Update MIXS:0000028 - observed biotic relationship

[raissameyer]

Current term details Please supply the current details of the term that you would like to update:

Term name - observed biotic relationship
Term ID -  MIXS:0000028
Structured comment name - biotic_relationship
Definition - Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object
Expected value - enumeration
Value syntax - [free living|parasitism|commensalism|symbiotic|mutualism]
Example - free living
Preferred unit - 
Package(s) - MIxS core

Suggested update(s) There is a mismatch between the definition and the value syntax and example (xRef DwC-MIxS TG #19). The term should be revised to offer a clear guidance on what is to be expected in the field.

[pbuttigieg]

Thanks for raising this important issue, @raissameyer: This was discussed in yesterday's CIG call with @pyilmaz @ramonawalls @only1chunts @lschriml and @pbuttigieg

As the call focused on the symbiont-associated package, this discussion was cut short. However, the relationship types for symbiosis will likely be moved to the type of symbiosis field (#170), and this field will only state "symbiosis". This seems convoluted, when this field could handle both needs.

There was a general intent to simplify the description to omit the range (i.e. the organism X, Y, etc), deferring that to fields like "host". This is unsatisfactory as there are biotic relationships that don't have "hosts" (e.g. predation).

As far as I see it, there are two credible ways forward:

1. Modify the value syntax to something like [relationship type]:[taxonID] or similar. This creates yet another bespoke and non-interoperable data structure in MIxS.
2. Add another field - like biotic relationship partner or similar - to handle the range of the relationship. In the current spreadsheet-like mode of MIxS, this cannot handle many-to-one, one-to-many, or many-to-many relationship types (unless we create another bespoke data structure). This of course disappears if we can repeat this field in RDF-like structures.

Until MIxS matures into something more computable, perhaps option 1 is a stop-gap solution. The need to atomise this specification to increase hopes of actual interoperability reaches across many fields.

[ramonawalls]

I cannot resolve this issue. @ndheilly can you please clarify if your intention is to include both the relationship type and target organism in the value field or just the relationship type?

[ramonawalls]

Sorry, i just reread our meeting notes. The change here is to include only free living and symbiotic in the value field. The more specific types of symbioses will be handled in #170 that describes the type of symbiosis. This is in core, not in the SA package. I did not change the core for now, as it does not affect the SA package.

[ndheilly]

Based on our discussions, I believe the conclusions were:

• to include in MIxS core a term to choose whether the organism from which the sample was collected from is free-living or a symbiotic organism
• to include in the MIxS package the other term that allows user to choose the type of symbiosis (if known): parasitism / mutualism / commensalism (#170). But we remove reference to the host of the symbiotic host organism. However I am supportive of adding a term that gives the user the option to indicate the relationship partner (as suggested above).

[only1chunts]

So this field is being reduced in scope to only accept "Free-Living" or "Symbiotic organism" as the values, is that correct?

If so, what is the definition of the term? My suggestion is:

Term name - observed biotic relationship
Term ID -  MIXS:0000028
Structured comment name - biotic_relationship
**Definition - Please indicate if the sampled organism was free-living or in some sort of symbiotic relationship at the time of sampling? If in a symbiotic relationship you may wish to consider adding terms for type_of_symbiosis [MIXS:0001307] and host_of_host term details.
Expected value - enumeration
** Value syntax - [free living|symbiotic]
Example - free living
Preferred unit - 
Package(s) - MIxS core

[raissameyer]

So this field is being reduced in scope to only accept "Free-Living" or "Symbiotic organism" as the values, is that correct?

This would now exclude other observed biotic relationships, such as predation, while introducing "free-living" which I would not consider as a biotic relationship. @only1chunts Is there a reason for doing that?

[only1chunts]

I believe the argument was that predation is considered a type of symbiosis, but hopefully someone can confirm that. And the type of symbiosis was to be held in a separate field.

On Mon, 5 Jul 2021, 17:12 Raissa Meyer, @.***> wrote:

So this field is being reduced in scope to only accept "Free-Living" or "Symbiotic organism" as the values, is that correct?

This would now exclude other observed biotic relationships, such as predation. Is there a reason for doing that?

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[ndheilly]

Hi,

I agree that "observed bitoic relationship" may not be the right term name anymore. The term rather focuses on whether the sampled organism was dependent on a host at the time of sampling. Indeed micropredation is a type of parasitism, and micro-predators are dependent on their hosts. However, predation itself is not considered as part of this definition.

If this term is included in the MIxS core, it can be confusing to talk about other terms that exist only in the SA package within the definition. Can we point out towards the SA package?

If yes, I suggest the following definition :

Term name - dependence to a host Term ID - MIXS:0000028 Structured comment name - dependence_host Definition - Please indicate if the sampled organism was free-living or in a symbiotic relationship at the time of sampling. For symbiotic organisms you may wish to consider using the symbiont-associated package that includes terms for type_of_symbiosis [MIXS:0001307] and host_of_host term details. Expected value - enumeration Value syntax - [free living|symbiotic] Example - free living Preferred unit - Package(s) - MIxS core

[only1chunts]

@ndheilly , I dont think the name change you suggest is appropriate as there is also a term proposed with the name "host_dependance". Although looking at the definition of that I'm still not sure how it differs from this?! see ticket #169 for host_dependence:

MIXS ID : MIXS:0001315
Term name - host dependence
Structured comment name - host_dependence   
Definition - Type of host dependence for the symbiotic host organism to its host.
Expected value - enumeration 
Value syntax - [facultative\|obligate]

@ramonawalls , @lschriml do you have any suggestions here? -Should prey/predator be included as options in the value syntax of observed biotic relationship [MIXS:0000028]? Personally, I think not as everything is either prey or predator to something. -Should the term name be adjusted to reflect the expected values of free-living or not? -Do we need to revisit the definition of MIXS:0001315 ? (if so, please add comments in #169 )