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Dev #59

Merged
merged 52 commits into from
Dec 8, 2023
Merged

Dev #59

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ada38d3
add list of element identifiers
srmnitc Dec 1, 2023
98aee13
update routine for element
srmnitc Dec 1, 2023
e332af2
update manifest
srmnitc Dec 1, 2023
4e7d19d
bug fix in assigning element identifiers
srmnitc Dec 1, 2023
2c880ea
add unit cell properties
srmnitc Dec 1, 2023
2574f6b
update graph, atoms work in progress
srmnitc Dec 1, 2023
af5ef9f
update atom mapping
srmnitc Dec 4, 2023
c73fe0a
update structure store
srmnitc Dec 4, 2023
6c5c13a
add identifiers
srmnitc Dec 4, 2023
8e35a46
add unique identifier
srmnitc Dec 4, 2023
bc5084e
update graph
srmnitc Dec 4, 2023
b02e4dc
update graph for uriref prep
srmnitc Dec 4, 2023
788e127
add skeleton for schema
srmnitc Dec 4, 2023
f74ae59
overhaul properties
srmnitc Dec 4, 2023
90842c5
add better data access
srmnitc Dec 4, 2023
21121f9
remove data
srmnitc Dec 4, 2023
adc5306
further fixes to remove data
srmnitc Dec 4, 2023
3eed167
fix minor bugs
srmnitc Dec 4, 2023
05f6261
update graphs
srmnitc Dec 4, 2023
f2cc569
Merge pull request #54 from pyscal/metaschema
srmnitc Dec 4, 2023
ae4362d
remove names
srmnitc Dec 4, 2023
bce40c2
remove BNodes
srmnitc Dec 4, 2023
40fae5e
remove stray BNodes
srmnitc Dec 4, 2023
f5d8dd0
update visualisation
srmnitc Dec 4, 2023
f75e530
Merge pull request #55 from pyscal/update_identifiers
srmnitc Dec 4, 2023
07f3ec3
save positions and species to file
srmnitc Dec 4, 2023
da135af
fix path name
srmnitc Dec 4, 2023
df19ce5
save file
srmnitc Dec 4, 2023
3542864
separate serialise function
srmnitc Dec 4, 2023
42d6c48
separate atom serialisation
srmnitc Dec 4, 2023
f3efffa
fix method to extract sample
srmnitc Dec 4, 2023
3cf07fa
add publish method
srmnitc Dec 4, 2023
7ca830f
add possibility to zip
srmnitc Dec 4, 2023
1049ee1
add possibility to zip
srmnitc Dec 4, 2023
43548d2
update unpack
srmnitc Dec 4, 2023
8c2369e
debug archive method
srmnitc Dec 5, 2023
dfe7f8c
Merge pull request #56 from pyscal/update_identifiers
srmnitc Dec 5, 2023
89670df
Merge pull request #57 from pyscal/restructure_atom_attributes
srmnitc Dec 5, 2023
88a8600
add archive functionality
srmnitc Dec 5, 2023
cc9dab0
Merge pull request #58 from pyscal/update_identifiers
srmnitc Dec 5, 2023
9b8bf9f
remove object store
srmnitc Dec 5, 2023
17599d3
update units
srmnitc Dec 5, 2023
739b9cc
add fix for viz
srmnitc Dec 5, 2023
b17ed80
add fix for viz
srmnitc Dec 5, 2023
a8c14af
add workflow view to visualisation
srmnitc Dec 6, 2023
f6a9a2b
add potential aso mappings
srmnitc Dec 6, 2023
bf3d0db
update ontology to ce1228377e5371e0306f1c70fc8711a088e66227
srmnitc Dec 8, 2023
d20aac2
update ontology mappings
srmnitc Dec 8, 2023
514cfcc
update docs
srmnitc Dec 8, 2023
f8ebc6f
Bump version: 0.0.18 → 0.1.0
srmnitc Dec 8, 2023
0763a07
update properties to return None
srmnitc Dec 8, 2023
0bb2141
Bump version: 0.1.0 → 0.1.1
srmnitc Dec 8, 2023
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2 changes: 1 addition & 1 deletion .bumpversion.cfg
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@@ -1,5 +1,5 @@
[bumpversion]
current_version = 0.0.18
current_version = 0.1.1
commit = True
tag = False

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2 changes: 1 addition & 1 deletion MANIFEST.in
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@@ -1 +1 @@
include pyscal_rdf/data/*.owl
include pyscal_rdf/data/*.??l
7,279 changes: 3,008 additions & 4,271 deletions examples/01_getting_started.ipynb
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52 changes: 40 additions & 12 deletions examples/02_grain_boundaries.ipynb
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1,087 changes: 1,087 additions & 0 deletions pyscal_rdf/data/asmo.owl
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165 changes: 116 additions & 49 deletions pyscal_rdf/data/cmso.owl
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Expand Up @@ -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">
Expand Down Expand Up @@ -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">
Expand All @@ -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>


Expand All @@ -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"/>
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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>


Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand Down Expand Up @@ -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">
Expand All @@ -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">
Expand All @@ -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">
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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>


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61 changes: 61 additions & 0 deletions pyscal_rdf/data/element.yml
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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
56 changes: 0 additions & 56 deletions pyscal_rdf/data/msmo.owl
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