Under laboratory or controlled conditions

[seltmann]

@jhpoelen in the dataset we have observations that are qualified as only being observed under laboratory or controlled conditions. Do you have a suggestion about how to express this in the spreadsheet? Right now I just have experimentalCondition as a column and TRUE if it is known.

[jhpoelen]

From your description you are describing something like:

specimen X interacted with specimen Y in a laboratory enviroment

which is very different to for example:

specimen X interacted with specimen Y in a forest

Is that a good description?

[jhpoelen]

I was hoping to find "laboratory environment" in the environment ontology https://www.ebi.ac.uk/ols/search?q=laboratory&ontology=envo , but alas!

@pbuttigieg @cmungall Is a laboratory environment not a natural habitat of researchers and should therefore be added to EnvO?

[seltmann]

I found that it is under "experimental conditions," which maybe one approach. http://purl.obolibrary.org/obo/XCO_0000000

[seltmann]

@jhpoelen you are correct in your statement below.

From your description you are describing something like: specimen X interacted with specimen Y in a laboratory environment

[jhpoelen]

That might work. Regardless of which term you end up using, I'd suggest to follow the pattern:

...	somethingId	somethingLabel	...
...	OBO:123	laboratory	...

instead of

...	inLaboratory	...
...	yes	...

But hey, as long as it is defined and you can convince your colleagues to use it . . . I favor consensus over the "best" way of doing it.

[seltmann]

@jhpoelen I think at this point it is good for me to understand the best way to do it, than move to consensus, which may change thinking behind what is best.

[pbuttigieg]

We can add it to ENVO, we have mesocosms etc, and we can express anthropised and anthropogenic environments

Is there anything specific about the lab conditions you're using?

[seltmann]

@pbuttigieg there is nothing specific about the lab conditions we are describing. I have 2 conditions. The first is an interaction that was observed "in nature" and the second "under laboratory conditions." Natural conditions or observations vs unnatural or controlled conditions.

Is there an ENVO class that could represents something observed in its natural setting?

[pbuttigieg]

We created a "natural environment " class for the non-anthropised world. There are anthropogenic environment classes, and I'll create one for lab conditions. More soon.

On Tue, 28 Aug 2018, 12:00 Katja Seltmann, notifications@github.com wrote:

@pbuttigieg https://github.com/pbuttigieg there is nothing specific about the lab conditions we are describing. I have 2 conditions. The first is an interaction that was observed "in nature" and the second "under laboratory conditions." Natural conditions or observations vs unnatural or controlled conditions.

Is there an ENVO class that could represents something observed in its natural setting?

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[pbuttigieg]

I've created a laboratory environment class under anthropogenic environment. It will have the PURL http://purl.obolibrary.org/obo/ENVO_01001405 (active after we make our next release)

[pbuttigieg]

I've also created laboratory facility if you wish to refer to the constructed entity (building or complex) rather than its internal environment. This will have the following PURL: http://purl.obolibrary.org/obo/ENVO_01001406

The ontology understands that the facility has the environment as a part.

[pbuttigieg]

This is the natural environment class: http://purl.obolibrary.org/obo/ENVO_01000951

This may be enough, but be warned that it doesn't let the machine know that you observed the organism in its natural environment. For that, we could create a subclass of habitat (e.g. 'vampire moth habitat') that overlaps with its usual range of environments (you'll have to help me out there).

[jhpoelen]

@pbuttigieg awesome! I am so happy that we know have a formal way to describe the lab environments that "host" researchers as well as their. often involuntary, test subjects. Curious to hear @seltmann take on the vampire moth habitat idea.

[seltmann]

@pbuttigieg thanks for adding this term. I used terrestrial natural environment http://purl.obolibrary.org/obo/ENVO_01001226 and laboratory environment http://purl.obolibrary.org/obo/ENVO_01001405.

I like the vampire moth habitat or its habitat idea because that is more exact and in line with what is being implied by the research statements. Its not just any natural habitat, but its this animals natural habitat.

[pbuttigieg]

@seltmann I've added vampire moth habitat with http://purl.obolibrary.org/obo/ENVO_01001452 This is not yet axiomatised with any environments as I'm having a bit of difficulty finding resources (see below). It is, however, axiomatised with NCBI Taxonomy's entry for Calyptra.

The EOL page (mirrored in Wikipedia) is not very helpful when it comes to finding out which environments the moth is found in, it's more focused on their range.

I found a U of Alberta page that lists "mesic meadows, edges and clearings".

Would you be able to provide a list of environments that these moths can maintain their populations in with growth rates > 0?