how to reference other phases/diffractograms?

[rowlesmr]

This was raised in the third dot point of @vaitkus #161 (comment)

What is the correct way to define a data item that is used to point to another place which contains the information you're after?

In the example below, there is a diffractogram with _pd_diffractogram.id having the value of DIFFRACTOGRAM_0020. It was quantified by the external method using the information contained in the PD_QPA_EXTERNAL_STD category data items (ie the K factor and standard MAC) associated with the key _pd_qpa_external_std.diffractogram_id which has the value SRM676A.

I've currently indicated that by having _pd_qpa_external_std.diffractogram_id SRM676A given inside the block containing DIFFRACTOGRAM_0020. The definition of _pd_qpa_external_std.diffractogram_id is below.

save_pd_qpa_external_std.diffractogram_id

    _definition.id                '_pd_qpa_external_std.diffractogram_id'
    _definition.update            2023-01-15
    _description.text
;
    The diffractogram (see _pd_diffractogram.id) which is being used to
    calculate the diffractometer constant.
;
    _name.category_id             pd_qpa_external_std
    _name.object_id               diffractogram_id
    _name.linked_item_id          '_pd_diffractogram.id'
    _type.purpose                 Link
    _type.source                  Related
    _type.container               Single
    _type.contents                Text

save_

Is this the correct way to do it, or should there be another data item used to point? Something like

save_pd_qpa_external_std.ref_diffractogram_id

    _definition.id                '_pd_qpa_external_std.ref_diffractogram_id'
    _definition.update            2023-06-26
    _description.text
;
    The diffractogram from which the diffractometer constant was calculated.
;
    _name.category_id             pd_qpa_external_std
    _name.object_id               ref_diffractogram_id
    _type.purpose                 Encode
    _type.source                  Related
    _type.container               Single
    _type.contents                Text

save_

where it isn't linked, but does Encode a diffractometer_id in order to find all the information?

#\#CIF_2.0

#######	Begin common information	#######
data_global
_diffrn_radiation_wavelength.value   1.7889847
#######	End common information	#######

#######	Begin powder diffraction data	#######
data_DIFFRACTOGRAM_0020
_pd_diffractogram.id	DIFFRACTOGRAM_0020

loop_
_pd_phase_mass.phase_id
_pd_phase_mass.percent
Goethite_0020	70.6(2)
Hematite_0020	8.11(17)
Quartz_0020 	6.48(6)
Kaolinite_0020	1.88(18)
Nacrite_0020	1.21(12)
Anatase_0020	0.35(3)
Rutile_0020 	0.44(4)
#amor 10.9(4)

_pd_qpa_external_std.diffractogram_id   SRM676A
_pd_char.mass_atten_coef_mu_calc        4.52708878
_pd_qpa_overall.method                  external_standard


loop_
	_pd_data.point_id
	_pd_meas.2theta_scan
	_pd_meas.counts_total
	_pd_calc.intensity_total
	_pd_proc.intensity_bkg_calc
1	5.007880	737	805.948339	805.681930	
#...
5713	95.008094	77	76.586601	63.972674
#######	End powder diffraction data	#######


#######	Begin External Standard information	#######
data_STD_Aluminium_oxide_alpha
_pd_phase.id	STD_Aluminium_oxide_alpha
#...

data_SRM676A
_pd_diffractogram.id	SRM676A

loop_
	_pd_phase_mass.phase_id
	_pd_phase_mass.percent
	_pd_phase_mass.percent_su
STD_Aluminium_oxide_alpha	99.02   1.11

_pd_qpa_external_std.k_factor           321.82
_pd_char.mass_atten_coef_mu_calc        4.87922752
_pd_qpa_overall.method                  external_standard
##
# _pd_qpa_external_std.diffractogram_id gets the value "SRM676A"
# solely due to the fact that _pd_diffractogram.id exists in this
# block, and has the value "SRM676A"
##

loop_
	_pd_data.point_id
	_pd_meas.2theta_scan
	_pd_meas.counts_total
	_pd_calc.intensity_total
	_pd_proc.intensity_bkg_calc
191	8.001585	66	62.572173	62.572174
#...
5713	95.008094	26	25.050297	23.441636
#######	End External Standard information	#######
    


#######	Begin powder crystal structures	#######
data_Goethite_0020
_pd_phase.id	Goethite_0020
#...
data_Hematite_0020
_pd_phase.id	Hematite_0020
#...
data_Quartz_0020
_pd_phase.id	Quartz_0020
#...
data_Kaolinite_0020
_pd_phase.id	Kaolinite_0020
#...
data_Nacrite_0020
_pd_phase.id	Nacrite_0020
#...
data_Anatase_0020
_pd_phase.id	Anatase_0020
#...
data_Rutile_0020
_pd_phase.id	Rutile_0020
#...
#######	End powder crystal structures	#######

[jamesrhester]

What is the correct way to define a data item that is used to point to another place which contains the information you're after?

The first thing to do is to not think in terms of "pointing" to a "place" that "contains" something. Instead, you are simply "identifying" something - a diffractogram, or a phase, or an instrument, etc. So your first definition (the current one) seems correct to me.

The example also seems correct to me. It is a little strange to think that _pd_qpa_external_std.diffractogram_id has the value SRM676A, but I guess it makes sense to say that it is also calibrating itself, as well as being used by other diffractograms.

# _pd_qpa_external_std.diffractogram_id gets the value "SRM676A"
# solely due to the fact that _pd_diffractogram.id exists in this
# block, and has the value "SRM676A"

[rowlesmr]

It is a little strange to think that _pd_qpa_external_std.diffractogram_id has the value SRM676A

To my mind, the SRM676A diffractogram owns the calibration value, and all other places are merely borrowing it.

Now that I think about it, as you need to collect the unknown data under identical circumstances, isn't the calibration owned by the diffrn.id? And then you need a seperate (hypothetical) _pd_diffrn.spec_id to identify each specimen for each diffraction experiment?

.

I don't know if I'm breaking out of my baliwick, but I'm trying to think up how to make a collection of powder CIF blocks into a single set of database tables, rather than a separate set for each block, and so I need to be able to uniquely identify things.

[jamesrhester]

I think PD_DIFFRACTOGRAM just needs a pointer to _diffrn.id, and then we have identified the conditions under which a diffractogram was measured. Sort of puzzled we don't have that yet, unless there's an indirect link.

Anyway, with that in place, SRM676A has a well-defined _diffrn.id, as do all other diffractograms, and they may differ slightly. A validation routine can decide if the variance is acceptable.

Not sure about the spec_id suggestion. The DIFFRN category does have a pointer to _exptl_crystal.id, which makes the particular crystal a part of the diffraction conditions, so by analogy spec_id has a place there as well. But spec_id is already pointed to by PD_DIFFRACTOGRAM so is already taken care of, I think.