Add proper docs - #130
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While writing the docs centered around the yaml files as modules, it became clear these two belong in the chemical entities module, not on the most upper ChemDCAT-AP level.
To make the schema easier to read
…s to SubstanceSample repsectively ChemicalReaction These subclasses are needed to demonstrate how the DCAT-AP+ classes should be specialized in Chem-DCAT-AP sub-profiles. This commit also adds two example files to test these new classes. As part of this the bug that `has_reaction_step` was not multivalued, was also fix for all to work.
…taset-001.yaml additionally as chebi:'chemical substance' and thereby fix that the `n-Buli` reactant was typed as a chebi:mixture, which is probably not wrong, since it will have some unknown residue. But chemical substance should be the standard.
…rizationDataset` and run `just gen-project`
Also declare all the example reaction details in the object provided from the dataset `is_about_activity` slot. It parts were previously declared there and in the `evaluated_activity` slot, where it is now only being referenced.
…ities_ap.yaml` As they are used for the ChemicalReaction as well.
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dalito
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dalito
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Some minor comments. Overall, it is a very good start for the documentations.
Some modelling decisions show that the development was driven from the molecular world but not chemical engineering. There may be room for a chemical engineering profile that could re-use parts of this profile.
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| - **By analysis method** → Find all datasets generated by heteronuclear single quantum coherence (HSQC) NMR spectroscopy, or by gas chromatography-mass spectrometry, or by X-ray powder diffraction. | ||
| - **By analysed substance** → Find all datasets about a specific molecule (via InChIKey), or about any compound containing a thiazole substructure (via SMILES substructure search on the `composed_of` chain). | ||
| - **By reaction characteristics** → Find all datasets about reactions that used a specific catalyst, produced a specific product, or achieved a yield above a threshold. |
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Isn't this a query into yield a query into the data (not metadata) and therefore not possible without looking into the data itself?
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Well, we do have yield as an attribute of a reaction, so if this field is used, one could do such a query. The ReactionMonitoringDataset-001.yaml has it. From my POV, I'd say the minimal metadata one should provide on a reaction are the inputs (starting material and reactants), the product, the yield (if possible) and at best also the reaction type using MOP or RXNO.
@dalito it would be great if we could have your thoughts on this in an issue, so we don't forget this and can discuss in how far we need things for this in ChemDCAT-AP already for such sub-profiles to work. |
Update references across documentation to point to the DCAT-AP+ 'latest' URLs (design-patterns, how-to-extend, etc.) and fix a malformed Metadata4cat link. Also refresh several dark-theme SVG assets and adjust related doc wording for consistent upstream links and guidance.
Co-authored-by: Philip Strömert <Philip.Stroemert@tib.eu>
merge: Improve-docs into Improve-docs2
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This PR adds a first draft of proper ChemDCAT documentation.
While writing these some minor issues where found that are also fixed by this PR, which are:
Closes #129