How to integrate abundance data with sosa with additional living organism data

[Mataivic]

Hello,

I am currently working on the data integration of a research project I'm working on, and I'm facing issues on how to integrate data such as the abundance of a living organism in a sample.

For example, for integrating the value of the abundance of a living organism in a metagenomic sample representative of an agricultural field, I would have an instance of sosa:Observation with linked properties to:

• The sample (labelled with its ID) as the sosa:Sample, but I'm not sure of the property to use to link the observation to the sample
• The field (labelled with its ID) as the sosa:FeatureOfInterest, but I'm not sure whether link it to the observation or the sample (I would say to the sample in case it is sampled several times, since each sample has its ID and its own observations)
• The abundance value linked to the sosa:Observation with the property sosa:hasSimpleResult
• At this point, the information on which species is observed is still missing. I am reluctant to consider the species as a sosa:ObservableProperty, since it is not really a intrisic feature. So i'm wondering if the solution is to add a property to link a sosa:Observation to a specific "LivingOrganism" entity, on which I could add other properties such as its taxonomy. The sosa:ObservableProperty would then just be used to specifies that the sosa:Observation is an abundance measure

I draw a summary figure for visual help ; is it a good start or am I doing this completely wrong ? Does anyone has ideas ?

[dr-shorthair]

Interesting use-case.

First I would recommend taking advantage of some of the enhancements to SSN that were introduced in the SSN Extensions, in particular the distinction between Proximate and Ultimate feature-of-interest. This has been rolled into the updated SSN/SOSA ontology, which nearing completion. This will allow you to acknowledge the agricultural field as the ultimate FoI, while still being more precise about the details of the observation.

(You will find that the Latest editor's draft link at the top of the Recommendation will lead you there.)

Then I would suggest that the proximate FoI is something like 'abundance of taxon X' which is characterized through two observations:

1. observedProperty = organism abundance
2. observedProperty = name of taxon X

If Taxon X is specified in advance, then the second observation is not needed.

[sgrellet]

I gues "LivingOrganism" refers to "LivingOrganismX"

along that line, we have use cases here where

• the uFoI could be : agricultural field
• the pFoi would be where the sample happens or specific sampleSquare (if revisited multiple times in the same agricutural field)
• the obsProp would be 'occurrence of taxon X', 'occurrence of taxon Y'

[Mataivic]

The Ultimate feature-of-interest property is actually very convenient, it indeed answers the issue concerning the sample and the field, many thanks. i also just fund ObservationCollection adn SampleCollection which could just fit for other parts of my data integration.

Bit it seems I'll have no choice but to set the abundances of taxon X/Y/Z as ObservableProperties ? Meanwhile, I realized I'll have other issues with taxa : some observed taxa will have abundances, some only an absence/presence. Proceed with two observations as suggested (organism abundance in the 1st case, only organism name in the 2d case) would manage that I believe ?

Finally, I just realized that my field samples can be associated to differents parts of the fields : crop roots, crop leaves, soil ... Is it possible to add a second ObservedProperty or FeatureOfInterest to a sample / observation?

[dr-shorthair]

Is it possible to add a second ObservedProperty or FeatureOfInterest to a sample / observation?

No. An Execution has one (proximate) FoI, and an Observation has one ObservedProperty.

You can group observations about the same OP, or a group of FoIs, using ObservationCollection which allows you to record some properties on the collection, so you don't have to repeat them on all the members.