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correct last URI and adjust table (#135)
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* correct last URI

* Recreate vibso_classes.owl from TSV

---------

Co-authored-by: Philip Strömert <[email protected]>
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@Zack-83 @StroemPhi
Zack-83 and StroemPhi authored Aug 9, 2024
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Showing 2 changed files with 12 additions and 12 deletions.
20 changes: 10 additions & 10 deletions src/ontology/components/vibso_classes.owl
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Expand Up @@ -24,7 +24,7 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)


Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_classes.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2024-08-08/components/vibso_classes.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2024-08-09/components/vibso_classes.owl>
Annotation(rdfs:comment "This component is derived from the manually edited 'src/templates/vibso_classes.tsv' template.")

Declaration(Class(obo:BFO_0000029))
Expand Down Expand Up @@ -67,7 +67,7 @@ Declaration(Class(obo:VIBSO_0000026))
Declaration(Class(obo:VIBSO_0000027))
Declaration(Class(obo:VIBSO_0000028))
Declaration(Class(obo:VIBSO_0000029))
Declaration(Class(obo:VIBSO_000030))
Declaration(Class(obo:VIBSO_0000030))
Declaration(ObjectProperty(obo:BFO_0000050))
Declaration(ObjectProperty(obo:OBI_0000293))
Declaration(ObjectProperty(obo:OBI_0000312))
Expand Down Expand Up @@ -425,15 +425,15 @@ 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)
# Class: obo:VIBSO_000030 (primary Raman data)
# Class: obo:VIBSO_0000030 (primary Raman data)
AnnotationAssertion(obo:IAO_0000115 obo:VIBSO_000030 "A data item that is obtained by processing raw Raman data."@en)
AnnotationAssertion(dc:contributor obo:VIBSO_000030 <http://orcid.org/0000-0002-1595-3213>)
AnnotationAssertion(dc:contributor obo:VIBSO_000030 <http://orcid.org/0000-0002-2239-3955>)
AnnotationAssertion(rdfs:label obo:VIBSO_000030 "primary Raman data"@en)
AnnotationAssertion(rdfs:seeAlso obo:VIBSO_000030 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132>)
SubClassOf(obo:VIBSO_000030 obo:IAO_0000027)
SubClassOf(obo:VIBSO_000030 ObjectSomeValuesFrom(obo:OBI_0000312 ObjectIntersectionOf(obo:OBI_0200000 ObjectSomeValuesFrom(obo:OBI_0000293 obo:VIBSO_0000028))))
AnnotationAssertion(obo:IAO_0000115 obo:VIBSO_0000030 "A data item that is obtained by processing raw Raman data."@en)
AnnotationAssertion(dc:contributor obo:VIBSO_0000030 <http://orcid.org/0000-0002-1595-3213>)
AnnotationAssertion(dc:contributor obo:VIBSO_0000030 <http://orcid.org/0000-0002-2239-3955>)
AnnotationAssertion(rdfs:label obo:VIBSO_0000030 "primary Raman data"@en)
AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000030 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132>)
SubClassOf(obo:VIBSO_0000030 obo:IAO_0000027)
SubClassOf(obo:VIBSO_0000030 ObjectSomeValuesFrom(obo:OBI_0000312 ObjectIntersectionOf(obo:OBI_0200000 ObjectSomeValuesFrom(obo:OBI_0000293 obo:VIBSO_0000028))))
)
4 changes: 2 additions & 2 deletions src/templates/vibso_classes.tsv
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Expand Up @@ -14,7 +14,7 @@ obo:VIBSO_0000010 groove density setting grating|grating setting https://github.
obo:VIBSO_0000011 diffraction grating https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/49 A device that is an optical component with a periodic structure that diffracts light into several beams travelling in different directions (i.e. different diffraction angles) https://en.wikipedia.org/wiki/Diffraction_grating owl:Class device ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000012 deprecated_excitation wavelength https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 A physical quality of the light source that is used used to excite a system to a higher energy state. owl:Class ORCID:0000-0002-1595-3213 This class is not needed, as PATO:wavelength is sufficient, if this quality of a Raman device is really needed. true failed exploratory term wavelength
obo:VIBSO_0000013 excitation wavelength setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 A setting datum that specifies the wavelength of an electromagnetic radiation source (e.g. a laser) which has the function to excite the energy state of a target material. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000014 objective magnification factor setting magnification|magnification setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24 A setting datum that specifies the magnification factor of the objective collecting the scattered light. owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100x
obo:VIBSO_0000014 objective magnification factor setting magnification|magnification setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24 A setting datum that specifies the magnification factor of the objective collecting the scattered light. owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100x
obo:VIBSO_0000015 spectral window range maximum acquisition band maximum https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31 A data item that is the part of a Raman spectrum which represents the maximum wavenumber included in the spectrum and which is calculated from the windows size and window center. owl:Class data item|('part of' some 'Raman spectrum') ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519 210 cm^-1 It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived.
obo:VIBSO_0000016 spectral window range minimum acquisition band minimum https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31 A data item that is the part of a Raman spectrum which represents the minimum wavenumber included in the spectrum and which is calculated from the windows size and window center. owl:Class data item|('part of' some 'Raman spectrum') ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519 1960 cm^-1 It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived.
obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components. owl:Class scalar measurement datum ORCID:0000-0001-7694-5519 200 mW The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot.
Expand All @@ -30,4 +30,4 @@ 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
obo:VIBSO_000030 primary Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132 A data item that is obtained by processing raw Raman data. owl:Class 'data item'|(is_specified_output_of some ('data transformation' and (has_specified_input some 'Raman raw data'))) ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955
obo:VIBSO_0000030 primary Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132 A data item that is obtained by processing raw Raman data. owl:Class 'data item'|(is_specified_output_of some ('data transformation' and (has_specified_input some 'Raman raw data'))) ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955

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