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Add core ecological interactions #2

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23 of 29 tasks
pbuttigieg opened this issue Aug 14, 2017 · 18 comments
Open
23 of 29 tasks

Add core ecological interactions #2

pbuttigieg opened this issue Aug 14, 2017 · 18 comments

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@pbuttigieg
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pbuttigieg commented Aug 14, 2017

Likely overlap with with REX and RO-ECO, often will specialise terms existing in these ( @cmungall )

Initial set

interactions

  • consumption
    • monophagy
    • oligophagy
    • mycophagy
    • herbivory
      • herbivorous grazing
      • seed predation
      • herbivorous browser
    • bactivory
    • parasitism
      • parasitoidism
    • carnivory
      • scavenging
      • predation ⚠️ (probably better under heterotrophy?)
        • trapping
        • hunting
        • social predation (e.g. wolves working together)
        • egg predation
        • cannibalism
          • oophagy ⚠️ (carnivory?)
    • insectivory
    • decomposition
      • detritivory
Misc
  • predator avoidance
    • pursuit deterrence / deterrent
      • stotting 🦌
    • escape
      • cryptic escape
    • avoiding detection
@cmungall
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Some of the classes me be more appropriate for NBO. Although I appreciate that NBO is not in an optimal state for ecologists right now - what do you think @pmidford?

The goal is to coordinate the ixn relations with classes using the obscure OWL pattern here:
https://github.com/oborel/obo-relations/wiki/InteractionRelations

@pmidford
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pmidford commented Aug 15, 2017

Yes, that predator avoidance subtree looks like it would belong in NBO. We will be adding terms from ABO (coming from a Behavioral Ecology/Ethology ground) soon. We've already updated some definitions in NBO, and will be adding synonyms and child terms soon. Reorganizing the core of NBO will be more of a challenge, but we (@aclark-binghamton-edu, @swmargulis, and myself) have a list of changes that would improve the core, with, we believe, little impact on existing use cases.

@aclark-binghamton-edu
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aclark-binghamton-edu commented Aug 15, 2017 via email

@pmidford
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pmidford commented Aug 15, 2017 via email

@swmargulis
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swmargulis commented Aug 15, 2017 via email

@pbuttigieg
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xref: #9
We've just set up the NBO import and are, of course, happy to synchronise to avoid duplication.

@pbuttigieg
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Some of the classes me be more appropriate for NBO. Although I appreciate that NBO is not in an optimal state for ecologists right now - what do you think @pmidford?

@cmungall @pmidford We're more than happy to import, we'd just need some fairly quick term creation for the initial stages. We need to represent the various forms of feeding (fungivory etc) as processes; this seems to be in accordance with the NBO definition for behavior , but isn't aligned to BFO.

ECOCORE would then host the classes for the fungivores, the heterotrophs, etc

[...] We will be adding terms from ABO (coming from a Behavioral Ecology/Ethology ground) soon.

@pmidford ETA?

@pmidford
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I think our part of the term additions could be done in 1-2 weeks, then we'll have to convince Robert it's time to do an update release.

@pbuttigieg
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I think our part of the term additions could be done in 1-2 weeks, then we'll have to convince Robert it's time to do an update release.

Great! Should we create issues on NBO for the terms we'd need?
We're adding a few seed terms to show what sort of defs we need (these can be obsoleted and moved to NBO, but we're at a hackathon and need to rally around some classes in the very short term). More here: a9a8415

We'll continue to create the defined terms for the organisms that realize such behaviours in ECOCORE.

@diatomsRcool
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What is the current state of this? Looks like we are waiting for a good time to do an NBO import into ecocore?

@diatomsRcool
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All checked terms are in ecocore-edit

@diatomsRcool
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I'm not sure that hunting, trapping, or viral predation are appropriate terms to add here

@diatomsRcool
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All checked terms are in latest release v2018-09-11

@diatomsRcool
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Whats the difference between plant trophism and herbivory? Maybe they should be synonyms.

@aclark-binghamton-edu
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aclark-binghamton-edu commented Jan 24, 2019 via email

@diatomsRcool
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hunting, ambush, and trapping added to NBO import

@diatomsRcool
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I'm requesting stotting be added to NBO. The others will wait until we have a need for more specific terms.
obo-behavior/behavior-ontology#108

@diatomsRcool
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Reminder to future Anne....you have editing rights in NBO

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