClassOf rdf:resource="AtomisticMethod"/>
-</owl:Class>
-
-<owl:Class rdf:about="MonteCarloMethod">
-  <rdfs:subClassOf rdf:resource="ComputationalMethod"/>
-</owl:Class>
-
-<owl:Class rdf:about="KineticMonteCarloMethod">
-  <rdfs:subClassOf rdf:resource="MonteCarloMethod"/>
-</owl:Class>
-
-<owl:Class rdf:about="MolecularDynamicsMinimization">
-  <rdfs:subClassOf rdf:resource="MolecularDynamics"/>
-</owl:Class>
-
-<owl:Class rdf:about="MolecularDynamicsNPT">
-  <rdfs:subClassOf rdf:resource="MolecularDynamics"/>
-</owl:Class>
-
-<owl:Class rdf:about="MolecularDynamicsNVT">
-  <rdfs:subClassOf rdf:resource="MolecularDynamics"/>
-</owl:Class>
-
-
-</rdf:RDF>
diff --git a/pyscal_rdf/network/ontology.py b/pyscal_rdf/network/ontology.py
index dc2c8f8..5e86ecb 100644
--- a/pyscal_rdf/network/ontology.py
+++ b/pyscal_rdf/network/ontology.py
@@ -10,11 +10,11 @@ def read_ontology():
 	cmso = OntologyNetwork(os.path.join(file_location,  'data/cmso.owl'))
 	pldo = OntologyNetwork(os.path.join(file_location,  'data/pldo.owl'))
 	podo = OntologyNetwork(os.path.join(file_location,  'data/podo.owl'))
-	msmo = OntologyNetwork(os.path.join(file_location,  'data/msmo.owl'))
+	#msmo = OntologyNetwork(os.path.join(file_location,  'data/msmo.owl'))
 	
 	#combine them
-	combo = cmso + pldo + podo + msmo	
-	#combo = cmso + pldo + podo
+	#combo = cmso + pldo + podo + msmo	
+	combo = cmso + pldo + podo
 
 	#add namespaces
 	combo.add_namespace('prov', 'http://www.w3.org/ns/prov#')
@@ -33,17 +33,17 @@ def read_ontology():
 	combo.add_term('http://www.w3.org/1999/02/22-rdf-syntax-ns#type', 'object_property', delimiter='#', namespace='rdf')
 	
 	#add paths
+	combo.add_path(('cmso:CrystalStructure', 'cmso:hasAltName', 'string'))
 	combo.add_path(('cmso:Material', 'cmso:hasDefect', 'pldo:PlanarDefect'))
 	combo.add_path(('cmso:Material', 'cmso:hasDefect', 'podo:Vacancy'))
 	combo.add_path(('cmso:SimulationCell', 'podo:hasVacancyConcentration', 'float'))
 	combo.add_path(('cmso:SimulationCell', 'podo:hasNumberOfVacancies', 'int'))
 	combo.add_path(('cmso:ComputationalSample', 'prov:wasDerivedFrom', 'cmso:ComputationalSample'))
-	combo.add_path(('cmso:ComputationalSample', 'prov:wasGeneratedBy', 'msmo:ComputationalMethod'))
-	combo.add_path(('msmo:ComputationalMethod', 'prov:wasAssociatedWith', 'prov:SoftwareAgent'))
 	combo.add_path(('cmso:ComputationalSample', 'rdf:type', 'prov:Entity'))
-	combo.add_path(('msmo:ComputationalMethod', 'rdf:type', 'prov:Activity'))
-	#for Alt Name, maybe this should not be here
-	combo.add_path(('cmso:CrystalStructure', 'cmso:hasAltName', 'string'))
+	#combo.add_path(('aso:StructureOptimization', 'rdf:type', 'prov:Activity'))	
+	#combo.add_path(('aso:StructureOptimization', 'prov:wasAssociatedWith', 'prov:SoftwareAgent'))
+	#combo.add_path(('cmso:ComputationalSample', 'prov:wasGeneratedBy', 'aso:StructureOptimization'))
+	
 	
 	#return
 	return combo
\ No newline at end of file