EnvironmentOntology
Map to LTER vocabulary
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 ***
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
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
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" [email protected] 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 .
I created a PCO issue at https://code.google.com/p/popcomm-ontology/issues/detail?id=20.
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"?
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
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.
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" [email protected] 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 .