Map to LTER vocabulary

[cmungall]

http://vocab.lternet.edu/

[cmungall]

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]

Requires review

• mapped: https://github.com/EnvironmentOntology/envo/blob/master/src/envo/mappings/lter-mapping.tsv
• unmapped: https://github.com/EnvironmentOntology/envo/blob/master/src/envo/mappings/lter-unmapped.tsv (2nd column shows the sub-root category)
• LTER:173 ! ecosystems
  • add to ENVO
• LTER:395 ! organisms
  • Belongs in NCBITaxon
• LTER:643 ! substances
  • Belongs in CHEBI
• LTER:651 ! disciplines
  • just use MESH here?
• LTER:655 ! processes
  • Consider for envo-process
• LTER:667 ! measurements
  • ENVO or PCO
• LTER:693 ! methods
  • BCO or something analogous?
• LTER:694 ! substrates
  • Do we need a specific category in ENVO here?
• LTER:698 ! events
  • Consider for envo-process
• LTER:799 ! organizational units
  • TBD

[cmungall]

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]

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

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[ramonawalls]

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

[ramonawalls]

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]

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]

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]

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!

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