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Move internal terms to ROBOT templates #710

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Move internal terms to ROBOT templates #710

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5c1bff8
First template formatting of internal terms
jmillanacosta Jul 16, 2024
74801dc
Some fixes
jmillanacosta Jul 16, 2024
b0aa7bd
Internal terms to templates
jmillanacosta Jul 16, 2024
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734 changes: 717 additions & 17 deletions internal-dev/bao-ext.owl
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149 changes: 147 additions & 2 deletions internal-dev/bfo-ext.owl
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Expand Up @@ -65,8 +65,6 @@
</owl:Class>




<!-- http://purl.enanomapper.org/onto/ENM_9000100 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_9000100">
Expand All @@ -75,6 +73,153 @@
<rdfs:label xml:lang="en">boiling point</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.org/onto/ENM_1200003 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_1200003">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000102"/>
<obo:IAO_0000115>A crystal structure following the formula ABX3</obo:IAO_0000115>
<rdfs:label xml:lang="en">perovskite</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.net/onto/ENM_8461735 -->

<owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_8461735">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000115>Increased energy price of a reaction due to steric effects (the atomic spacial arrangement in a molecule or ion)</obo:IAO_0000115>
<rdfs:label xml:lang="en">Steric hindrance</rdfs:label>
</owl:Class>


<!-- http://purl.enanomapper.net/onto/ENM_6390284 -->

<owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_6390284">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000101"/>
<obo:IAO_0000115>Point defects in the bulk or surface of a material</obo:IAO_0000115>
<rdfs:label xml:lang="en">Oxygen vacancies</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.net/onto/ENM_0310210 -->

<owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_0310210">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<rdfs:label xml:lang="en">Interaction potential</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.org/onto/ENM_3991469 -->

<owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_3991469">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0000973"/>
<rdfs:label xml:lang="en">mesoporosity</rdfs:label>
<dc:source rdf:resource="https://doi.org/10.1351/pac199466081739"/>
<obo:IAO_0000115>Structural quality of a material containing pores with diameters between 2 and 50 nm</obo:IAO_0000115>
</owl:Class>

<!-- http://purl.enanomapper.org/onto/ENM_8000101 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000101">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>Electronic chemical potential, μ, is a measure of the escaping tendency of an electronic cloud and corresponds to the negative of the electronegativity c. Considering a finite difference approximation and a quadratic dependence of energy on the number of electrons, the electronegativity approximates the loss or gain in charge by the ionization potential IP and electron affinity EA, that is χMU is approximately (IP+EA)/2=-μ , χMU is Mulliken electronegativity.</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">electronic chemical potential</rdfs:label>
</owl:Class>


<!-- http://purl.enanomapper.org/onto/ENM_8000102 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000102">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>Mulliken electronegativity = -α, where α = the average of the HOMO and LUMO energies, i.e., α = ½(εhomo+ εlumo) http://openmopac.net/manual/super.html</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">Mullikens electronegativity Xc</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000103 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000103">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>Parr &amp; Pople absolute hardness = ½(εhomo- εlumo) http://openmopac.net/manual/super.html</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">parr and poples absolute hardness</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000104 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000104">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>Polarizability derived from the dipole moment Ad</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">polarizability derived from the dipole moment ad</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000105 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000105">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>Polarizability derived from the heat of formation Ahof.</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">polarizability derived from the heat of formation ahof</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000106 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000106">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>Schuurmann MO shift alpha = α, where α = the average of the HOMO and LUMO energies, i.e., α = ½(εhomo+ εlumo) http://openmopac.net/manual/super.html</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">schuurmann mo shift alpha</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000107 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000107">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>The solvent accessible surface is a continuous surface of the molecule which can be reached by the center of charge of a solvent molecule. http://openmopac.net/manual/cosmo.html</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">solvent accessible surface</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000108 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000108">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>Total energy equals to (Eelect + Enuc), where Eelect is the electronic energy, Enuc is the nuclear-nuclear repulsion energy. http://openmopac.net/manual/SCF_calc_hof.html</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">total energy</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000109 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000109">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>The total softness S is defined as S=0.5*η, where η is the absolute hardness. Defined in page 629 of: Molecular descriptors for chemoinformatics (2 volumes), Roberto Todeschini, Viviana Consonni, 2009, Volume 41, Wiley-VCH.</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">total softness</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000110 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000110">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>The valence band is the highest range of electron energies in which electrons are normally present at absolute zero temperature. https://en.wikipedia.org/wiki/Valence_and_conduction_bands</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">valence band</rdfs:label>
</owl:Class>



<!-- http://purl.enanomapper.org/onto/ENM_8000111 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000111">
<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_8000027"/>
<rdfs:isDefinedBy>Zeta potential derived from Quantum Mechanics Calculations.</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">zeta potential</rdfs:label>
</owl:Class>


</rdf:RDF>
73 changes: 0 additions & 73 deletions internal-dev/cheminf-ext.owl
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Expand Up @@ -33,13 +33,7 @@
<owl:AnnotationProperty rdf:about="http://purl.enanomapper.org/onto/ENM_8000222">
<rdfs:label xml:lang="en">PrefLabel</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>



<!--
Expand All @@ -50,76 +44,9 @@
///////////////////////////////////////////////////////////////////////////////////////
-->

<!-- http://purl.enanomapper.org/onto/ENM_8000030 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000030">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000123"/>
<obo:IAO_0000115>Descriptors that have been obtained through modelling.</obo:IAO_0000115>
<rdfs:label xml:lang="en">predicted descriptors</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.org/onto/ENM_8000031 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000031">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000123"/>
<obo:IAO_0000115>Descriptors that have been obtained through modelling.</obo:IAO_0000115>
<rdfs:label xml:lang="en">calculated descriptors</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.org/onto/ENM_8000032 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_8000032">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000123"/>
<obo:IAO_0000115>A class of descriptors derived using CDK, the Chemistry Development Kit.</obo:IAO_0000115>
<rdfs:label xml:lang="en">cdk descriptors</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.org/onto/ENM_1200002 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_1200002">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000464"/>
<obo:IAO_0000115>PMCID is a unique identifier for publications archived in PubMed Central, which may also be indexed in PubMed. </obo:IAO_0000115>
<rdfs:label xml:lang="en">PubMedCentral Identifier (PMCID)</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.org/onto/ENM_1200003 -->

<owl:Class rdf:about="http://purl.enanomapper.org/onto/ENM_1200003">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000102"/>
<obo:IAO_0000115>A crystal structure following the formula ABX3</obo:IAO_0000115>
<rdfs:label xml:lang="en">perovskite</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.net/onto/ENM_8461735 -->

<owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_8461735">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000115>Increased energy price of a reaction due to steric effects (the atomic spacial arrangement in a molecule or ion)</obo:IAO_0000115>
<rdfs:label xml:lang="en">Steric hindrance</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.net/onto/ENM_6390284 -->

<owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_6390284">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000101"/>
<obo:IAO_0000115>Point defects in the bulk or surface of a material</obo:IAO_0000115>
<rdfs:label xml:lang="en">Oxygen vacancies</rdfs:label>
</owl:Class>


<!-- http://purl.enanomapper.net/onto/ENM_5933788 -->

<owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_5933788">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000247"/>
<rdfs:label xml:lang="en">BET surface area endpoint</rdfs:label>
</owl:Class>

<!-- http://purl.enanomapper.net/onto/ENM_0310210 -->

<owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_0310210">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<rdfs:label xml:lang="en">Interaction potential</rdfs:label>
</owl:Class>
</rdf:RDF>


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