From 3041fdfeb7a39116cdbc54122ab3e1da944cdf01 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Mon, 27 Feb 2023 11:41:27 +0100 Subject: [PATCH 01/13] Update competency_questions.md --- docs/competency_questions.md | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/docs/competency_questions.md b/docs/competency_questions.md index ac16d8a..d3aead2 100644 --- a/docs/competency_questions.md +++ b/docs/competency_questions.md @@ -4,20 +4,29 @@ Competency questions can be understood as the test cases with which one can chec As previously mentioned, VIBSO's scope is the semantic description of vibrational spectroscopy research data. So far we have thus identified the following competency questions: - * What kind of vibrational spectroscopy was performed? +### Questions addressing one single data set + + * What kind of vibrational spectroscopy was performed (as detailed as possible: enhanced, resonant, stimulated, coherent, anti-Stokes...)? * In what context was it performed, e.g. as part of what study or investigation? +> Requires to clarify the hierarchy in the ontology: e.g. experiment < investigation < project - * What protocol and devices were used? + ~* What protocol and devices were used?~ +> Somehow redundant with the following one; "what protocol" meaningful only within a workgroup * What were the protocol parameters & device configurations? - * Who was involved in the assay, e.g. PI, PhD, lab assistant etc.? (identified by a PID like ORCID at best) + * Who was involved in the assay? (identified by a PID like ORCID at best) + > It is more probable that the users document the names of the co-authors than the academic degree / role + + * What was the assayed sample, including its relevant attributes (e.g. substrate, production procedure, pre-treatment)? + + * What is the dimensionality of the experiment (e.g. single spectra, line maps, surface maps, volume scans...)? - * What was the assayed sample, including its relevant attributes? + * What kind of post-processing (e.g. smoothing, baseline subtraction, band integration, peak recognition, image reconstruction) was done? - * What assay outputs were produced, such as what spectra (e.g. different formats)? +### Questions addressing the full database - * What kind of pre- and post-processing was done? +* -This list represents only a first draft and needs to be thoroughly discussed with the domain experts and the NFDI4Chem community. \ No newline at end of file +This list represents only a first draft and needs to be thoroughly discussed with the domain experts and the NFDI4Chem community. From ca01d9758043685f60486d1acb23a873e0e89eec Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Mon, 27 Feb 2023 11:45:56 +0100 Subject: [PATCH 02/13] Update docs/competency_questions.md --- docs/competency_questions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/competency_questions.md b/docs/competency_questions.md index d3aead2..c369c87 100644 --- a/docs/competency_questions.md +++ b/docs/competency_questions.md @@ -27,6 +27,6 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa ### Questions addressing the full database -* +* Find me all Raman spectra of wolfram wires on a silicium substrate covering the range 600-1800 cm^-1. This list represents only a first draft and needs to be thoroughly discussed with the domain experts and the NFDI4Chem community. From 51a23315c7749f7dd3c1648b363ad754e2e2b589 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Mon, 27 Feb 2023 11:49:14 +0100 Subject: [PATCH 03/13] Update docs/competency_questions.md --- docs/competency_questions.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/competency_questions.md b/docs/competency_questions.md index c369c87..eb843ee 100644 --- a/docs/competency_questions.md +++ b/docs/competency_questions.md @@ -29,4 +29,6 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa * Find me all Raman spectra of wolfram wires on a silicium substrate covering the range 600-1800 cm^-1. +* Find me which is a safe range of incoming laser powers to perform Raman experiments at wavelength Z on probe XY. + This list represents only a first draft and needs to be thoroughly discussed with the domain experts and the NFDI4Chem community. From 908d038eef538030e9ebe6c1014d3eeaa162a515 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Mon, 27 Feb 2023 11:52:18 +0100 Subject: [PATCH 04/13] Update docs/competency_questions.md --- docs/competency_questions.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/competency_questions.md b/docs/competency_questions.md index eb843ee..c33011b 100644 --- a/docs/competency_questions.md +++ b/docs/competency_questions.md @@ -31,4 +31,6 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa * Find me which is a safe range of incoming laser powers to perform Raman experiments at wavelength Z on probe XY. +* Find me a suitable solvent which is compatible with sample XY, i.e. which does not have any Raman peak or band between wavenumbers W1 and W2. + This list represents only a first draft and needs to be thoroughly discussed with the domain experts and the NFDI4Chem community. From f2619ab9c6d647507ff4684a4527d0a61f0a53e5 Mon Sep 17 00:00:00 2001 From: RainerStosch <121162130+RainerStosch@users.noreply.github.com> Date: Mon, 27 Feb 2023 11:53:23 +0100 Subject: [PATCH 05/13] Update competency_questions.md --- docs/competency_questions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/competency_questions.md b/docs/competency_questions.md index c33011b..43878ac 100644 --- a/docs/competency_questions.md +++ b/docs/competency_questions.md @@ -29,7 +29,7 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa * Find me all Raman spectra of wolfram wires on a silicium substrate covering the range 600-1800 cm^-1. -* Find me which is a safe range of incoming laser powers to perform Raman experiments at wavelength Z on probe XY. +* Find me which is a safe range of incoming laser powers to perform Raman experiments at wavelength Z on sample XY. * Find me a suitable solvent which is compatible with sample XY, i.e. which does not have any Raman peak or band between wavenumbers W1 and W2. From 467e73c1847e8d252aa524427e93e265a77cfd32 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Thu, 3 Aug 2023 11:52:51 +0200 Subject: [PATCH 06/13] Tabular template for multiple term requests --- ...w-multiple-term-request-issue-template.md} | 23 +++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) rename .github/ISSUE_TEMPLATE/{new-term-request-issue-template.md => new-multiple-term-request-issue-template.md} (55%) diff --git a/.github/ISSUE_TEMPLATE/new-term-request-issue-template.md b/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md similarity index 55% rename from .github/ISSUE_TEMPLATE/new-term-request-issue-template.md rename to .github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md index c4ee359..bd98083 100644 --- a/.github/ISSUE_TEMPLATE/new-term-request-issue-template.md +++ b/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md @@ -1,6 +1,6 @@ --- -name: New term request issue template -about: Please use this template to request a new term for the ontology +name: New multiple term request issue template +about: Please use this template to request one or multiple new terms for the ontology title: "[NTR]" labels: New Term Request assignees: '' @@ -9,6 +9,18 @@ assignees: '' For new term requests (NTRs), please provide the following information: +| Preferred term label | Synonyms | Textual definition | Link to [CHARISMA Wiki equivalent] | Suggested parent term | Axiomatization | Examples | Remarks | +| -------------------- | -------- | ------------------ | ---------------------------------- | --------------------- | -------------- | -------- | ------- | +| | | [definition1] | | | | | [note1] | + + +[definition1]: ## "You may use this syntax for lengthy sentences, in order to maintain the code of the table legible. This applies specially to definitions and remarks. The text becomes visible upon hovering the mouse pointer over the placeholder text." + +[note1]: ## "..." + + + + ## Preferred term label (e.g., spectral window range maximum) @@ -21,7 +33,7 @@ For new term requests (NTRs), please provide the following information: The definition should be understandable even for non-specialists. Include a DOI or URL to refer to any relevant publication that provides additional information about the suggested term. -## Link to [CHARISMA Wiki equivalent](https://wiki.charisma.ideaconsult.net/wiki/List_of_all_terms) +## Link to [CHARISMA Wiki equivalent] The CHARISMA project wiki contains terms for Raman specific and related concepts identified by domain experts of the CHARISMA team. In order to reuse this expertise, we've agreed with the CHARISMA team to link between the terms in this wiki and the terms in VISBO. For example https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 is mentioned as definition source for the VIBSO class *region of interest*. ## Suggested parent term @@ -34,4 +46,7 @@ Please provide a more detailed description that examplifies how the term is supp ## Attribution -If you would like a nanoattribution, please indicate your ORCID id +If you would like a nanoattribution, please indicate your ORCID id. (out of the table) + +[CHARISMA Wiki equivalent]: https://wiki.charisma.ideaconsult.net/wiki/List_of_all_terms + From 548f79b086391f90b1d2e5754ec9c23455e51e72 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Thu, 3 Aug 2023 11:57:39 +0200 Subject: [PATCH 07/13] restore file deleted by error --- .../new-term-request-issue-template.md | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/new-term-request-issue-template.md diff --git a/.github/ISSUE_TEMPLATE/new-term-request-issue-template.md b/.github/ISSUE_TEMPLATE/new-term-request-issue-template.md new file mode 100644 index 0000000..c4ee359 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/new-term-request-issue-template.md @@ -0,0 +1,37 @@ +--- +name: New term request issue template +about: Please use this template to request a new term for the ontology +title: "[NTR]" +labels: New Term Request +assignees: '' + +--- + +For new term requests (NTRs), please provide the following information: + +## Preferred term label + +(e.g., spectral window range maximum) + +## Synonyms + +(e.g., acquisition band maximum) + +## Textual definition + +The definition should be understandable even for non-specialists. Include a DOI or URL to refer to any relevant publication that provides additional information about the suggested term. + +## Link to [CHARISMA Wiki equivalent](https://wiki.charisma.ideaconsult.net/wiki/List_of_all_terms) +The CHARISMA project wiki contains terms for Raman specific and related concepts identified by domain experts of the CHARISMA team. In order to reuse this expertise, we've agreed with the CHARISMA team to link between the terms in this wiki and the terms in VISBO. For example https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 is mentioned as definition source for the VIBSO class *region of interest*. + +## Suggested parent term + +Please look in the hierarchy in a browser such as the [NFDI4Chem TS](https://terminology.nfdi4chem.de/ts/ontologies/vibso) + +## Examples + +Please provide a more detailed description that examplifies how the term is supposed to be used, in terms of what it is suppose to repesent (e.g. a concept or a relation). + +## Attribution + +If you would like a nanoattribution, please indicate your ORCID id From d278aff55419779bfdaaf2195ab62922bb056735 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Fri, 13 Oct 2023 10:26:09 +0200 Subject: [PATCH 08/13] Update docs/competency_questions.md --- docs/competency_questions.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/competency_questions.md b/docs/competency_questions.md index ef82bb1..e4daa16 100644 --- a/docs/competency_questions.md +++ b/docs/competency_questions.md @@ -11,8 +11,6 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa * In what context was it performed, e.g. as part of what study or investigation? > Requires to clarify the hierarchy in the ontology: e.g. experiment < investigation < project - ~* What protocol and devices were used?~ -> Somehow redundant with the following one; "what protocol" meaningful only within a workgroup * What devices were used? From 9f23d7096fff1480ea3860f712353dcb35c44cf7 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Fri, 13 Oct 2023 10:26:29 +0200 Subject: [PATCH 09/13] Update docs/competency_questions.md --- docs/competency_questions.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/competency_questions.md b/docs/competency_questions.md index e4daa16..e3577f4 100644 --- a/docs/competency_questions.md +++ b/docs/competency_questions.md @@ -11,7 +11,6 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa * In what context was it performed, e.g. as part of what study or investigation? > Requires to clarify the hierarchy in the ontology: e.g. experiment < investigation < project - * What devices were used? * What were the protocol parameters & device configurations? From 8eb7e49b7f476019f59a8f7b86959c010c1e92df Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Mon, 6 Nov 2023 10:32:35 +0100 Subject: [PATCH 10/13] Update .github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md --- .../new-multiple-term-request-issue-template.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md b/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md index bd98083..bc183f1 100644 --- a/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md +++ b/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md @@ -10,8 +10,8 @@ assignees: '' For new term requests (NTRs), please provide the following information: | Preferred term label | Synonyms | Textual definition | Link to [CHARISMA Wiki equivalent] | Suggested parent term | Axiomatization | Examples | Remarks | -| -------------------- | -------- | ------------------ | ---------------------------------- | --------------------- | -------------- | -------- | ------- | -| | | [definition1] | | | | | [note1] | +| --- | --- | ------------- | --- | --- | --- | --- | ------- | +| | | [definition1] | | | | | [note1] | [definition1]: ## "You may use this syntax for lengthy sentences, in order to maintain the code of the table legible. This applies specially to definitions and remarks. The text becomes visible upon hovering the mouse pointer over the placeholder text." From 1422872928d57c20d83c6b89b3e6ec0447ca6789 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Fri, 9 Aug 2024 09:49:42 +0200 Subject: [PATCH 11/13] beautify table --- src/templates/vibso_classes.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 92cc2f0..84de951 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -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. @@ -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_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 From 1d3dfc9dac57a88e02fb60c75a66a2f2221aaa35 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Fri, 9 Aug 2024 10:02:32 +0200 Subject: [PATCH 12/13] fix "measurment" --- src/templates/vibso_classes.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 84de951..da21384 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -28,6 +28,6 @@ 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) -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_0000028 Raman raw data raw Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 A measurement 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 From 85c9f71a0eb8a8cc7457fc753321718b0a5a4883 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Mon, 11 Nov 2024 07:53:39 +0100 Subject: [PATCH 13/13] sort columns according to #145 --- src/templates/vibso_classes.tsv | 66 ++++++++++++++++----------------- 1 file changed, 33 insertions(+), 33 deletions(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index da21384..abd946a 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -1,33 +1,33 @@ -id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage comment editor note obsoleted obsolescence reason term replaced by -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 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 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. -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. -obo:VIBSO_0000018 region of interest imaging region of interest|ROI https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 owl:Class site ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 -obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the width (length in the X direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 1 mm region of interest width = (point distance X) * (number of measurements X) -obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the height (length in the Y direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.5 mm region of interest breadth = (point distance Y) * (number of measurements Y) -obo:VIBSO_0000021 region of interest depth ROI depth|ROI vertical length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the depth (length in the Z direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.1 mm region of interest depth = (point distance Z) * (number of measurements Z) -obo:VIBSO_0000022 point distance X sampling pace in the X direction|sampling step in the X direction|voxel distance in the X direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 20 µm point distance X = (region of interest width) / (number of measurements X) -obo:VIBSO_0000023 point distance Y sampling pace in the Y direction|sampling step in the Y direction|voxel distance in the Y direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Y = (region of interest breadth) / (number of measurements Y) -obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling step in the Z direction|voxel distance in the Z direction|vertical mapping distance|axial mapping distance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Z = (region of interest depth) / (number of measurements Z) -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) -obo:VIBSO_0000028 Raman raw data raw Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 A measurement 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 +id label alternative term super class definition definition source URI comment example of usage editor note obsoleted obsolescence reason term replaced by contributor URI link(s) to issue(s) type +ID AL rdfs:label@en AL IAO:0000118@en SPLIT=| SC % SPLIT=| AL IAO:0000115@en >AI dc11:source SPLIT=| AL rdfs:comment@en SPLIT=| AL IAO:0000112@en AL IAO:0000116@en SPLIT=| AT owl:deprecated^^xsd:boolean AI IAO:0000231 AI IAO:0100001 AI dc11:contributor SPLIT=| AI rdfs:seeAlso SPLIT=| TYPE +obo:VIBSO_0000000 vibrational spectrometer configuration specification setting datum A setting datum that specifies the needed settings of a spectrometer used in vibrational spectroscopy. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/39 owl:Class +obo:VIBSO_0000001 Raman spectrometer configuration device setting 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, ...). The set of meassured configuration characteristics of a Raman spectrometer, like the operating temperature of a Raman spectrometer. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/47 owl:Class +obo:VIBSO_0000002 integration time setting integration time|integration period setting setting datum 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 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 owl:Class +obo:VIBSO_0000003 preamplifier gain setting setting datum A setting datum that specifies the preamplifier gain in CCD sensors. This class should better be defined in a more general device ontology. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/41 owl:Class +obo:VIBSO_0000004 horizontal shift speed setting setting datum A setting datum that specifies the horizontal shift speed in CCD sensors. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 owl:Class +obo:VIBSO_0000005 vertical shift speed setting setting datum A setting datum that specifies the vertical shift speed in CCD sensors. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 owl:Class +obo:VIBSO_0000006 device temperature setting setting datum A setting datum that specifies the operating temperature of a device. This class should better be defined in a more general device ontology. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/43 owl:Class +obo:VIBSO_0000007 number of accumulations number of acquisitions setting datum 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. This class might better be defined in a more general device ontology. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 owl:Class +obo:VIBSO_0000008 CCD sensor binning read mode setting setting datum A setting datum that specifies the binning read mode of a device with a CCD sensor. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/46 owl:Class +obo:VIBSO_0000009 groove density groove frequency physical quality 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 temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541) ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 owl:Class +obo:VIBSO_0000010 groove density setting grating|grating setting setting datum A setting datum that specifies the number of grooves in a diffraction grating device. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 owl:Class +obo:VIBSO_0000011 diffraction grating device 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 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/49 owl:Class +obo:VIBSO_0000012 deprecated_excitation wavelength A physical quality of the light source that is used used to excite a system to a higher energy state. 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 ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 owl:Class +obo:VIBSO_0000013 excitation wavelength setting setting datum 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. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 owl:Class +obo:VIBSO_0000014 objective magnification factor setting magnification|magnification setting setting datum A setting datum that specifies the magnification factor of the objective collecting the scattered light. 100x ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24 owl:Class +obo:VIBSO_0000015 spectral window range maximum acquisition band maximum data item|('part of' some 'Raman spectrum') 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. 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. ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31 owl:Class +obo:VIBSO_0000016 spectral window range minimum acquisition band minimum data item|('part of' some 'Raman spectrum') 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. 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. ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31 owl:Class +obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample scalar measurement datum 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. 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. 200 mW ORCID:0000-0001-7694-5519 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 owl:Class +obo:VIBSO_0000018 region of interest imaging region of interest|ROI site A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length setting datum A setting datum that specifies the width (length in the X direction) of the region of interest. region of interest width = (point distance X) * (number of measurements X) 1 mm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length setting datum A setting datum that specifies the height (length in the Y direction) of the region of interest. region of interest breadth = (point distance Y) * (number of measurements Y) 0.5 mm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000021 region of interest depth ROI depth|ROI vertical length setting datum A setting datum that specifies the depth (length in the Z direction) of the region of interest. region of interest depth = (point distance Z) * (number of measurements Z) 0.1 mm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000022 point distance X sampling pace in the X direction|sampling step in the X direction|voxel distance in the X direction setting datum A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. point distance X = (region of interest width) / (number of measurements X) 20 µm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000023 point distance Y sampling pace in the Y direction|sampling step in the Y direction|voxel distance in the Y direction setting datum A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. point distance Y = (region of interest breadth) / (number of measurements Y) 10 µm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling step in the Z direction|voxel distance in the Z direction|vertical mapping distance|axial mapping distance setting datum A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy. point distance Z = (region of interest depth) / (number of measurements Z) 10 µm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line setting datum 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. number of measurements X = (region of interest width) / (point distance X) 50 ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer setting datum 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. number of measurements = (region of interest breadth) / (point distance Y) 100 ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition setting datum 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. number of measurements Z = (region of interest depth) / (point distance Z) 10 ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000028 Raman raw data raw Raman data measurement datum A measurement 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 ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 owl:Class +obo:VIBSO_0000029 lens numerical aperture numerical aperture setting datum 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 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 ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76 owl:Class +obo:VIBSO_000030 primary Raman data 'data item'|(is_specified_output_of some ('data transformation' and (has_specified_input some 'Raman raw data'))) A data item that is obtained by processing raw Raman data. ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132 owl:Class