diff --git a/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md b/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md new file mode 100644 index 0000000..bc183f1 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/new-multiple-term-request-issue-template.md @@ -0,0 +1,52 @@ +--- +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: '' + +--- + +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) + +## 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] +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. (out of the table) + +[CHARISMA Wiki equivalent]: https://wiki.charisma.ideaconsult.net/wiki/List_of_all_terms + diff --git a/docs/competency_questions.md b/docs/competency_questions.md index 45a08f1..28cece5 100644 --- a/docs/competency_questions.md +++ b/docs/competency_questions.md @@ -6,9 +6,12 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa ### Questions addressing one single data set - * What kind of vibrational spectroscopy was performed (as detailed as possible: enhanced, resonant, stimulated, + * 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 devices were used? * What is the software version? * Whats the instrument manufacturer? @@ -21,7 +24,7 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa * What is the unit of the measurement? * What file output format is the measurement in? * What is the types of acquisition for this measurement? - * What was the humidity and temperature of the collection environment? + * What was the humidity and temperature of the collection environment? * What are the light conditions around the sample? (closed or open space) * Which laser wavelength was used for the measurement? * What grating was used for the spectrum acquisition/measurement? @@ -34,20 +37,23 @@ As previously mentioned, VIBSO's scope is the semantic description of vibrationa * Did you correct for the dark spectrum of the detector? (ie noise correction from detector) * What kind of filters do you use for your measurement? * Which slit position was used? Standard or high confocality? - * Has the autofocus been used? + * Has the autofocus been used? * Have the data been acquired with an automatic cosmic ray removal? * 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/static scan, line maps, surface maps, volume scans...)? + * What is the dimensionality of the experiment (e.g. single spectra/static scan, line maps, surface maps, volume scans...)? * If the spectrum is a static scan, what is the center of the spectrum? * What kind of preprocessing was done to the spectra? * What kind of preprocessing was done on the sample? - * What kind of post-processing (e.g. smoothing, baseline subtraction, band integration, peak recognition, image + * What kind of post-processing (e.g. smoothing, baseline subtraction, band integration, peak recognition, image reconstruction) was done? * Do you perform correction for spectral shifts? * What were the data extraction steps that have been done on the spectra? * For baseline correction, what are the applied baseline correction methods? - * If the cosmic ray removal was applied manually, what are the applied processing steps to do the cosmic ray + * If the cosmic ray removal was applied manually, what are the applied processing steps to do the cosmic ray removal? * What kind of preprocessing was done on the sample? * Has the SNR been maintained for all measurements at expected levels? @@ -58,4 +64,5 @@ 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 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. -This list represents only a first draft and needs to be thoroughly discussed with the domain experts and the NFDI4Chem community. + +This list represents only a first draft and needs to be thoroughly discussed with the domain experts and the NFDI4Chem community. diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 92cc2f0..da21384 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. @@ -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 +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