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add numerical aperture (#123)
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* Add numerical aperture class to TSV

* Update owl component from TSV

* Update TBox graphs for the docs

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Co-authored-by: Philip Strömert <[email protected]>
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@Zack-83 @StroemPhi
Zack-83 and StroemPhi authored May 13, 2024
1 parent d6e6839 commit cc7c6ba
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8 changes: 4 additions & 4 deletions docs/images/VIBSO_T-Box_graph_views.drawio
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<mxfile host="app.diagrams.net" modified="2024-05-13T08:12:30.625Z" agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:109.0) Gecko/20100101 Firefox/115.0" etag="57ZWlL_0ZOLiXTzs_Ei3" version="24.4.0" type="device" pages="5">
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<diagram id="R2lEEEUBdFMjLlhIrx00" name="VIBSO T-Box">
<mxGraphModel dx="2074" dy="7724" grid="0" gridSize="5" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="4681" pageHeight="3300" math="0" shadow="0" extFonts="Permanent Marker^https://fonts.googleapis.com/css?family=Permanent+Marker">
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<root>
<mxCell id="0" />
<mxCell id="1" parent="0" />
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<mxCell id="QKKoRjnMVttNz9pZIT6n-1" value="&lt;div&gt;&lt;a href=&quot;https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000656&quot;&gt;CHMO:Raman spectroscopy&lt;/a&gt;&lt;/div&gt;" style="rounded=0;whiteSpace=wrap;html=1;fillColor=#f8cecc;strokeColor=#b85450;" parent="1" vertex="1">
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<mxCell id="QKKoRjnMVttNz9pZIT6n-2" value="&lt;a href=&quot;https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77&quot;&gt;VIBSO:raw Raman data&lt;/a&gt;" style="rounded=0;whiteSpace=wrap;html=1;fillColor=#dae8fc;strokeColor=#6c8ebf;arcSize=15;glass=0;shadow=0;strokeWidth=1;align=center;" parent="1" vertex="1">
<mxCell id="QKKoRjnMVttNz9pZIT6n-2" value="&lt;a href=&quot;https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FVIBSO_0000028&quot;&gt;VIBSO:raw Raman data&lt;/a&gt;" style="rounded=0;whiteSpace=wrap;html=1;fillColor=#dae8fc;strokeColor=#6c8ebf;arcSize=15;glass=0;shadow=0;strokeWidth=1;align=center;" parent="1" vertex="1">
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<mxCell id="yY9HiGbYDIGNY1c0d9uf-41" value="&lt;div&gt;optical&amp;nbsp;&lt;/div&gt;&lt;div&gt;settings&lt;/div&gt;" style="whiteSpace=wrap;html=1;align=left;verticalAlign=top;fillColor=default;" parent="Nw7-E2_MfOwgosX6pQGJ-2" vertex="1">
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<mxCell id="lnHGb59-9foJHnMW3seC-17" value="&lt;a href=&quot;https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76&quot;&gt;NTR:numerical aperture&lt;/a&gt;" style="text;whiteSpace=wrap;html=1;fillColor=#dae8fc;strokeColor=#FF0000;verticalAlign=middle;align=center;strokeWidth=5;" parent="Nw7-E2_MfOwgosX6pQGJ-2" vertex="1">
<mxCell id="lnHGb59-9foJHnMW3seC-17" value="&lt;a href=&quot;https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FVIBSO_0000029&quot;&gt;VIBSO:numerical aperture&lt;/a&gt;" style="text;whiteSpace=wrap;html=1;fillColor=#dae8fc;strokeColor=#6c8ebf;verticalAlign=middle;align=center;strokeWidth=1;" parent="Nw7-E2_MfOwgosX6pQGJ-2" vertex="1">
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<mxCell id="-qVNJrEobh2uuxl9ESg2-140" value="&lt;a href=&quot;https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000013&quot;&gt;&lt;span style=&quot;font-size: 12px; color: rgb(0, 0, 0); font-weight: normal; text-decoration: none; font-style: normal; text-decoration-skip-ink: none;&quot;&gt;VIBSO:exitation wavelength setting&lt;/span&gt;&lt;/a&gt;" style="rounded=0;whiteSpace=wrap;html=1;fontSize=12;fontFamily=Helvetica;fillColor=#dae8fc;strokeColor=#6c8ebf;strokeWidth=1;verticalAlign=middle;" parent="Nw7-E2_MfOwgosX6pQGJ-2" vertex="1">
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2 changes: 1 addition & 1 deletion docs/images/VIBSO_TBox_graph_views.html
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13 changes: 13 additions & 0 deletions src/ontology/components/vibso_classes.owl
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Expand Up @@ -65,6 +65,7 @@ Declaration(Class(obo:VIBSO_0000025))
Declaration(Class(obo:VIBSO_0000026))
Declaration(Class(obo:VIBSO_0000027))
Declaration(Class(obo:VIBSO_0000028))
Declaration(Class(obo:VIBSO_0000029))
Declaration(ObjectProperty(obo:BFO_0000050))
Declaration(AnnotationProperty(obo:IAO_0000112))
Declaration(AnnotationProperty(obo:IAO_0000115))
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AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000028 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77>)
SubClassOf(obo:VIBSO_0000028 obo:IAO_0000109)

# Class: obo:VIBSO_0000029 (lens numerical aperture)

AnnotationAssertion(obo:IAO_0000112 obo:VIBSO_0000029 "The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm."@en)
AnnotationAssertion(Annotation(dc:source Wikipedia:Numerical_aperture) Annotation(dc:source <https://wiki.charisma.ideaconsult.net/wiki/Item:Q385>) obo:IAO_0000115 obo:VIBSO_0000029 "A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located."@en)
AnnotationAssertion(obo:IAO_0000116 obo:VIBSO_0000029 "possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA"@en)
AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000029 "numerical aperture"@en)
AnnotationAssertion(dc:contributor obo:VIBSO_0000029 <http://orcid.org/0000-0002-1595-3213>)
AnnotationAssertion(dc:contributor obo:VIBSO_0000029 <http://orcid.org/0000-0002-2239-3955>)
AnnotationAssertion(rdfs:label obo:VIBSO_0000029 "lens numerical aperture"@en)
AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000029 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76>)
SubClassOf(obo:VIBSO_0000029 obo:IAO_0000140)
)
1 change: 1 addition & 0 deletions src/templates/vibso_classes.tsv
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Expand Up @@ -33,3 +33,4 @@ obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|n
obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 "A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest.
Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z)
obo:VIBSO_0000028 Raman raw data raw Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 A measurment datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam. https://wiki.charisma.ideaconsult.net/wiki/Item:Q64 owl:Class measurement datum ORCID:0000-0002-2239-3955
obo:VIBSO_0000029 lens numerical aperture numerical aperture https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76 A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located. https://wiki.charisma.ideaconsult.net/wiki/Item:Q385|https://en.wikipedia.org/wiki/Numerical_aperture owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm. possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA

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