reorganizing antimicrobial agent and chemical resistance phenotypes

[dsiegele]

• antimicrobial agent resistance phenotype should be a child of chemical resistance phenotype
  • xx
• some of the compound classes listed as antimicrobial agents are not antimicrobial agents and need to be moved to be children of chemical resistance phenotype
  • moved OMP:0000455 and changed name to alkaloid chemical resistance phenotype

[dsiegele]

I think we need to make it easier to use the antimicrobial resistance and chemical resistance phenotype terms.

We started with grouping resistance phenotypes for antimicrobial agents that shared a common structure, such as beta-lactams and aminoglycosides. As we started to come across antimicrobial agents or chemicals didn't fall into generally recognized groupings such as these, I tried to identify chemical groupings in the CHEBI ontology. This quickly became problematic. Many compounds have more than one is_a CHEBI parent term. For such cases, we need to set criteria for choosing which parent term to use. We also need to set criteria for how granular these parent terms should be.

An example, 'OMP:0007380 benzamides resistance phenotype' - included synonyms for sulfamonomethoxine and CHIR-090. Both of these compounds are

• Moved synonym 'sulfamonomethoxine resistance phenotype (CHEBI:32164)' from benzamides antimicrobial agents to sulfonamide antimicrobial agents

• Moved synonym 'CHIR-090 resistance phenotype' from benzamides antimicrobial agents to sulfonamide antimicrobial agents.

• moved synonym 'benzamide resistance phenotype' from benzamides antimicrobial agents to sulfonamide antimicrobial agents.

make benzamides resistance phenotype obsolete? merge into another term?

[dsiegele]

Another issue that comes up is keeping separate chemicals that are classified as antimicrobial agents and chemicals that aren't. For example, experiments might look at resistance/sensitivity to a chemical that isn't an antimicrobial agent, but is in the same chemical class as some antimicrobial agents. One way to deal with this is to incorporate 'antimicrobial agent' into the term names for resistance phenotypes related to an antimicrobial agent.

[dsiegele]

• OMP:0007474 changed named to phenolic antimicrobial agent resistance phenotype removed triclosan as a synonym because it is not a member of the class phenols deleted narrow synonyms phenol red and rose bengal because these are not classified as antimicrobial agents in CHEBI ** left antimicrobial agents phenol, triclosan, and EGCG as narrow synonyms

• created OMP:0007848 phenolic chemical resistance phenotype ** added narrow synonyms phenol red and rose bengal resistance phenotypes

• need to find or create a class that includes the antimicrobial agent triclosan as a narrow synonym

[dsiegele]

2018-08-17: Further discussion with Jim and Peter about precomposition and postcomposition of chemical and antimicrobial agent resistance phenotype terms. If there is a group of compounds where information about resistance/sensitivity to one member of the group is likely to be informative about other members of the group, then we should make a specific branch for that group in OMP. Examples would be: 'OMP:0000336 beta-lactam antimicrobial agent resistance phenotype' and 'OMP:0006062 tetracycline antimicrobial agent resistance phenotype.'

When a phenotype annotation is made for a member of a group, a group phenotype term will be used and put the CHEBI ID (or other identifier) for the particular chemical or antimicrobial agent into the Annotation Extension field.

When there is not a natural group, use one of the general terms and put the CHEBI ID (or other identifier) for the particular chemical or antimicrobial agent into the Annotation Extension field.

Terms to use for antimicrobial agents: OMP:0007876 resistant to an antimicrobial agent OMP:0007877 not resistant to an antimicrobial agent OMP:0007134 altered resistance to an antimicrobial agent OMP:0007878 increased resistance to an antimicrobial agent OMP:000 7879 decreased resistance to an antimicrobial agent OMP:0007880 abolished resistance to an antimicrobial agent

Terms to use for chemicals that are not classified as antimicrobial agents: OMP:0007247 resistant to a chemical OMP:0007246 not resistant to a chemical OMP:0007248 altered chemical resistance OMP:0007250 increased resistance to a chemical OMP:0007249 decreased resistance to a chemical OMP:0007883 abolished chemical resistance

[dsiegele]

The following terms were made obsolete. OMP:0007533 urea derivative resistance phenotype OMP:0007535 | not resistant to a urea derivative OMP:0007534 | resistant to a urea derivative OMP:0007536 | altered resistance to a urea derivative OMP:0007538 | decreased resistance to a urea derivative OMP:0007539 | abolished resistance to a urea derivative OMP:0007537 | increased resistance to a urea derivative

Added the following replacement terms and put an explanation in the comments field of each obsoleted term. OMP:0007248 chemical resistance phenotype OMP:0007247 resistant to a chemical OMP:0007246 not resistant to a chemical OMP:0007248 altered chemical resistance OMP:0007250 increased resistance to a chemical OMP:0007249 decreased resistance to a chemical OMP:0007883 abolished chemical resistance