dsiegele
commented
8 years ago 2013-01-23 Jonathan Herrera: Difference between state and relative Relative phenotypes are comparative in nature. Like if we knock out this gene, then the cell swims SLOWER than if we did not do the knockout. Slower as compared to what? Compared to a non-knockout. So it is relative. State phenotypes are not comparative in nature, i.e. they are what they are. For example, a MOTILE organism has the inherent capacity to swim in any situation, whether or not it does. So for an E. coli cell with some reduced swimming capacity, we'd say it is:
- MOTILE (the state phenotype)
- DECREASED MOTILITY (the relative phenotype) I will try to get those defs in there soon. But FYI, those are just large grouping terms, and the terms "relative phenotype" and "state phenotype" will not be used for annotation, per se.
2012-10-02 Jonathan Herrera The following is only a partial list, the rest of the terms not found here are on the tracker already (ex. rifampins). For Nicer looking version of this Please see the google doc here: https://docs.google.com/document/d/1KhEducmHePja1F56pZtCVfbaqkW_KgR0RX14WLqvPQs/edit#
[NOTE FROM ADMIN Marcus Chibucos: Links like the one above, while helpful for internal project personnel, might not be accessible by most people reading this thread. Consider adding such information to a wiki (either the OMPwiki or this development site wiki?), where everyone can read it.]
ANTIMICROBIAL Compound Increase/Decrease RESISTANCE Synonyms: Antibiotics, Antifungals, Antivirals, Antimetabolite Definition: Any compounds that kills (microbiocidal) or inhibit growth (microbiostatic) of bacteria. This is different from bacteriocins with the same function but are proteins. We should also do a redirect for increase/decrease sensitivity.
Increase/Decrease Macrolides Resistance (Antibiotic) -- Increase/decrease resistance to macrolides Definitions: Structure characterized by 14-, 15- or 16-membered lactone ring, substituted with several neutral or amino sugars. (1) Macrolide antibiotics are effective inhibitors of bacterial protein biosynthesis. They bind to the large 50S ribosomal subunit at or near the peptidyl transferase center and block the elongation of the peptide chain. (2) Terms that should redirect to Macrolides Erythromycin, Clarithromycin, Azithromycin, Dirithromycin, Roxithromycin, Telithromycin, Carvomycin A, Josamycin, Troleandomycin, Spectinomycin, Spiramycin Other: *There are several more (see: http://en.wikipedia.org/wiki/Category:Macrolide_antibiotics) but these listed I have verified through pubmed as macrolides. . Sources:
Increase/Decrease resistance to Diaminopyrimidine Compound (several) Definition: Is an organic chemical compound that includes many dihydrofolate inhibitors, but not all dihydrofolate inhibitors are Diaminopyrimidine. Structure: Are compounds with a pyrimidine ring with 2 attached amine groups. Redirects from searches to here:
Beta Lactams (Antibiotics) This needs more info - ecocyc has none Definition: A broad class cyclic amide where most work by proteins synthesis inhibition. Structure: It is a 4 membered cyclic amide with the amide attached to the beta position to the carbonyl group. --increase/decrease resistance to b-lactams Searched terms that should redirect here: Subclass antibiotics - penicillin, ampicillin, cephaloxporins, cefoxitin, monobactams, carbapenams. Beta Lactams are divided further into subclasses. Not sure if we want to divide to that level. see: http://www.aafp.org/afp/2000/0801/p611.html Link to resources Antibiotic list http://en.wikipedia.org/wiki/List_of_antibiotics Beta-lactam info http://en.wikipedia.org/wiki/Beta-lactam_antibiotic#cite_note-pmid10950216-0
Sideromycins (Antibiotics) Synonyms (1967): Sideramines & siderochromes. --Incease/decrease resistance to sideromycins Sideromycins Are iron carriers (Fe3+ siderophores) that are covalently linked to the antibiotic Moiety. Searches that should redirect here: Antibiotics - Albomycin, salmycin References: PMID:19130258
Azole Class (An Antifungal) -Increase/Decrease Resistance to Triazole Definition: Inhibits enzyme (lanosterol 14 α-demethylase) necessary to convert lanosterol to ergosterol which is important for fungal membrane structure and function. Structure: Azoles are nitrogen heterocyclic rings with one other non-carbon atom (sulfure, oxygen or nitrogen). Searched terms that should redirect to Azole: Triazole- acts against bacteria There are several other classes of azole antifungal but we do not know if they act as anti bacterial agents. Should we add these as well? A more complete list can be found on Wikipedia.
Chloramphenicol or Nitrobeneze (antibiotic-unclassifiable) Synonyms: chlornitromycin, Chloromycetin (Other brand names on wikipedia), *Chloramphenicol, in bacteria, inhibits protein synthesis by binding to 50s subunit, thus preventing peptide bond formation, chain elongation, by peptidyl transferase. nitrobenzene moiety in its structure. Nitrobenzene is a very broad classification so I am not sure if we should group chloramphenicol as a nitrobenzene antimicrobial agent. Before this is incorporated I want to figure this out. http://en.wikipedia.org/wiki/List_of_antibiotics - lists it as others http://www.merckmanuals.com/professional/infectious_diseases/bacteria_and_antibacterial_drugs/chloramphenicol.html?qt=&sc=&alt= http://www.scribd.com/doc/2024490/Tetracyclines-Chloramphenicol-and-Mis
Quinolones (Antibiotic) Searches that should redirect to quinolones: Antibiotics: Nalidixic Acid,Ciproflixacin, Levofloxacin, Trovafloxacin, 2-Quinolones, 4-Quinolones