Skip to content

Commit

Permalink
Add synonyms requested in #66 (#100)
Browse files Browse the repository at this point in the history 
* Update vibso_classes.tsv

#66 (comment)

* recreate OWL components from TSV and delete dummy ID artefact

---------

Co-authored-by: StroemPhi <[email protected]>
  • Loading branch information
@Zack-83 @StroemPhi
Zack-83 and StroemPhi authored Aug 10, 2023
1 parent e8f21ae commit 906add5
Show file tree
Hide file tree
Showing 3 changed files with 8 additions and 5 deletions.
5 changes: 4 additions & 1 deletion src/ontology/components/vibso_classes.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ 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/2023-06-21/components/vibso_classes.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2023-08-10/components/vibso_classes.owl>
Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_classes.tsv', which is edited manually by domain experts.")

Declaration(Class(obo:BFO_0000029))
Expand Down Expand Up @@ -100,6 +100,7 @@ SubClassOf(obo:VIBSO_0000001 obo:OBI_0000654)
AnnotationAssertion(Annotation(dc:source <https://www.oceaninsight.com/knowledge-hub/glossary/#i>) obo:IAO_0000115 obo:VIBSO_0000002 "A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed."@en)
AnnotationAssertion(obo:IAO_0000116 obo:VIBSO_0000002 "This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices."@en)
AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000002 "integration period setting"@en)
AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000002 "integration time"@en)
AnnotationAssertion(dc:contributor obo:VIBSO_0000002 <http://orcid.org/0000-0002-1595-3213>)
AnnotationAssertion(rdfs:label obo:VIBSO_0000002 "integration time setting"@en)
AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000002 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40>)
Expand Down Expand Up @@ -174,6 +175,8 @@ SubClassOf(obo:VIBSO_0000009 obo:PATO_0001018)

AnnotationAssertion(obo:IAO_0000115 obo:VIBSO_0000010 "A setting datum that specifies the number of grooves in a diffraction grating device."@en)
AnnotationAssertion(obo:IAO_0000116 obo:VIBSO_0000010 "This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices."@en)
AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000010 "grating"@en)
AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000010 "grating setting"@en)
AnnotationAssertion(dc:contributor obo:VIBSO_0000010 <http://orcid.org/0000-0002-1595-3213>)
AnnotationAssertion(rdfs:label obo:VIBSO_0000010 "groove density setting"@en)
AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000010 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45>)
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/components/vibso_object_properties.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)


Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_object_properties.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2023-06-21/components/vibso_object_properties.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2023-08-10/components/vibso_object_properties.owl>
Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_object_properties.tsv', which is edited manually by domain experts.")


Expand Down
6 changes: 3 additions & 3 deletions src/templates/vibso_classes.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,15 +2,15 @@ id label alternative term link(s) to issue(s) definition definition source URI t
ID AL rdfs:label@en AL IAO:0000118@en SPLIT=| AI rdfs:seeAlso SPLIT=| AL IAO:0000115@en >AI dc11:source SPLIT=| TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL rdfs:comment@en SPLIT=| AL IAO:0000116@en SPLIT=| AT owl:deprecated^^xsd:boolean AI IAO:0000231 AI IAO:0100001
obo:VIBSO_0000000 vibrational spectrometer configuration specification https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/39 A setting datum that specifies the needed settings of a spectrometer used in vibrational spectroscopy. owl:Class setting datum ORCID:0000-0002-1595-3213
obo:VIBSO_0000001 Raman spectrometer configuration https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/47 A device setting that represents the measured or set physical qualities which make up the configuration state of a Raman spectrometer at the time of a measurement (e.g. operating temperature, exitation wavelength, groove density, ...). owl:Class device setting ORCID:0000-0002-1595-3213 The set of meassured configuration characteristics of a Raman spectrometer, like the operating temperature of a Raman spectrometer.
obo:VIBSO_0000002 integration time setting integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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_0000002 integration time setting integration time|integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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_0000003 preamplifier gain setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/41 A setting datum that specifies the preamplifier gain in CCD sensors. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology.
obo:VIBSO_0000004 horizontal shift speed setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 A setting datum that specifies the horizontal shift speed in CCD sensors. 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_0000005 vertical shift speed setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 A setting datum that specifies the vertical shift speed in CCD sensors. 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_0000006 device temperature setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/43 A setting datum that specifies the operating temperature of a device. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology.
obo:VIBSO_0000007 number of accumulations number of acquisitions https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio. owl:Class setting datum ORCID:0000-0002-1595-3213 This class might better be defined in a more general device ontology.
obo:VIBSO_0000008 CCD sensor binning read mode setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/46 A setting datum that specifies the binning read mode of a device with a CCD sensor. 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_0000009 groove density groove frequency https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter. Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range owl:Class physical quality ORCID:0000-0002-1595-3213 temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541)
obo:VIBSO_0000010 groove density setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A setting datum that specifies the number of grooves in a diffraction grating device. 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_0000010 groove density setting grating|grating setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A setting datum that specifies the number of grooves in a diffraction grating device. 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_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.
Expand All @@ -31,4 +31,4 @@ obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling ste
obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X)
obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y)
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)
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)

0 comments on commit 906add5

Please sign in to comment.