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EcologicalSemantics / ecocore

An ontology of core ecological entities
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Add core ecological interactions #2

Open pbuttigieg opened 6 years ago

pbuttigieg commented 6 years ago

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

Initial set

interactions

Misc
cmungall commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

HI Peter

I didn’t get the intermediary email or response…can you fill me in on what your response is a reply to??

Thanks,

Anne Anne B. Clark, Ph.D. Biological Sciences Binghamton University Binghamton, NY 13902 1-607-777-6228, Fax -777-6521 C. 607-222-0905

We are speaking where we stand and we shall stand afterwards in the presence of what we have said.--Wendell Berry—"Standing By Words"

On Aug 15, 2017, at 12:03 PM, Peter E. Midford notifications@github.com wrote:

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 https://github.com/aclark-binghamton-edu, @swmargulis https://github.com/swmargulis, and myself) have a list of changes that would improve the core, with, we believe, little impact on existing use cases.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/EcologicalSemantics/ecocore/issues/2#issuecomment-322510187, or mute the thread https://github.com/notifications/unsubscribe-auth/AOl5ls8RHIpPZJFxXcF_NJllOaw-Aj5Rks5sYcFogaJpZM4O25Fb.

pmidford commented 6 years ago

At the bottom of the email, there is a link to the GitHub issue. The whole conversation will be there. If you can't find the link, l can send it when I get in.

On Aug 15, 2017 09:12, "aclark-binghamton-edu" notifications@github.com wrote:

HI Peter

I didn’t get the intermediary email or response…can you fill me in on what your response is a reply to??

Thanks,

Anne Anne B. Clark, Ph.D. Biological Sciences Binghamton University Binghamton, NY 13902 1-607-777-6228 <(607)%20777-6228>, Fax -777-6521 C. 607-222-0905 <(607)%20222-0905>

We are speaking where we stand and we shall stand afterwards in the presence of what we have said.--Wendell Berry—"Standing By Words"

On Aug 15, 2017, at 12:03 PM, Peter E. Midford notifications@github.com wrote:

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 < https://github.com/aclark-binghamton-edu>, @swmargulis < https://github.com/swmargulis>, and myself) have a list of changes that would improve the core, with, we believe, little impact on existing use cases.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ EcologicalSemantics/ecocore/issues/2#issuecomment-322510187, or mute the thread https://github.com/notifications/unsubscribe- auth/AOl5ls8RHIpPZJFxXcF_NJllOaw-Aj5Rks5sYcFogaJpZM4O25Fb.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/EcologicalSemantics/ecocore/issues/2#issuecomment-322513315, or mute the thread https://github.com/notifications/unsubscribe-auth/AAX3jsFC3ipRjXY8cCMOft1FFsp7yUxyks5sYcN1gaJpZM4O25Fb .

swmargulis commented 6 years ago

I didn't get it either.

Sent from my iPhone

On Aug 15, 2017, at 12:12 PM, aclark-binghamton-edu notifications@github.com<mailto:notifications@github.com> wrote:

HI Peter

I didn’t get the intermediary email or response…can you fill me in on what your response is a reply to??

Thanks,

Anne Anne B. Clark, Ph.D. Biological Sciences Binghamton University Binghamton, NY 13902 1-607-777-6228, Fax -777-6521 C. 607-222-0905

We are speaking where we stand and we shall stand afterwards in the presence of what we have said.--Wendell Berry—"Standing By Words"

On Aug 15, 2017, at 12:03 PM, Peter E. Midford notifications@github.com<mailto:notifications@github.com> wrote:

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 https://github.com/aclark-binghamton-edu, @swmargulis https://github.com/swmargulis, and myself) have a list of changes that would improve the core, with, we believe, little impact on existing use cases.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/EcologicalSemantics/ecocore/issues/2#issuecomment-322510187, or mute the thread https://github.com/notifications/unsubscribe-auth/AOl5ls8RHIpPZJFxXcF_NJllOaw-Aj5Rks5sYcFogaJpZM4O25Fb.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/EcologicalSemantics/ecocore/issues/2#issuecomment-322513315, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AOl4sTWsl4oxxeP8LLAw1zr3KLsb8ZCGks5sYcN1gaJpZM4O25Fb.

pbuttigieg commented 6 years ago

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

pbuttigieg commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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: https://github.com/EcologicalSemantics/ecocore/commit/a9a8415c3365e1bf7cce89edf4363e89d3347abc

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

diatomsRcool commented 6 years ago

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

diatomsRcool commented 5 years ago

All checked terms are in ecocore-edit

diatomsRcool commented 5 years ago

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

diatomsRcool commented 5 years ago

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

diatomsRcool commented 5 years ago

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

aclark-binghamton-edu commented 5 years ago

At most they should be synonyms--that is the only definition of plant trophism. Looking at usage, depending on English language speakers, plant trophism is often confused with plant TROPISM. Make it a synonym.

Also note need for reorganization of heirarchy to simplify and clarify. Viral predation of bacteria belongs under Bacterivory (if that is a term in common use) Carnivory belongs under heterotrophy but under carnivory, the list should be scavenging, predation (or depredation), and under predation, egg predation OR oophagy (synonyms?) and cannibalism. The various methods of predation are elaborated in NBO--the ABO part of it.

Anne

On Thu, Jan 24, 2019 at 10:05 AM diatomsRcool notifications@github.com wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/EcologicalSemantics/ecocore/issues/2#issuecomment-457229329, or mute the thread https://github.com/notifications/unsubscribe-auth/AOl5lq0qOwItFJdarWn4nDxTYRyvIKfoks5vGcukgaJpZM4O25Fb .

-- Anne B. Clark, Ph.D. Biological Sciences Binghamton University Binghamton, NY 13902-6000

(607) 777-6228 (office) (607) 222-0905 (cell) (607) 777-6521 (fax-Dept office)

diatomsRcool commented 3 years ago

hunting, ambush, and trapping added to NBO import

diatomsRcool commented 3 years ago

I'm requesting stotting be added to NBO. The others will wait until we have a need for more specific terms. https://github.com/obo-behavior/behavior-ontology/issues/108

diatomsRcool commented 3 years ago

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