add Fe,Al,Mn extraction procedures

[pvgenuchten]

resolves #130

[ldesousa]

@pvgenuchten Please submit your pull requests against develop, not master.

On the content: there are three new procedures, but no new observations, nor results (and perhaps properties). Those are necessary within the SOSA/STA framework.

[pvgenuchten]

Thanks for reviewing Luis, i rebased to develop.

For your second comment, is it correct to assume these aspects are managed by a script. I wanted to wait with the script until the PR had its first review. Or would you recommend to run the script now?

[ldesousa]

Without observations it is not possible to correctly evaluate the introduction of these new procedures. As presented now they cannot be applied by a user of the ontology, and I cannot be sure what do they actually add anew.

[pvgenuchten]

Can you point me to where I can add the observations?

Also I noticed the script to transform the csv runs at deploy time, so no need to run locally?

glosis/.github/workflows/codelists.yml

Line 39 in 7f288f1

python transform_to_csv.py ../../glosis_procedure.ttl ../../csv_codelists/glosis_procedure

[bkempen]

@pvgenuchten @ldesousa thanks! Good to see this progress. The addition looks good although I do not fully understand @ldesousa coments. I opened this issue (#130) because typical extraction procedures for Al, Mn, Fe, Si were missing in the first version of the methods vocab we did in our vocab viewer. I ran into that when I was for looking for vocab entries for the Soils4Africa soil analyses. I had to provide URLs describing these analyses to Calisto but these were not available.

The extraction methods that I referred to are commonly used methods to measure different fractions of extracted Al, Fe, Mn, Si. And are typically part of the 'standard package' of chemical soil analyses. With Ad we are currently defining observations these methods apply to.

One comment from my side, the literature reference is relevant as far as I can judge, but it is not open access. We can look for another source if needed.

[pvgenuchten]

Comment by Ad van Oostrum:

Data using this procedures is described in https://www.isric.org/sites/default/files/ISM_SM1.pdf p10 and https://www.isric.org/sites/default/files/ISM_SM2.pdf

Ad also indicates that many citations in the laboratory domain describing procedures are in closed access journals

An additional challenge here is that many of these generic procedures have local differences in how they are applied, these differences are generally not described at all

NRCS – Kellog lab provides a lab manual for the 3 procedures mentioned: page 620 (digital) or p. 596 (hard copy).

An alternative is this isric manual chapter 12

For describing the property that is measured (‘operational definition’) only the “extraction part” is important / the most important; composition, shaking ratio (temperature), extraction time etc. Both references are then equivalent.

For certain applications (criteria) it is important that you use the matching / prescribed lab method. Details in the prescription can be more important there. When describing in your database you should therefore take into account “what the user is looking for”; and that jargon is also not always clear.

[bkempen]

Thanks, Paul. This is helpful. I propose not to worry about 'local differences' otherwise we get nowhere with this. References to procedure manuals of well recognized laboratories (e.g. Kellog) would be fine I think.