Skip to content

Commit 690d2fe

Browse files
github-actions[bot]github-actions[bot]
committed
updated ontology
1 parent 5c436b8 commit 690d2fe

9 files changed

Lines changed: 773 additions & 1 deletion

File tree

‎src/ontology/cryo-base.owl‎

Lines changed: 146 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -188,6 +188,18 @@
188188

189189

190190

191+
<!-- http://purl.obolibrary.org/obo/RO_0000080 -->
192+
193+
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000080"/>
194+
195+
196+
197+
<!-- http://purl.obolibrary.org/obo/RO_0001025 -->
198+
199+
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001025"/>
200+
201+
202+
191203
<!-- http://purl.obolibrary.org/obo/RO_0009006 -->
192204

193205
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0009006"/>
@@ -420,6 +432,12 @@ RO&apos;s &apos;quality of&apos; is functional i.e., a-&gt;b, a-&gt;c =&gt; b=c.
420432

421433

422434

435+
<!-- http://purl.obolibrary.org/obo/BFO_0000029 -->
436+
437+
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000029"/>
438+
439+
440+
423441
<!-- http://purl.obolibrary.org/obo/BFO_0000030 -->
424442

425443
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000030"/>
@@ -3834,6 +3852,134 @@ The molar ratio of carbon dioxide to average atmosphere air is 420 ppm as of 202
38343852

38353853

38363854

3855+
<!-- https://w3id.org/pmd/cryo/CRYO_0000000 -->
3856+
3857+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000000">
3858+
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000029"/>
3859+
<rdfs:label xml:lang="en">unit cell</rdfs:label>
3860+
<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>
3861+
</owl:Class>
3862+
3863+
3864+
3865+
<!-- https://w3id.org/pmd/cryo/CRYO_0000001 -->
3866+
3867+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000001">
3868+
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000029"/>
3869+
<rdfs:subClassOf>
3870+
<owl:Restriction>
3871+
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
3872+
<owl:someValuesFrom rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000000"/>
3873+
</owl:Restriction>
3874+
</rdfs:subClassOf>
3875+
<rdfs:subClassOf>
3876+
<owl:Restriction>
3877+
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
3878+
<owl:someValuesFrom rdf:resource="https://w3id.org/pmd/co/PMD_0020003"/>
3879+
</owl:Restriction>
3880+
</rdfs:subClassOf>
3881+
<rdfs:comment xml:lang="en">TODO:
3882+
1. check if located in is meant to be used this way
3883+
2. Is there a better alternative to has part?</rdfs:comment>
3884+
<rdfs:label xml:lang="en">lattice</rdfs:label>
3885+
<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>
3886+
</owl:Class>
3887+
3888+
3889+
3890+
<!-- https://w3id.org/pmd/cryo/CRYO_0000002 -->
3891+
3892+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000002">
3893+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/co/PMD_0040001"/>
3894+
<rdfs:subClassOf>
3895+
<owl:Restriction>
3896+
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000080"/>
3897+
<owl:allValuesFrom rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000000"/>
3898+
</owl:Restriction>
3899+
</rdfs:subClassOf>
3900+
<rdfs:label xml:lang="en">lattice parameter</rdfs:label>
3901+
<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>
3902+
</owl:Class>
3903+
3904+
3905+
3906+
<!-- https://w3id.org/pmd/cryo/CRYO_0000003 -->
3907+
3908+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000003">
3909+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000002"/>
3910+
<rdfs:label xml:lang="en">a lattice parameter</rdfs:label>
3911+
<skos:definition xml:lang="en">A length of a unit cell along its x-axis</skos:definition>
3912+
</owl:Class>
3913+
3914+
3915+
3916+
<!-- https://w3id.org/pmd/cryo/CRYO_0000004 -->
3917+
3918+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000004">
3919+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000002"/>
3920+
<rdfs:label xml:lang="en">b lattice parameter</rdfs:label>
3921+
<skos:definition xml:lang="en">A length of a unit cell along its y-axis</skos:definition>
3922+
</owl:Class>
3923+
3924+
3925+
3926+
<!-- https://w3id.org/pmd/cryo/CRYO_0000005 -->
3927+
3928+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000005">
3929+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000002"/>
3930+
<rdfs:label xml:lang="en">c lattice parameter</rdfs:label>
3931+
<skos:definition xml:lang="en">A length of a unit cell along its z-axis</skos:definition>
3932+
</owl:Class>
3933+
3934+
3935+
3936+
<!-- https://w3id.org/pmd/cryo/CRYO_0000006 -->
3937+
3938+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000006">
3939+
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000145"/>
3940+
<rdfs:subClassOf>
3941+
<owl:Restriction>
3942+
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000080"/>
3943+
<owl:allValuesFrom rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000000"/>
3944+
</owl:Restriction>
3945+
</rdfs:subClassOf>
3946+
<rdfs:comment>TODO check the naming conventions</rdfs:comment>
3947+
<rdfs:label xml:lang="en">angular lattice parameter</rdfs:label>
3948+
<skos:definition xml:lang="en">Angular lattice parameter is a relational quality between two axes in a unit cell</skos:definition>
3949+
</owl:Class>
3950+
3951+
3952+
3953+
<!-- https://w3id.org/pmd/cryo/CRYO_0000007 -->
3954+
3955+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000007">
3956+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000006"/>
3957+
<rdfs:label xml:lang="en">α lattice parameter</rdfs:label>
3958+
<skos:definition xml:lang="en">α lattice parameter is an anlge between y- and z-directions in a unit cell</skos:definition>
3959+
</owl:Class>
3960+
3961+
3962+
3963+
<!-- https://w3id.org/pmd/cryo/CRYO_0000008 -->
3964+
3965+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000008">
3966+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000006"/>
3967+
<rdfs:label xml:lang="en">β lattice parameter</rdfs:label>
3968+
<skos:definition xml:lang="en">β lattice parameter is an anlge between x- and z-directions in a unit cell</skos:definition>
3969+
</owl:Class>
3970+
3971+
3972+
3973+
<!-- https://w3id.org/pmd/cryo/CRYO_0000009 -->
3974+
3975+
<owl:Class rdf:about="https://w3id.org/pmd/cryo/CRYO_0000009">
3976+
<rdfs:subClassOf rdf:resource="https://w3id.org/pmd/cryo/CRYO_0000006"/>
3977+
<rdfs:label xml:lang="en">γ lattice parameter</rdfs:label>
3978+
<skos:definition xml:lang="en">γ lattice parameter is an anlge between x- and z-directions in a unit cell</skos:definition>
3979+
</owl:Class>
3980+
3981+
3982+
38373983
<!--
38383984
///////////////////////////////////////////////////////////////////////////////////////
38393985
//

‎src/ontology/cryo-base.ttl‎

Lines changed: 102 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -123,6 +123,14 @@ obo:RO_0000056 rdf:type owl:ObjectProperty .
123123
obo:RO_0000058 rdf:type owl:ObjectProperty .
124124

125125

126+
### http://purl.obolibrary.org/obo/RO_0000080
127+
obo:RO_0000080 rdf:type owl:ObjectProperty .
128+
129+
130+
### http://purl.obolibrary.org/obo/RO_0001025
131+
obo:RO_0001025 rdf:type owl:ObjectProperty .
132+
133+
126134
### http://purl.obolibrary.org/obo/RO_0009006
127135
obo:RO_0009006 rdf:type owl:ObjectProperty .
128136

@@ -282,6 +290,10 @@ obo:BFO_0000024 rdf:type owl:Class .
282290
obo:BFO_0000027 rdf:type owl:Class .
283291

284292

293+
### http://purl.obolibrary.org/obo/BFO_0000029
294+
obo:BFO_0000029 rdf:type owl:Class .
295+
296+
285297
### http://purl.obolibrary.org/obo/BFO_0000030
286298
obo:BFO_0000030 rdf:type owl:Class .
287299

@@ -2753,6 +2765,96 @@ co:PMD_0050157 rdf:type owl:Class ;
27532765
"Examples include shapes like cubes, spheres, and pyramids."@en .
27542766

27552767

2768+
### https://w3id.org/pmd/cryo/CRYO_0000000
2769+
<https://w3id.org/pmd/cryo/CRYO_0000000> rdf:type owl:Class ;
2770+
rdfs:subClassOf obo:BFO_0000029 ;
2771+
rdfs:label "unit cell"@en ;
2772+
skos:definition "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."@en .
2773+
2774+
2775+
### https://w3id.org/pmd/cryo/CRYO_0000001
2776+
<https://w3id.org/pmd/cryo/CRYO_0000001> rdf:type owl:Class ;
2777+
rdfs:subClassOf obo:BFO_0000029 ,
2778+
[ rdf:type owl:Restriction ;
2779+
owl:onProperty obo:BFO_0000051 ;
2780+
owl:someValuesFrom <https://w3id.org/pmd/cryo/CRYO_0000000>
2781+
] ,
2782+
[ rdf:type owl:Restriction ;
2783+
owl:onProperty obo:RO_0001025 ;
2784+
owl:someValuesFrom co:PMD_0020003
2785+
] ;
2786+
rdfs:comment """TODO:
2787+
1. check if located in is meant to be used this way
2788+
2. Is there a better alternative to has part?"""@en ;
2789+
rdfs:label "lattice"@en ;
2790+
skos:definition "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."@en .
2791+
2792+
2793+
### https://w3id.org/pmd/cryo/CRYO_0000002
2794+
<https://w3id.org/pmd/cryo/CRYO_0000002> rdf:type owl:Class ;
2795+
rdfs:subClassOf co:PMD_0040001 ,
2796+
[ rdf:type owl:Restriction ;
2797+
owl:onProperty obo:RO_0000080 ;
2798+
owl:allValuesFrom <https://w3id.org/pmd/cryo/CRYO_0000000>
2799+
] ;
2800+
rdfs:label "lattice parameter"@en ;
2801+
skos:definition "Lattice parameter is a quality of a unit cell which describes the length of (three) dimensions along of thwe unit cell's x-, y-, and z-directions."@en .
2802+
2803+
2804+
### https://w3id.org/pmd/cryo/CRYO_0000003
2805+
<https://w3id.org/pmd/cryo/CRYO_0000003> rdf:type owl:Class ;
2806+
rdfs:subClassOf <https://w3id.org/pmd/cryo/CRYO_0000002> ;
2807+
rdfs:label "a lattice parameter"@en ;
2808+
skos:definition "A length of a unit cell along its x-axis"@en .
2809+
2810+
2811+
### https://w3id.org/pmd/cryo/CRYO_0000004
2812+
<https://w3id.org/pmd/cryo/CRYO_0000004> rdf:type owl:Class ;
2813+
rdfs:subClassOf <https://w3id.org/pmd/cryo/CRYO_0000002> ;
2814+
rdfs:label "b lattice parameter"@en ;
2815+
skos:definition "A length of a unit cell along its y-axis"@en .
2816+
2817+
2818+
### https://w3id.org/pmd/cryo/CRYO_0000005
2819+
<https://w3id.org/pmd/cryo/CRYO_0000005> rdf:type owl:Class ;
2820+
rdfs:subClassOf <https://w3id.org/pmd/cryo/CRYO_0000002> ;
2821+
rdfs:label "c lattice parameter"@en ;
2822+
skos:definition "A length of a unit cell along its z-axis"@en .
2823+
2824+
2825+
### https://w3id.org/pmd/cryo/CRYO_0000006
2826+
<https://w3id.org/pmd/cryo/CRYO_0000006> rdf:type owl:Class ;
2827+
rdfs:subClassOf obo:BFO_0000145 ,
2828+
[ rdf:type owl:Restriction ;
2829+
owl:onProperty obo:RO_0000080 ;
2830+
owl:allValuesFrom <https://w3id.org/pmd/cryo/CRYO_0000000>
2831+
] ;
2832+
rdfs:comment "TODO check the naming conventions" ;
2833+
rdfs:label "angular lattice parameter"@en ;
2834+
skos:definition "Angular lattice parameter is a relational quality between two axes in a unit cell"@en .
2835+
2836+
2837+
### https://w3id.org/pmd/cryo/CRYO_0000007
2838+
<https://w3id.org/pmd/cryo/CRYO_0000007> rdf:type owl:Class ;
2839+
rdfs:subClassOf <https://w3id.org/pmd/cryo/CRYO_0000006> ;
2840+
rdfs:label "α lattice parameter"@en ;
2841+
skos:definition "α lattice parameter is an anlge between y- and z-directions in a unit cell"@en .
2842+
2843+
2844+
### https://w3id.org/pmd/cryo/CRYO_0000008
2845+
<https://w3id.org/pmd/cryo/CRYO_0000008> rdf:type owl:Class ;
2846+
rdfs:subClassOf <https://w3id.org/pmd/cryo/CRYO_0000006> ;
2847+
rdfs:label "β lattice parameter"@en ;
2848+
skos:definition "β lattice parameter is an anlge between x- and z-directions in a unit cell"@en .
2849+
2850+
2851+
### https://w3id.org/pmd/cryo/CRYO_0000009
2852+
<https://w3id.org/pmd/cryo/CRYO_0000009> rdf:type owl:Class ;
2853+
rdfs:subClassOf <https://w3id.org/pmd/cryo/CRYO_0000006> ;
2854+
rdfs:label "γ lattice parameter"@en ;
2855+
skos:definition "γ lattice parameter is an anlge between x- and z-directions in a unit cell"@en .
2856+
2857+
27562858
#################################################################
27572859
# Individuals
27582860
#################################################################

0 commit comments

Comments
 (0)