Organization of terms that describe environmental effects on growth of a microbial population

[dsiegele]

OMP:0007192 ! population growth range phenotype and its children

When we first created OMP terms to describe the effects of environmental factors, such as temperature, pH, and osmolarity, on growth, the definitions referred to "a cell or cells." Because these phenotypes are usually assayed by monitoring population growth, we moved these phenotype terms to be children of 'OMP:0007167 ! population growth phenotype.' However, the term names and definition were not edited. I have started working on editing these terms and creating missing terms that are needed to annotate the phenotypes in Nichols et al.

[dsiegele]

• Created the following terms:

OMP:0007919 ! presence of cell population growth

OMP:0007920 ! absence of cell population growth

OMP:0007926 ! increased anaerobic population growth

OMP:0007927 ! decreased anaerobic population growth def. "An altered anaerobic population growth phenotype where growth of a microbial population in the absence of O2 is decreased relative to a designated control." *Added comment "Altered population growth may result from changes in population growth rate or population growth yield. Consider using a more specific term if either of these parameters was determined in the experiments."

OMP:0007928 ! abolished anaerobic population growth *Moved OMP:0007928 to OMP:0007927 from OMP:0005192

• Edited names and definitions of the following terms. Following are the new names and definitions.

OMP:0000039 ! def. "A population growth range phenotype related to how growth of a microbial population is affected by different concentrations of oxygen gas (O2) in the environment."

Changed name of OMP:0000087 from "facultative anaerobe" to "facultative anaerobe population growth" def. "A population growth phenotype where a microbial population does not require oxygen gas (O2) for growth but growth is better in the presence of O2."

Changed name of OMP:0000105 from "aerotolerant anaerobe" to "aerotolerant anaerobe population growth" def. "A population growth phenotype where a microbial population grows equally well in the presence or absence of oxygen."

OMP:0005189 ! anaerobic population growth phenotype def. "A population growth range phenotype related to whether a microbial population can grow in the absence of oxygen."

OMP:0005190 presence of anaerobic population growth def. "A population growth range phenotype where a microbial population is able to grow in the absence of oxygen."

OMP:0005191 ! absence of anaerobic population growth def. "An anaerobic growth range phenotype where a microbial population cannot grow in the absence of oxygen."

OMP:0005192 ! altered anaerobic population growth def. "A population growth range phenotype where the ability of a microbial population to grow in the absence of oxygen is altered relative to a designated control." *[Added comment "Altered population growth may result from changes in population growth rate or population growth yield. Consider using a more specific term if either of these parameters was determined in the experiments."]

OMP:0005193 ! increased anaerobic population growth yield *Moved OMP:0005193 to OMP:0007926 from OMP:0005192

OMP:0005194 ! decreased anaerobic population growth yield *Moved OMP:0005194 to OMP:0007927 from OMP:0005192

OMP:0005195 ! abolished anaerobic population growth def. An altered anaerobic population growth phenotype where growth of a microbial population in the absence of oxygen is abolished." Moved OMP:0005195 to OMP:0007927 from OMP:0005192 Created link OMP:0005195 -OBO_REL:is_a-> OMP:0005191 ! absence of

OMP:0005196 ! increased anaerobic population growth rate *OMP:0005196 to OMP:0007926 from OMP:0005192

OMP:0005197 ! decreased anaerobic population growth rate *Moved OMP:0005197 to OMP:0007927 from OMP:0005192

OMP:0007192 ! population growth range phenotype def. "A population growth phenotype related to how non-nutrient environmental factors affect growth of a microbial population."

*Added comment "This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype." to the following terms: OMP:0000039, OMP:0007794

*The following terms were added to category qc_do_not_annotate and category qc_do_not_manually_annotate]: OMP:0000039, OMP:0007167, OMP:0007794

[dsiegele]

The group went over the proposed changes in today's OMP call.

• We discussed my proposal of using the existing terms and modifying the names and definitions to make it clear that these terms are to be used for population phenotypes. Best ontology practice would be to obsolete the existing terms and create new sets of terms: one set to describe cell phenotypes and one set to describe population phenotypes. However, because at this point in time our group is the main consumer of the ontology and, as far as we know, no one else has used these terms, we will go ahead and use the existing terms to describe population phenotypes. Terms to describe cell phenotypes can be created as called for.

• The group reviewed the changes I had made to the branch of the ontology describing the effects of O2 on population growth. The subclasses 'aerobic population growth phenotype' and 'anaerobic population growth phenotype' were agreed on, and Michelle requested a subclass for 'microaerophilic population growth phenotypes.'

Michelle pointed out a problem with the terms I had suggested for 'facultative anaerobe population growth' and 'aerotolerant anaerobe population growth,' etc. The problem she pointed out is that for any given microbial population, it will be growing either in the presence or absence of O2. Phenotype terms such as aerotolerant anaerobe or hyperthermophile were created to capture types of information that are commonly used in identifying microorganisms.

We want to have these "bergey's-manual-esque" terms in OMP, but aren't sure where they belong in the ontology. Consensus was that they should be grouped together at some high level in the ontology. Jim suggested we think about the structure of GO in terms of process terms and molecular function terms.

Action item: I will revert to the original names of these terms (see crossed out changes in the previous comment) and move them to a temporary high level branch.

Consensus was that these