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PopulationAndCommunityOntology / pco

An ontology about groups of interacting organisms such as populations and communities
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NewTerm: operational taxonomic unit (OTU) #9

Open ramonawalls opened 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/14

Please provide the following information:

Primary label for the proposed term: operational taxonomic unit

alternate label: OTU

Definition: Need to get a definition and source

Definition source:

Name of submitter: Ramona

ORCID of submitter (if known):

Any other information:
OBI is creating a new class called "OTU matrix", defined as "Operational 
Taxonomic Unit matrix  is a data item, organized as a table, where organismal 
taxonomic units, computed by sequence analysis and genetic distance 
calculation, are counted in a set of biological or environmental samples. The 
table is  used to appraise biodiversity of a population or community of living 
organism." We should create a term for OTU that they can use to define this.

Original issue reported on code.google.com by rlwalls2...@gmail.com on 17 Nov 2014 at 5:39

ramonawalls commented 9 years ago

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

An initial stab...

From Wikipedia:

----------
The definition given by NCBI is:[2]

"Taxonomic level of sampling selected by the user to be used in a study, such 
as individuals, populations, species, genera, or bacterial strains."

Another definition:[3] [ Wooley, John C. "A Primer on Metagenomics". PLOS 
Computational Biology. Retrieved 14 November 2012.]

"Operational taxonomic unit, species distinction in microbiology. Typically 
using rRNA and a percent similarity threshold for classifying microbes within 
the same, or different, OTUs" 

-----------

Perhaps to generalise the def...
OTU := a taxonomic unit which includes biological entities that possess an 
arbitrarily defined minimal similarity to one or more biological entities used 
as OTU references, as determined through a planned process of OTU 
identification.

...where biological entities can be individuals, populations, communities, etc.
...the reference biological entity can have_role "OTU reference"
...taxonomic unit would be the superclass
...one could create a process "OTU definition process" which has as parts 
concepts such as "similarity threshold", the algorithm used, etc. 
...Comment: usually relevant to the definition of taxonomic units based on 
nucleotide sequence similarity of a suitable molecular marker gene such as the 
16S rRNA gene.

In fact, a sub-class specific to the OTU used by the meta-omic community would 
be needed to describe there studies (and thus capture what OBI is trying to do):

"sequence-similarity-based OTU":= an OTU which includes biological entities 
that possess and arbitrarily defined minimal sequence similarity to the 
sequence(s) of (part of) a phylogenetic marker gene of one or more biological 
entities used as OTU references, as determined through a planned process of OTU 
identification.

Cursory, but a place to kick off. Note that different OTU generating algorithms 
will treat the whole thing (sequences, references, thresholds, clustering) 
differently. Also, the algorithm may have only one "reference sequence" which 
is, in fact, an information artefact derived from multiple, identical copies of 
a gene in a collection of microbes.

Original comment by p.buttig...@gmail.com on 6 Feb 2015 at 5:22

ramonawalls commented 4 years ago

Also see OBI's http://purl.obolibrary.org/obo/OBI_0001968 for OTU matrix.

ramonawalls commented 4 years ago

Now that it is 2020, we should also add a term for ASV (amplicon sequence variant)

ramonawalls commented 4 years ago

I am debating whether to make this a subclass of taxon as collection of organisms (TACOO) or information content entity. For the use cases I am aware of, I think TACOO makes a better parent. For example:

  1. To define a TACOO in biodiversity studies where there is no named taxon
  2. To define the elements of OBI's operational taxonomic unit matrix (http://purl.obolibrary.org/obo/OBI_0001968), which specifies that it is about some material entity.
  3. To refer to taxa in NCBI, which, in NCBITaxon ontology, are considered organisms.

@pbuttigieg @cmungall can you think of other use cases where and ICE makes more sense?

I am going to postpone this to the next release so I have more time to think about it.