Merge pull request #59 from pyscal/dev

Dev
pyscal · Dec 8, 2023 · 764ac01 · 764ac01
2 parents 6fd1c06 + 0bb2141
commit 764ac01
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.18
+current_version = 0.1.1
 commit = True
 tag = False
 

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +1 @@
-include pyscal_rdf/data/*.owl
+include pyscal_rdf/data/*.??l
diff --git a/examples/01_getting_started.ipynb b/examples/01_getting_started.ipynb
diff --git a/examples/02_grain_boundaries.ipynb b/examples/02_grain_boundaries.ipynb
diff --git a/pyscal_rdf/data/asmo.owl b/pyscal_rdf/data/asmo.owl
diff --git a/pyscal_rdf/data/cmso.owl b/pyscal_rdf/data/cmso.owl
@@ -231,17 +231,6 @@
 
 
 
-    <!-- http://purls.helmholtz-metadaten.de/cmso/hasAtom -->
-
-    <owl:ObjectProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasAtom">
-        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/AtomicScaleSample"/>
-        <rdfs:range rdf:resource="http://purls.helmholtz-metadaten.de/cmso/Atom"/>
-        <rdfs:label>has atom</rdfs:label>
-        <skos:definition>The relation between an atomic scale sample and the atoms it contains.</skos:definition>
-    </owl:ObjectProperty>
-
-
-
     <!-- http://purls.helmholtz-metadaten.de/cmso/hasBasis -->
 
     <owl:ObjectProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasBasis">
@@ -322,25 +311,6 @@
 
 
 
-    <!-- http://purls.helmholtz-metadaten.de/cmso/hasPositionVector -->
-
-    <owl:ObjectProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasPositionVector">
-        <rdfs:subPropertyOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/hasVector"/>
-        <rdfs:domain>
-            <owl:Class>
-                <owl:unionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purls.helmholtz-metadaten.de/cmso/Atom"/>
-                    <rdf:Description rdf:about="http://purls.helmholtz-metadaten.de/cmso/Basis"/>
-                </owl:unionOf>
-            </owl:Class>
-        </rdfs:domain>
-        <rdfs:range rdf:resource="http://purls.helmholtz-metadaten.de/cmso/PositionVector"/>
-        <rdfs:label>has position vector</rdfs:label>
-        <skos:definition>The relation between an atom or basis and its position vector.</skos:definition>
-    </owl:ObjectProperty>
-
-
-
     <!-- http://purls.helmholtz-metadaten.de/cmso/hasSimulationCell -->
 
     <owl:ObjectProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasSimulationCell">
@@ -366,10 +336,10 @@
     <!-- http://purls.helmholtz-metadaten.de/cmso/hasSpecies -->
 
     <owl:ObjectProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasSpecies">
-        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/Material"/>
+        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/ComputationalSample"/>
         <rdfs:range rdf:resource="http://purls.helmholtz-metadaten.de/cmso/ChemicalSpecies"/>
         <rdfs:label>has species</rdfs:label>
-        <skos:definition>The relation between a material and the species that constitutes it.</skos:definition>
+        <skos:definition>The relation between a computational sample and the species that constitutes it.</skos:definition>
     </owl:ObjectProperty>
 
 
@@ -392,6 +362,7 @@
             <owl:Class>
                 <owl:unionOf rdf:parseType="Collection">
                     <rdf:Description rdf:about="http://purls.helmholtz-metadaten.de/cmso/Angle"/>
+                    <rdf:Description rdf:about="http://purls.helmholtz-metadaten.de/cmso/AtomAttribute"/>
                     <rdf:Description rdf:about="http://purls.helmholtz-metadaten.de/cmso/CalculatedProperty"/>
                     <rdf:Description rdf:about="http://purls.helmholtz-metadaten.de/cmso/Length"/>
                     <rdf:Description rdf:about="http://purls.helmholtz-metadaten.de/cmso/Vector"/>
@@ -514,6 +485,18 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cmso/hasAtomicPercent -->
+
+    <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasAtomicPercent">
+        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/ChemicalElement"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+        <rdfs:comment>abbreviated at.%</rdfs:comment>
+        <rdfs:label>has atomic percent</rdfs:label>
+        <skos:definition>A data property linking a chemical element with atomic percentage present in the material.</skos:definition>
+    </owl:DatatypeProperty>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cmso/hasChemicalSymbol -->
 
     <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasChemicalSymbol">
@@ -559,24 +542,25 @@
 
 
 
-    <!-- http://purls.helmholtz-metadaten.de/cmso/hasCoordinationNumber -->
+    <!-- http://purls.helmholtz-metadaten.de/cmso/hasElementRatio -->
 
-    <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasCoordinationNumber">
-        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/Atom"/>
-        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#integer"/>
-        <rdfs:label>has coordination number</rdfs:label>
-        <skos:definition>A data property linking an atom with its coordination number. The coordination number of an atom in an extended structure is the number of nearest neighbors.</skos:definition>
+    <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasElementRatio">
+        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/ChemicalElement"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+        <rdfs:comment>Indicated with a value from 0 to 1.</rdfs:comment>
+        <rdfs:label>has element ratio</rdfs:label>
+        <skos:definition>A data property linking a chemical element with the ratio or fraction of it in the material.</skos:definition>
     </owl:DatatypeProperty>
 
 
 
-    <!-- http://purls.helmholtz-metadaten.de/cmso/hasElementRatio -->
+    <!-- http://purls.helmholtz-metadaten.de/cmso/hasIdentifier -->
 
-    <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasElementRatio">
-        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/Material"/>
+    <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasIdentifier">
+        <rdfs:domain rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
         <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
-        <rdfs:label>has element ratio</rdfs:label>
-        <skos:definition>A data property linking a material with the ratio or fraction of an element that constitutes it. Comment: indicated with a value from 0 to 1.</skos:definition>
+        <rdfs:label>has identifier</rdfs:label>
+        <skos:definition>A data property linking an entity with an identifier (internal or external) that represents the entity.</skos:definition>
     </owl:DatatypeProperty>
 
 
@@ -657,6 +641,17 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cmso/hasPath -->
+
+    <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasPath">
+        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/AtomAttribute"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
+        <rdfs:label>has path</rdfs:label>
+        <skos:definition>A data property linking an atom attribute (per atom quantity) with the path pointing to the file where the data is stored.</skos:definition>
+    </owl:DatatypeProperty>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cmso/hasReference -->
 
     <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasReference">
@@ -756,6 +751,18 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cmso/hasWeightPercent -->
+
+    <owl:DatatypeProperty rdf:about="http://purls.helmholtz-metadaten.de/cmso/hasWeightPercent">
+        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cmso/ChemicalElement"/>
+        <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+        <rdfs:comment>abbreviated wt.%</rdfs:comment>
+        <rdfs:label>has weight percent</rdfs:label>
+        <skos:definition>A data property linking a chemical element with percentage by mass present in the material.</skos:definition>
+    </owl:DatatypeProperty>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -799,6 +806,36 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cmso/AtomAttribute -->
+
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/AtomAttribute">
+        <rdfs:label>Atom Attribute</rdfs:label>
+        <skos:definition>Atom attribute refers to the features or quantities per atom of an atomic scale sample.</skos:definition>
+    </owl:Class>
+
+
+
+    <!-- http://purls.helmholtz-metadaten.de/cmso/AtomicForce -->
+
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/AtomicForce">
+        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/AtomAttribute"/>
+        <rdfs:label>Atomic Force</rdfs:label>
+        <skos:definition>Atomic force refers to the vector that represents the force of each atom.</skos:definition>
+    </owl:Class>
+
+
+
+    <!-- http://purls.helmholtz-metadaten.de/cmso/AtomicPosition -->
+
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/AtomicPosition">
+        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/AtomAttribute"/>
+        <rdfs:comment>Cartesian coordinates are preferred over direct (or fractional) coordinates.</rdfs:comment>
+        <rdfs:label>Atomic Position</rdfs:label>
+        <skos:definition>Atomic position refers to the vector that represents the position of each atom.</skos:definition>
+    </owl:Class>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cmso/AtomicScaleSample -->
 
     <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/AtomicScaleSample">
@@ -809,6 +846,16 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cmso/AtomicVelocity -->
+
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/AtomicVelocity">
+        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/AtomAttribute"/>
+        <rdfs:label>Atomic Velocity</rdfs:label>
+        <skos:definition>Atomic velocity refers to the vector that represents the velocity of each atom.</skos:definition>
+    </owl:Class>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cmso/Basis -->
 
     <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/Basis">
@@ -827,6 +874,15 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cmso/ChemicalComposition -->
+
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/ChemicalComposition">
+        <rdfs:label>Chemical Composition</rdfs:label>
+        <skos:definition>Chemical composition refers to the type, arrangement and ratio of the chemical elements of a compound (or material).</skos:definition>
+    </owl:Class>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cmso/ChemicalElement -->
 
     <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/ChemicalElement">
@@ -857,6 +913,17 @@
 
 
 
+    <!-- http://purls.helmholtz-metadaten.de/cmso/CoordinationNumber -->
+
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/CoordinationNumber">
+        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/AtomAttribute"/>
+        <rdfs:comment>In the case of molecules, it refers to the number of atoms, molecules or ions bonded to a central atom of the molecule. Also known as ligancy.</rdfs:comment>
+        <rdfs:label>Coordination Number</rdfs:label>
+        <skos:definition>Coordination number refers to the number of neighbors of each atom.</skos:definition>
+    </owl:Class>
+
+
+
     <!-- http://purls.helmholtz-metadaten.de/cmso/CrystalDefect -->
 
     <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/CrystalDefect">
@@ -1013,13 +1080,13 @@
 
 
 
-    <!-- http://purls.helmholtz-metadaten.de/cmso/PositionVector -->
+    <!-- http://purls.helmholtz-metadaten.de/cmso/Occupancy -->
 
-    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/PositionVector">
-        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/Vector"/>
-        <rdfs:comment>Cartesian coordinates are preferred over direct (or fractional) coordinates.</rdfs:comment>
-        <rdfs:label>Position Vector</rdfs:label>
-        <skos:definition>The position vector is a vector that represents the position of the atoms.</skos:definition>
+    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cmso/Occupancy">
+        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cmso/AtomAttribute"/>
+        <rdfs:comment>Note the difference from a total ratio or percentage of the occupancy of a site in the crystal structure (as defined in CIF)</rdfs:comment>
+        <rdfs:label>Occupancy</rdfs:label>
+        <skos:definition>Occupancy refers to the atom type at each lattice site.</skos:definition>
     </owl:Class>
 
 

diff --git a/pyscal_rdf/data/element.yml b/pyscal_rdf/data/element.yml
@@ -0,0 +1,61 @@
+Ac: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33337
+Ag: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30512
+Al: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28984
+Ar: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49475
+Au: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29287
+Ba: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32594
+Be: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30501
+Ca: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:22984
+Cd: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:22977
+Ce: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33369
+Co: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27638
+Cr: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28073
+Cs: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30514
+Cu: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28694
+Dy: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33377
+Er: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33379
+Eu: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32999
+Fe: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18248
+Gd: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33375
+Ge: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30441
+He: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30217
+Hf: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33343
+Ho: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49648
+Ir: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49666
+Kr: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49696
+La: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33336
+Li: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30145
+Lu: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33382
+Mg: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:25107
+Mo: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28685
+Na: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:26708
+Nb: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33344
+Nd: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33372
+Ne: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33310
+Ni: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28112
+Os: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30687
+Pb: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:25016
+Pd: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33363
+Po: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33313
+Pr: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49828
+Pt: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33364
+Rb: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33322
+Re: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49882
+Rh: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33359
+Ru: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30682
+Sc: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33330
+Se: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27568
+Si: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27573
+Sr: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33324
+Ta: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33348
+Tb: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33376
+Tc: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33353
+Te: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30452
+Th: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33385
+Ti: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33341
+Tl: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30440
+Tm: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33380
+Xe: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49957
+Yb: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33381
+Zn: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27363
+Zr: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33342
diff --git a/pyscal_rdf/data/msmo.owl b/pyscal_rdf/data/msmo.owl