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PopulationAndCommunityOntology / pco

An ontology about groups of interacting organisms such as populations and communities
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Community species richness & diversity #1

Closed ramonawalls closed 9 years ago

ramonawalls commented 9 years ago

Issue by GoogleCodeExporter Thursday Jun 11, 2015 at 23:48 GMT Originally opened as https://github.com/rlwalls2008/pco/issues/3

def: "The number of species present in a community."
is_a: quality (inferred)

Are numbers qualities? [a question for BFO not you]

I initially thought this a curious definition - "richness" in the general sense 
is typically more nuanced than simply a count.

But wikipedia agreess with PCO:
http://en.wikipedia.org/wiki/Species_richness

Will you add definition sources as axiom annotations on your definitions?

I also encourage links to wikipedia whether you use them in defs or not. E.g. 
Wikipedia:species_richness foaf:is_about pco:species richness. Up to you though.

Finally: is http://en.wikipedia.org/wiki/Species_diversity in scope for PCO?

Original issue reported on code.google.com by cmung...@gmail.com on 14 Mar 2013 at 5:50

ramonawalls commented 9 years ago

Comment by GoogleCodeExporter Thursday Jun 11, 2015 at 23:48 GMT

Richness is generally considered just the number of species; diversity is 
number of species plus other information (like abundance).

I plan to add definition sources for all terms, preferably from authoritative 
books, but will look into adding wikipedia refs too. 

Species diversity is definitely in scope, but I haven't added it yet because it 
is more complicated than richness (there are many ways of measuring diversity).

Original comment by rlwalls2...@gmail.com on 21 Mar 2013 at 9:11

ramonawalls commented 9 years ago

Comment by GoogleCodeExporter Thursday Jun 11, 2015 at 23:48 GMT

Chris, if I want to add links like "Wikipedia:species_richness foaf:is_about 
pco:species richness" do I add Wikipedia:species_richness as an instance or a 
class? Can you point me to an example of an ontology that is doing this 
(correctly)?  

I did see the obo-discuss thread about how to properly reference wikipedia 
(http://obo-discuss.2851485.n2.nabble.com/Referencing-wikipedia-a-suggestion-td7
572983.html).

Original comment by rlwalls2...@gmail.com on 21 Mar 2013 at 11:01

ramonawalls commented 9 years ago

Comment by GoogleCodeExporter Thursday Jun 11, 2015 at 23:48 GMT

You're right, modeling the wikipedia relationship properly is a lot of faff. 
You could do this the way everyone else does it, with an oboInOwl:xref from the 
class to the wikipedia URL (and count on the fact we'll all be using the same 
transform later on)

This is just to say that they're talking about the same thing. The thread was 
in part about provenance for definitions. I think it's important to record the 
specific version as David says, but I think if you're going to that trouble, 
why not go to source material, authoritative reviews/text book and use that?

Original comment by cmung...@gmail.com on 21 Mar 2013 at 11:41

ramonawalls commented 9 years ago

Comment by GoogleCodeExporter Thursday Jun 11, 2015 at 23:48 GMT

At the 2/6/2015 call we agreed that we should stick with the most general 
definitiosn of these for now.

Original comment by rlwalls2...@gmail.com on 6 Feb 2015 at 4:17

ramonawalls commented 9 years ago

Comment by GoogleCodeExporter Thursday Jun 11, 2015 at 23:48 GMT

Original comment by rlwalls2...@gmail.com on 6 Feb 2015 at 5:05

ramonawalls commented 9 years ago

See notes from discussion on 7/24/15 https://docs.google.com/document/d/1-xzkHEF-D0PLLSYgck_aNrOz2TpWh0GDDMi3i1MjZqw/edit