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NFDI4Chem / VibrationalSpectroscopyOntology

WORK IN PROGRESS - The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR.
https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/
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Add terms defined in Parameters_and_Units_IR_and_Raman_for_VIBSO.xlsx #66

Open StroemPhi opened 1 year ago

StroemPhi commented 1 year ago

Lars Meyer (BASF) was so kind to provide Parameters_and_Units_IR_and_Raman_for_VIBSO.xlsx in which he provided a list of parameters and their unist that are relevant in IR and Raman spectroscopy. We thus need to check which of these we already have, need to mint or import.

StroemPhi commented 1 year ago

I went over the terms listed in the XLSX and checked if they are already in VIBSO and/or the CHARISMA wiki.

Terms that are already in VIBSO or have an existing issues:

| needed term | VIBSO term or issue | CHARISMA link | comments | | ---- | ---- | ---- | ---- | | Magnification | [objective magnification factor setting](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000014) | | add synonyms `magnification` and maybe `magnification #setting`, no CHARISMA term yet | Wavelength | [PATO:wavelength](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0001242) | [Wavelength](https://wiki.charisma.ideaconsult.net/wiki/Item:Q36)| unclear what this is needed for, if we there is a wavelenght measured somewhere, we need a measuremtn datum for it | | Grating | [groove density setting](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000010) || add synonyms `grating` and `grating setting`| | Integration time | [integration time setting](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000002) | ???[Integration period](https://wiki.charisma.ideaconsult.net/wiki/Item:Q346)???| add synonym `integration time`| | Instrument | [spectrometer](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0001234) & [manufacturer](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000835) |[Spectrometer](https://wiki.charisma.ideaconsult.net/wiki/Item:Q9) & [Spectrograph](https://wiki.charisma.ideaconsult.net/wiki/Item:Q420) | | | Laser (wavelength of laser) | [excitation wavelength setting](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000013) | [Laser wavelength](https://wiki.charisma.ideaconsult.net/wiki/Item:Q189) | add better synonyms? | | Laser power | [incident light power datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000017)| [Laser power](https://wiki.charisma.ideaconsult.net/wiki/Item:Q188) | | | Number of acumulations | [number of accumulations](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000007)| | | | Method | | | unclear if this refers to the mapping mode discussed in #28 or to the various existig subclasses of [laser Raman spectroscopy](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0002515) | | Sampling accessory | [diffraction grating](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000011), [microscope](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0400169), [spectrometer](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0001234), [Raman spectrometer](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0001235), [Raman microscope](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0001814) | | Other devices need to be defined yet in NTRs. Which are really necessary from a POV centered around finding the right dataset, not reproducing the research?| | gain | [preamplifier gain setting](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000003) | | | | | | | |

Terms that already exist but not in VIBSO yet need to be imported from external ontologies:

| needed term | existing external term | CHARISMA link | comments | | ---- | ---- | ---- | ---- | | concentration quality| [PATO:concentration of](https://terminology.nfdi4chem.de/ts/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000033) | [Concentration](https://wiki.charisma.ideaconsult.net/wiki/Item:Q316)|| | Model | [iao:model number](https://terminology.nfdi4chem.de/ts/ontologies/iao/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000017) || to be able to further denote the specific kind of spectrometer used, if the chmo:spectrometer class might not suffice for this| | Mass (weight of sample, solvent, reagent, etc.) | [IAO:mass measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/iao/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000414) | ---- | ---- | | Solvent | [OBI:solvent role](https://terminology.nfdi4chem.de/ts/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302732) | | Chemicals that are used as solvents will have this solvent role in RDF | | Density |[pato:mass density](https://terminology.nfdi4chem.de/ts/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0001019) | | |

Terms needed to be minted in VIBSO or requested in external ontologies:

| needed term | possible parent | CHARISMA link | definition | comments | | ---- | ---- | ---- | ---- | ---- | | Absorbance | need to adapt [absorbance](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0001157) placed under [iao:measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) | [Absorbance](https://wiki.charisma.ideaconsult.net/wiki/Item:Q287) ?|https://doi.org/10.1351/goldbook|https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86| | Absorbance maximum or Peak position | [IAO:scalar measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000032) | [Absorption band](https://wiki.charisma.ideaconsult.net/wiki/Item:Q288) | | https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/89| | concentration| actually it is [CHMO:concentration](https://terminology.nfdi4chem.de/ts/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0002820), but it should be a [IAO:scalar measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000032)| [concentration](https://wiki.charisma.ideaconsult.net/wiki/Item:Q316)| | https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/90 | | Pathlength | a [length measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/iao/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000408) | [Sample pathlength](https://wiki.charisma.ideaconsult.net/wiki/Item:Q24) | Thickness of layer, film, cuvette, deposit --> IR or Raman, if latter difference to [region of interest depth](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVIBSO_0000021) needs to be made clear if there is any | Content (Amount of any type per mass of liquid or gas or solid system) | | | https://doi.org/10.1351/goldbook | | | Particle area | [iao:scalar measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000032) | | area of particles in IR/Raman microscopy relative to total area | do we need the total illuminated surface area of the sample then as well? And is this related to https://pubmed.ncbi.nlm.nih.gov/27671141/? | | Scans (number of scans used to measure a spectrum) | need to adapt from [nmrCV:number of scans](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv/terms?iri=http%3A%2F%2FnmrML.org%2FnmrCV%23NMR%3A1400087)|| is related to discussion in #30| | Particle count | [iao:count](https://terminology.nfdi4chem.de/ts/ontologies/iao/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FAPOLLO_SV_00000032) | | number of counted particles in IR/Raman microscopy | | | Peak Area | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) --> adapt [afo:peak area](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0001073) | | | | | Peak Height (measurement datum) | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) --> adapt [afo:peak height](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0000948) | | absolute Peak Height | | | Raman Intensity | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) --> adapt from [AFO:Raman Intensity](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0001589) | | | | | Raman shift | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) --> adapt from [Raman wavenumber shift](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0001591) | | | | | Reflectance | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) --> adapt from [reflectance](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0002260) | | | | | relative Peak Area | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) --> adapt from [relative peak area](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0001165) | | | | | relative Peak Height | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) --> adapt from [relative peak height](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0000949) | | | | | Wavenumber | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) --> adapt from [wavenumber](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0001592) | [Wavenumber](https://wiki.charisma.ideaconsult.net/wiki/Item:Q37) | | | | viscosity value | measurement datum of [pato:viscosity](https://terminology.nfdi4chem.de/ts/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000992) --> adapt [afo:viscosity](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0002641) | | | | resolution | [setting datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000140) --> adapt from [resolution](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0001619) | | | | | Hydroxyl value | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) | | [In analytical chemistry, the hydroxyl value is defined as the number of milligrams of potassium hydroxide (KOH) required to neutralize the acetic acid taken up on acetylation of one gram of a chemical substance that contains free hydroxyl groups.](https://en.wikipedia.org/wiki/Hydroxyl_value) | | | acid value | [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) | | [In chemistry, acid value (AV, acid number, neutralization number or acidity) is a number used to quantify the acidity of a given chemical substance. It is the quantity of base (usually potassium hydroxide (KOH)), expressed as milligrams of KOH required to neutralize the acidic constituents in 1 gram of a sample.](https://en.wikipedia.org/wiki/Acid_value) | | | | Content of water in sample | a [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) | | | | | content of active ingredient | a [measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000109) | | | ppm | | calculated content AI | a content of active ingredient | | | | | average content AI | a content of active ingredient | | | | | dilution factor | a [data item](https://terminology.nfdi4chem.de/ts/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000027) adapt from [afo:dilution factor](https://terminology.nfdi4chem.de/ts/ontologies/afo/terms?iri=http%3A%2F%2Fpurl.allotrope.org%2Fontologies%2Fresult%23AFR_0002758) | | | | | refractive index | a [data item](https://terminology.nfdi4chem.de/ts/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000027) adapt from [cheminf:refractive index descriptor](https://terminology.nfdi4chem.de/ts/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_000253) | | | CHEMINF hs issues preventing it from being imported directly | | Pressure | a [data item](https://terminology.nfdi4chem.de/ts/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000027) adapt from [cheminf:vapour pressure descriptor](https://terminology.nfdi4chem.de/ts/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_000419) | | A [iao:scalar measurement datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000032) or [setting datum](https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000140) that is about a [PATO:pressure](https://terminology.nfdi4chem.de/ts/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0001025) Are we talking about a setting or measurement? |CHEMINF has issues preventing it from being imported directly | | pH value | a [data item](https://terminology.nfdi4chem.de/ts/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000027) adapt from [proco:solution pH datum](https://terminology.nfdi4chem.de/ts/ontologies/proco/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPROCO_0000216) or [cheminf:pH descriptor](https://terminology.nfdi4chem.de/ts/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_000442)| | needed axiomatization [CHMO:pH measurement](https://terminology.nfdi4chem.de/ts/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0002354) of [PATO:acidity](https://terminology.nfdi4chem.de/ts/ontologies/pato/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0001842)| * date & time of the measurement --> assuming this refers to the date/time a Raman record or a part thereof was created, we'd use standard terms from the Dublin Core ontology like [DC:created](https://terminology.tib.eu/ts/ontologies/dcterms/props?iri=http%3A%2F%2Fpurl.org%2Fdc%2Fterms%2Fcreated) or [DC:date](https://terminology.tib.eu/ts/ontologies/dcterms/props?iri=http%3A%2F%2Fpurl.org%2Fdc%2Fterms%2Fdate) Terms mentioned in the XLSX that remain unclear and need to be discussed/described further: * Kubelka Munk * Identity (Identity of Sample) * First derivative * Second derivative * Log (1/R) * Quotient (e.g. Relative peak/area heights) * number of scans used to measure a spectrum --> difference to number of accumulations = creation of mean spectrum?
StroemPhi commented 1 year ago

Any help from others for making NTR issues for the terms listed in the third table is highly welcome.

StroemPhi commented 1 year ago

accidentally closed this with #100