request for new P01 term: bodyPart

[sformel-usgs]

Problem:

We need to describe stable isotope measurements from various body parts of the same sampled organism. There are 2-3 measurements per body part (e.g. gill, muscle, shell) per organism. The S12 terms could completely meet our needs for MeasurementValue but I couldn't find a good way to indicate a MeasurmentType of bodyPart. I don't think it's useful to incorporate it into many terms as a subcomponent because (1) it would be useful to be able to group this data by body part value and (2) it will result in taxon x body part # of terms, which feels excessive.

Request

Create a new P01 term, bodyPart. This term would be used in eMOF MeasurementType and allow the specification of terms from S12 as MeasurementValue.

Suggested Definition

any part of an organism, such as an organ or extremity defined in vocabulary S12.

[roswri]

Hi @sformel-usgs,

As you have pointed out, there are two ways to handle this within the Darwin Core format:

1. Create new P01 codes for each combination of stable isotope and body part e.g. "Concentration of [stable isotope] per unit dry/wet weight of biota {biological entity specified elsewhere [Subcomponent: gill/muscle/shell]}" this would allow you to have one sample event for each organism rather than one event per body part per organism. There would be more parameter codes, they would not be challenging to create, but potentially more complicated to keep track of in your data.
2. Create new P01 codes for each stable isotope e.g. "Concentration of [stable isotope] per unit dry/wet weight of biota {biological entity specified elsewhere}", and a new P01 for "Body part of biological entity specified elsewhere". I think for this option to work you would need to have one event per body part per organism so you could then link the eMOF for the concentration measurement and the eMOF describing the body part.

If I understand correctly there's 2-3 stable isotope measurements per body part which is only ~9 P01 terms if we went with option 1. Option 2 could result in a more complicated event table. Could you let me know which option you would prefer?

Many thanks, Roseanna

[sformel-usgs]

@roswri thank you for the thoughtful response, and my apologies for the delayed answer. I would prefer the second option, with the new P01 term for body part. I think this aligns with the response from #28.

[gwemon]

@sformel-usgs Option 2 is indeed attractive and it saves us from creating many combinations for various body parts however we discussed this ticket at the OBIS vocab group meeting today and we were wondering how would the appropriate body part be linked to their respective stable isotope measurement value if they sit under the same occurrence ID? I understand that it is not currently possible to do this. Could you explain how you would see this working?

[EliLawrence]

I found the parentMeasurementID thread we were wondering about yesterday (https://github.com/tdwg/dwc/issues/362) and based on that, I wonder if such data could be formatted like:

Occurrence table eventID	occurrenceID	occurrenceStatus	basisOfRecord	scientificName
e-1	occ1	present	materialSample	Salmo salar
e-1	occ2	present	materialSample	Salmo salar

eMoF Table 

eventID	occurrenceID	parentMeasurementID	measurementID	measurementType	measurementValue
e-1	occ1		occ1_gill	body part	gill
e-1	occ1	occ1_gill	spp1_gill_isotope	Concentration of isotope	10
e-1	occ1		occ1_muscle	body part	muscle
e-1	occ1	occ1_muscle	occ1_muscle_isotope	Concentration of isotope	20
e-1	occ2		occ2_gill	body part	gill
e-1	occ2	occ2_gill	occ2_gill_isotope	Concentration of isotope	10
e-1	occ2		occ2_muscle	body part	muscle
e-1	occ2	occ2_muscle	occ2_muscle_isotope	Concentration of isotope	20

But I am not sure if parentMeasurementID is implemented in the IPT, or if there is an issue in having multiple measurementType: body part linked to the same occurenceID..