Tabular template for multiple term requests

.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
+

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.

src/templates/vibso_classes.tsv

@@ -15,8 +15,8 @@ obo:VIBSO_0000011	diffraction grating		device	A device that is an optical compon
 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	setting datum	A setting datum that specifies the upper boundary of the spectral window range utilized during the acquisition of spectroscopic data.			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	setting datum	A setting datum that specifies the lower boundary of the spectral window range utilized during the acquisition of spectroscopic data.			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_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