Adding has_habitat and biotically_interacts_with predicates

[diatomsRcool]

I want to add predicates to the model that represent associations between an organism or organism taxon and their environments or other organisms. I am doing this in the context of eco-kg and importing EOL TraitBank data. In addition to trait data, EOLTraitBank contains information about where an organism has been observed and its organism interactions.

I would like to add has_habitat as a child of located_in. I can use located_in to describe political/geographical locations, like countries or mountains. I need something a bit different for habitat types, like saying an organism lives in a swamp or a boreal forest. I would like to add biotically_interacts_with as a child of interacts_with. I need to represent the collection of trophic interactions represented in the eco subset of RO. I will likely need more predicates as children of biotically_interacts_with, but cross that bridge.

Any objections?

@sierra-moxon @justaddcoffee @jhpoelen

[jhpoelen]

@diatomsRcool no objections here: I much like the idea of increasing the reach of species interactions data!

Also, much, if not all, of EOL TraitBank interaction data comes from GloBI (https://globalbioticinteractions.org) . And, I'd be happy to help produce/update a GloBI data product that would help make it easier to import/link the continuously updating species interaction data into the eco-kg.

Curious to learn more!

[jhpoelen]

cc-ing EOL TraitBank collaborators @katjaschulz and @jhammock .

[sierra-moxon]

@wdduncan tagging you for feedback too

[cmungall]

See https://github.com/oborel/obo-relations/issues/453 for coordinating with RO

• a specific panda instance and a zoo it lives in
• a clade of birds and the two ecosystems it spends its summers and winters in
• bears and the urban biomes they encroach in
• a taxon such as certain bats and the structures they sleep in (e.g. caves)
• an interaction between two taxa and a location - e.g. shark attacking seals near the shores

[wdduncan]

Some of the classes in the envo hierarchy might be of use here. For example,

• The panda lives in a particular zoological garden.
• Birds may inhabit a particular tropical environment.
• Bears encroach on a particular urban biome
• etc.

[diatomsRcool]

I think I was mostly thrown by the definitions for located in found in RO and in BioLink. The BioLink definition is very broad, which isn't necessarily a problem. The RO definition seems maybe a little too "physical". I think has habitat almost says more about the organism and its adaptations. Does that make sense? Maybe I'm thinking too much.

[wdduncan]

MIxS has properties for env_broad_scale, env_local_scale, env_medium. Guidance on how evno uses them is document here.

These properties are described as: env_broad_scale

In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). | We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428

env_local_scale

In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen.

env_medium

In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling

The labels for these properties are cryptic. I find the labels env_biome, env_feature, and env_material more intuitive.

@diatomsRcool if these properties were added to the biolink model, would that help you?

[sierra-moxon]

Per slack conversation, I believe located_in was selected as the predicate in this use case. @diatomsRcool ok to close?

[diatomsRcool]

yes, this can be closed.