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A community-driven ontology for the representation of environments
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Map to LTER vocabulary #135

Open cmungall opened 9 years ago

cmungall commented 9 years ago

http://vocab.lternet.edu/

cmungall commented 9 years ago

population and community properties should go to PCO. cc @rlwalls2008

  is_a LTER:674 ! population and community properties ***
   is_a LTER:115 ! community composition ***
   is_a LTER:166 ! diversity ***
    is_a LTER:542 ! species composition ***
    is_a LTER:543 ! species diversity ***
    is_a LTER:546 ! species richness ***
    is_a LTER:64 ! biodiversity ***
     is_a LTER:432 ! plant species composition ***
     is_a LTER:543 ! species diversity ***
     is_a LTER:546 ! species richness ***
   is_a LTER:468 ! respiration rates ***
   is_a LTER:554 ! standing crop ***
   is_a LTER:6 ! abundance ***
    is_a LTER:462 ! relative abundance ***
    is_a LTER:52 ! bacterial abundance ***
   is_a LTER:603 ! trophic structure ***
cmungall commented 9 years ago

Requires review

cmungall commented 9 years ago

The BP subbranch of the process hierarchy is also a candidate for PCO. Although many labels look like GO terms, I think many of these are populations of processes. E.g. mereological sum of photosynthesis processes in an area of land over some time; LTER:mortality = mereological sum of GO:deaths. This could be seen as term inflation though. Depends how these are to be used. cc @rlwalls2008

 / LTER:655 ! processes
  is_a LTER:656 ! biological processes 
   is_a LTER:155 ! disease
   is_a LTER:186 ! evolution
    is_a LTER:14 ! adaptation
    is_a LTER:188 ! extinction
    is_a LTER:357 ! mutation
    is_a LTER:360 ! natural selection
    is_a LTER:540 ! speciation
   is_a LTER:298 ! life history
    is_a LTER:113 ! colonization
    is_a LTER:156 ! dispersal
     is_a LTER:495 ! seed dispersal
    is_a LTER:226 ! germination
    is_a LTER:236 ! growth
     is_a LTER:428 ! plant growth
     is_a LTER:597 ! tree growth
    is_a LTER:237 ! habitat selection
    is_a LTER:264 ! incubation
    is_a LTER:353 ! mortality
     is_a LTER:598 ! tree mortality
    is_a LTER:461 ! regeneration
    is_a LTER:465 ! reproduction
    is_a LTER:572 ! survival
   is_a LTER:305 ! litterfall
   is_a LTER:338 ! microbial activity
   is_a LTER:449 ! production
    is_a LTER:417 ! photosynthesis
    is_a LTER:428 ! plant growth
    is_a LTER:447 ! primary production
     is_a LTER:363 ! net primary production
      is_a LTER:36 ! annual net primary production
    is_a LTER:5 ! aboveground production
    is_a LTER:53 ! bacterial production
   is_a LTER:544 ! species interactions
    is_a LTER:120 ! competition
    is_a LTER:233 ! grazing
    is_a LTER:244 ! herbivory
    is_a LTER:401 ! parasitism
    is_a LTER:444 ! predation
    is_a LTER:575 ! symbiosis
    is_a LTER:74 ! browsing
   is_a LTER:686 ! succession
   is_a LTER:689 ! translocation
   is_a LTER:88 ! carbon cycling
    is_a LTER:467 ! respiration
    is_a LTER:87 ! carbon assimilation
pbuttigieg commented 9 years ago

Populations of processes seems a bit odd, but not wrong. Perhaps a process that has as parts processes that have as participants (one or more ecological) populations (or communities). We can remain agnostic towards area at this level, I think, as this would be an instance-level issue. Some can be linked to ENVO classes directly, e.g. "litterfall" to the leaf litter layer.

This can be the foundation for some ecosystem services or some of the concepts NCEAS was interested in. On 1 Apr 2015 03:41, "Chris Mungall" notifications@github.com wrote:

The BP subbranch of the process hierarchy is also a candidate for PCO. Although many labels look like GO terms, I think many of these are populations of processes. E.g. mereological sum of photosynthesis processes in an area of land over some time; LTER:mortality = mereological sum of GO:deaths. This could be seen as term inflation though. Depends how these are to be used. cc @rlwalls2008 https://github.com/rlwalls2008

/ LTER:655 ! processes is_a LTER:656 ! biological processes is_a LTER:155 ! disease is_a LTER:186 ! evolution is_a LTER:14 ! adaptation is_a LTER:188 ! extinction is_a LTER:357 ! mutation is_a LTER:360 ! natural selection is_a LTER:540 ! speciation is_a LTER:298 ! life history is_a LTER:113 ! colonization is_a LTER:156 ! dispersal is_a LTER:495 ! seed dispersal is_a LTER:226 ! germination is_a LTER:236 ! growth is_a LTER:428 ! plant growth is_a LTER:597 ! tree growth is_a LTER:237 ! habitat selection is_a LTER:264 ! incubation is_a LTER:353 ! mortality is_a LTER:598 ! tree mortality is_a LTER:461 ! regeneration is_a LTER:465 ! reproduction is_a LTER:572 ! survival is_a LTER:305 ! litterfall is_a LTER:338 ! microbial activity is_a LTER:449 ! production is_a LTER:417 ! photosynthesis is_a LTER:428 ! plant growth is_a LTER:447 ! primary production is_a LTER:363 ! net primary production is_a LTER:36 ! annual net primary production is_a LTER:5 ! aboveground production is_a LTER:53 ! bacterial production is_a LTER:544 ! species interactions is_a LTER:120 ! competition is_a LTER:233 ! grazing is_a LTER:244 ! herbivory is_a LTER:401 ! parasitism is_a LTER:444 ! predation is_a LTER:575 ! symbiosis is_a LTER:74 ! browsing is_a LTER:686 ! succession is_a LTER:689 ! translocation is_a LTER:88 ! carbon cycling is_a LTER:467 ! respiration is_a LTER:87 ! carbon assimilation

— Reply to this email directly or view it on GitHub https://github.com/EnvironmentOntology/envo/issues/135#issuecomment-88307447 .

ramonawalls commented 9 years ago

I created a PCO issue at https://code.google.com/p/popcomm-ontology/issues/detail?id=20.

ramonawalls commented 9 years ago

I have never used the phrase "population of processes". To me that sounds like a group of processes that do not have any parthood relations among them. I've always just said that one process has other processes as parts. But maybe Chris just meant to say "population process"?

cmungall commented 9 years ago

it's just a 4D extensions of the concept of 'population'. Just as we may be interested in talking about a population of plants (as distinct from an individual plant) we may want to talk about a population of photosynthesis instances

ramonawalls commented 9 years ago

That sounds okay to me! In fact, we wrote about something like that in a meeting report, to distinguish population qualities that are sum (or some other stat) of the individual qualities versus those that only exist in populations. Same idea can apply to processes.

pbuttigieg commented 9 years ago

Yes, that makes sense. Some may say it's shorthand (for processes that have participants that are in the same population of material entities), but it's no more so than most populations of material entities. On 3 Apr 2015 02:16, "Ramona Walls" notifications@github.com wrote:

That sounds okay to me!

— Reply to this email directly or view it on GitHub https://github.com/EnvironmentOntology/envo/issues/135#issuecomment-89090254 .