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PopulationAndCommunityOntology / pco

An ontology about groups of interacting organisms such as populations and communities
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NTRs: Shannon and Simpson diversity #94

Closed kaiiam closed 4 years ago

kaiiam commented 4 years ago

For the UA-SRC project we'll need to represent some data which has to do with diversity metric calculated upon microbial 16S sequence data. Specifically, Richness, Shannon, Simpson, and Inverse Simpson diversity.

We currently have the term community species richness suitable for Richness under the quality of an ecological community hierarchy.

Perhaps we could add the following terms?

community species shannon diversity index

Definition:

A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi).

Parent class

community species diversity

References

https://doi.org/10.1002%2Fj.1538-7305.1948.tb01338.x

http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html

community species simpson diversity index

Definition:

A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi).

Parent class

community species diversity

Reference

http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html

community species inverse simpson diversity index

Definition:

A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi).

Comment:

The inverse simpson diversity index is the reciprocal of the (standard) simpson diversity index.

Parent class

community species diversity

References

http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html

https://mothur.org/wiki/invsimpson/

@ramonawalls let me know what you think and please double check me on this. Do we want to try and add this to the July 2020 release?

ramonawalls commented 4 years ago

Thanks @kaiiam! I'll get this in the release today. I will use the wikipedia references, though, since I think they are more stable than the .edu ones.