Skip to content

Commit 5c436b8

Browse files
cmllezrcmllezr
committed
added some classes
1 parent 25792ae commit 5c436b8

3 files changed

Lines changed: 210 additions & 18 deletions

File tree

‎src/ontology/components/cryo-axioms-shared.owl‎

Lines changed: 46 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,21 +1,61 @@
11
<?xml version="1.0"?>
2-
<rdf:RDF
3-
xml:base="https://w3id.org/pmd/"
4-
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
2+
<rdf:RDF xmlns="https://w3id.org/pmd/cryo/components/cryo-axioms-shared.owl/"
3+
xml:base="https://w3id.org/pmd/cryo/components/cryo-axioms-shared.owl/"
4+
xmlns:co="https://w3id.org/pmd/co/"
5+
xmlns:dc="http://purl.org/dc/elements/1.1/"
6+
xmlns:obo="http://purl.obolibrary.org/obo/"
57
xmlns:owl="http://www.w3.org/2002/07/owl#"
6-
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
8+
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
79
xmlns:xml="http://www.w3.org/XML/1998/namespace"
810
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
911
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
10-
xmlns:obo="http://purl.obolibrary.org/obo/">
12+
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
13+
xmlns:terms="http://purl.org/dc/terms/"
14+
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
1115
<owl:Ontology rdf:about="https://w3id.org/pmd/cryo/components/cryo-axioms-shared.owl">
1216
<owl:imports rdf:resource="https://w3id.org/pmd/cryo/components/cryo-entities.owl"/>
1317
<owl:imports rdf:resource="https://w3id.org/pmd/cryo/components/cryo-qualities.owl"/>
1418
</owl:Ontology>
1519

1620

1721

22+
<!--
23+
///////////////////////////////////////////////////////////////////////////////////////
24+
//
25+
// Classes
26+
//
27+
///////////////////////////////////////////////////////////////////////////////////////
28+
-->
29+
30+
1831

1932

20-
<!-- This is a placeholder, it will be regenerated when makefile is first executed -->
33+
<!-- https://w3id.org/pmd/cryo/CRYO_0000002 -->
34+
35+
<rdf:Description rdf:about="https://w3id.org/pmd/cryo/CRYO_0000002">
36+
<rdfs:subClassOf>
37+
<owl:Restriction>
38+
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000080"/>
39+
<owl:allValuesFrom rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000000"/>
40+
</owl:Restriction>
41+
</rdfs:subClassOf>
42+
</rdf:Description>
43+
44+
45+
46+
<!-- https://w3id.org/pmd/cryo/CRYO_0000006 -->
47+
48+
<rdf:Description rdf:about="https://w3id.org/pmd/cryo/CRYO_0000006">
49+
<rdfs:subClassOf>
50+
<owl:Restriction>
51+
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000080"/>
52+
<owl:allValuesFrom rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000000"/>
53+
</owl:Restriction>
54+
</rdfs:subClassOf>
55+
</rdf:Description>
2156
</rdf:RDF>
57+
58+
59+
60+
<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->
61+

‎src/ontology/components/cryo-entities.owl‎

Lines changed: 59 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,69 @@
11
<?xml version="1.0"?>
2-
<rdf:RDF
3-
xml:base="https://w3id.org/pmd/"
4-
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
2+
<rdf:RDF xmlns="https://w3id.org/pmd/cryo/components/cryo-entities.owl/"
3+
xml:base="https://w3id.org/pmd/cryo/components/cryo-entities.owl/"
4+
xmlns:co="https://w3id.org/pmd/co/"
5+
xmlns:dc="http://purl.org/dc/elements/1.1/"
6+
xmlns:obo="http://purl.obolibrary.org/obo/"
57
xmlns:owl="http://www.w3.org/2002/07/owl#"
6-
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
8+
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
79
xmlns:xml="http://www.w3.org/XML/1998/namespace"
810
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
911
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
10-
xmlns:obo="http://purl.obolibrary.org/obo/">
12+
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
13+
xmlns:terms="http://purl.org/dc/terms/"
14+
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
1115
<owl:Ontology rdf:about="https://w3id.org/pmd/cryo/components/cryo-entities.owl">
1216
<owl:imports rdf:resource="https://w3id.org/pmd/cryo/components/cryo-shared.owl"/>
1317
</owl:Ontology>
18+
19+
20+
21+
<!--
22+
///////////////////////////////////////////////////////////////////////////////////////
23+
//
24+
// Classes
25+
//
26+
///////////////////////////////////////////////////////////////////////////////////////
27+
-->
28+
29+
30+
31+
32+
<!-- https://w3id.org/pmd/cryo/CRYO_0000000 -->
1433

15-
<!-- This is a placeholder, it will be regenerated when makefile is first executed -->
34+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000000">
35+
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000029"/>
36+
<rdfs:label xml:lang="en">unit cell</rdfs:label>
37+
<skos:definition xml:lang="en">Unit cell is a site which is a part of a crystal lattice and represents the smallest volume, where the lattice can be constructed by translational displacements. Thus, unit cell is characterized by the length of its sides and their angular relations.</skos:definition>
38+
</owl:Class>
39+
40+
41+
42+
<!-- https://w3id.org/pmd/cryo/CRYO_0000001 -->
43+
44+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000001">
45+
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000029"/>
46+
<rdfs:subClassOf>
47+
<owl:Restriction>
48+
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
49+
<owl:someValuesFrom rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000000"/>
50+
</owl:Restriction>
51+
</rdfs:subClassOf>
52+
<rdfs:subClassOf>
53+
<owl:Restriction>
54+
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
55+
<owl:someValuesFrom rdf:resource="https://w3id.org/pmd/co/PMD_0020003"/>
56+
</owl:Restriction>
57+
</rdfs:subClassOf>
58+
<rdfs:comment xml:lang="en">TODO:
59+
1. check if located in is meant to be used this way
60+
2. Is there a better alternative to has part?</rdfs:comment>
61+
<rdfs:label xml:lang="en">lattice</rdfs:label>
62+
<skos:definition xml:lang="en">Lattice is a site that is formed by a two- or three-dimensional periodic array of points in space, which describes the arrangement of atoms or molecules in a crystal.</skos:definition>
63+
</owl:Class>
1664
</rdf:RDF>
65+
66+
67+
68+
<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->
69+

‎src/ontology/components/cryo-qualities.owl‎

Lines changed: 105 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,115 @@
11
<?xml version="1.0"?>
2-
<rdf:RDF
3-
xml:base="https://w3id.org/pmd/"
4-
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
2+
<rdf:RDF xmlns="https://w3id.org/pmd/cryo/components/cryo-qualities.owl/"
3+
xml:base="https://w3id.org/pmd/cryo/components/cryo-qualities.owl/"
4+
xmlns:co="https://w3id.org/pmd/co/"
5+
xmlns:dc="http://purl.org/dc/elements/1.1/"
6+
xmlns:obo="http://purl.obolibrary.org/obo/"
57
xmlns:owl="http://www.w3.org/2002/07/owl#"
6-
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
8+
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
79
xmlns:xml="http://www.w3.org/XML/1998/namespace"
810
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
911
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
10-
xmlns:obo="http://purl.obolibrary.org/obo/">
12+
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
13+
xmlns:terms="http://purl.org/dc/terms/"
14+
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
1115
<owl:Ontology rdf:about="https://w3id.org/pmd/cryo/components/cryo-qualities.owl">
1216
<owl:imports rdf:resource="https://w3id.org/pmd/cryo/components/cryo-shared.owl"/>
1317
</owl:Ontology>
18+
19+
20+
21+
<!--
22+
///////////////////////////////////////////////////////////////////////////////////////
23+
//
24+
// Classes
25+
//
26+
///////////////////////////////////////////////////////////////////////////////////////
27+
-->
28+
29+
30+
31+
32+
<!-- https://w3id.org/pmd/cryo/CRYO_0000002 -->
33+
34+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000002">
35+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/co/PMD_0040001"/>
36+
<rdfs:label xml:lang="en">lattice parameter</rdfs:label>
37+
<skos:definition xml:lang="en">Lattice parameter is a quality of a unit cell which describes the length of (three) dimensions along of thwe unit cell&apos;s x-, y-, and z-directions.</skos:definition>
38+
</owl:Class>
39+
40+
41+
42+
<!-- https://w3id.org/pmd/cryo/CRYO_0000003 -->
43+
44+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000003">
45+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000002"/>
46+
<rdfs:label xml:lang="en">a lattice parameter</rdfs:label>
47+
<skos:definition xml:lang="en">A length of a unit cell along its x-axis</skos:definition>
48+
</owl:Class>
49+
50+
51+
52+
<!-- https://w3id.org/pmd/cryo/CRYO_0000004 -->
53+
54+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000004">
55+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000002"/>
56+
<rdfs:label xml:lang="en">b lattice parameter</rdfs:label>
57+
<skos:definition xml:lang="en">A length of a unit cell along its y-axis</skos:definition>
58+
</owl:Class>
59+
60+
61+
62+
<!-- https://w3id.org/pmd/cryo/CRYO_0000005 -->
1463

15-
<!-- This is a placeholder, it will be regenerated when makefile is first executed -->
64+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000005">
65+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000002"/>
66+
<rdfs:label xml:lang="en">c lattice parameter</rdfs:label>
67+
<skos:definition xml:lang="en">A length of a unit cell along its z-axis</skos:definition>
68+
</owl:Class>
69+
70+
71+
72+
<!-- https://w3id.org/pmd/cryo/CRYO_0000006 -->
73+
74+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000006">
75+
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000145"/>
76+
<rdfs:comment>TODO check the naming conventions</rdfs:comment>
77+
<rdfs:label xml:lang="en">angular lattice parameter</rdfs:label>
78+
<skos:definition xml:lang="en">Angular lattice parameter is a relational quality between two axes in a unit cell</skos:definition>
79+
</owl:Class>
80+
81+
82+
83+
<!-- https://w3id.org/pmd/cryo/CRYO_0000007 -->
84+
85+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000007">
86+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000006"/>
87+
<rdfs:label xml:lang="en">α lattice parameter</rdfs:label>
88+
<skos:definition xml:lang="en">α lattice parameter is an anlge between y- and z-directions in a unit cell</skos:definition>
89+
</owl:Class>
90+
91+
92+
93+
<!-- https://w3id.org/pmd/cryo/CRYO_0000008 -->
94+
95+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000008">
96+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000006"/>
97+
<rdfs:label xml:lang="en">β lattice parameter</rdfs:label>
98+
<skos:definition xml:lang="en">β lattice parameter is an anlge between x- and z-directions in a unit cell</skos:definition>
99+
</owl:Class>
100+
101+
102+
103+
<!-- https://w3id.org/pmd/cryo/CRYO_0000009 -->
104+
105+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000009">
106+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000006"/>
107+
<rdfs:label xml:lang="en">γ lattice parameter</rdfs:label>
108+
<skos:definition xml:lang="en">γ lattice parameter is an anlge between x- and z-directions in a unit cell</skos:definition>
109+
</owl:Class>
16110
</rdf:RDF>
111+
112+
113+
114+
<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->
115+

0 commit comments

Comments
 (0)