muthuvenkat
commented
18 years ago Logged In: YES user_id=802919
I like "biological role" more than "biological function" even though we probably have to keep both terms.
I hope to incorporate most definitions before the release.
However...
Nutrient
I have problems with the above definition because it mixes the two categories: elements (=atoms) and compounds. Its children are micronutrients and macronutrients. Micronutrients are almost universally understood as elements, while macronutrients means either elements (in biology) or compounds such as proteins, carbohydrats and fats (in nutrition) => see http://en.wikipedia.org/wiki/Macronutrient
I am in favour of defining nutrients as elements, not compounds. Vitamins are often included in nutrients but probably should be not.
As for "food": it is not synonymous with nutrients. It belongs to application ontology, not biology. Both food and fertilizer contain nutrients. On the other hand, some components of food are practically not metabolised and therefore cannot be said to be nutrients in either sense.
After our exchange of "reagent" definitions, I don't see why laboratory chemical should be replaced by reagent: reagent is_a laboratory chemical. We already mentioned buffer components and solvents. Inert gases like argon that are used in the lab to create "anaerobic" conditions are not reagents (supposedly they do not react).
I agree that "health care products" is an awful term and any alternative will be welcome. However this is placeholder for the stuff used in medicine (veterinary medicine, dentistry, etc) includig drugs and diagnostic aid, probably something else, like antiseptics.
As for drugs: the fact that they are used on model organisms does not change their use as drugs.
Kirill
Original comment by: kiri11
Kirill and friends,
I attach a small text file with some changes to the function and application nodes of chebi, with some suggestions for definitions.
I have not reduced the number of function nodes (which I suggest we call 'biological role'), but have increased its depth a bit.
I hope that this is interpretable.
Michael
Application ontology.
CHEBI:25944 pesticides > pesticide CHEBI:22153 acaricides > acaricide CHEBI:23092 chemosterilants > chemosterilant CHEBI:24527 herbicides > herbicide CHEBI:24852 insecticides > insecticide CHEBI:25491 nematicides > nematicide ... add nematocide as synonym CHEBI:25943 pesticide synergists > pesticide synergist CHEBI:33288 rodenticides > rodenticide CHEBI:33289 avicides > avicide CHEBI:33281 antimicrobial agents > antimicrobial agent ... move up one level, I do not regard these as pesticides CHEBI:27780 detergents > ... suggest we replace by surfactant. synonym wetting agent CHEBI:33286 agrochemicals > agrochemical CHEBI:33287 fertilizers > fertilizer CHEBI:33290 food > nutrient ; CHEBI:33284 ... food has (now) only one child. I am not sure I can think of any other children that would be single compounds. CHEBI:33229 vitamins > vitamin CHEBI:27027 micronutrients > micronutrient CHEBI:33293 health care products ... I do NOT like this one, as many drugs will be used eg on model organisms so I suggest putting drug and diagnostic agent at the top level and getting rid of health care product(s) CHEBI:33294 pharmaceuticals > pharmaceutical CHEBI:23888 drugs > drug CHEBI:33295 diagnostic aid > diagnostic agent CHEBI:33291 laboratory chemicals > reagent CHEBI:33292 fuel
agrochemical defn: A substance used in agricultural practice.
fuel defn: A substance from which energy may be converted in form.
antimicrobial agent defn: A chemical that kills or slows the growth of microbes, i.e., viruses, bacteria, fungi or other microbial eukaryotes.
pharmaceutical defn: A substance with medicinal properties, usually in human or animals, but may be used in the context of studies with model organisms.
pesticide defn: A substance used to destroy pests of any sort. pesticide synergist defn: A substance that increases the efficacy of a pesticide. acaricide defn: A substance used to destroy pests of the Class Arachnida. insecticide defn: A substance used to destroy pests of the Class Insecta. nematicide defn: A substance used to destroy pests of the Phylum Nematoda. avicide defn: A substance used to destroy pests of the Class Aves. rodenticide defn: A substance used to destroy pests of the Order Rodentia. herbicide defn: A substance used to destroy plant pests.
Add fungicide defn: A substance used to destroy fungal pests. molluscicide defn: A substance used to destroy pests of the Phylum Mollusca.
chemosterilant defn: A substance intended for sterilise any organism.
reagent: A substance that is added to a system in order to bring about a reaction, to modulate a reaction or to see whether a reaction occurs (e.g. an analytical reagent).
surfactant defn: A substance that lowers the surface tension of a liquid.
one suggested isa child of reagent: buffer defn: A reagent that, in solution (normally aqueous), resists change in pH upon addition of small amounts of acid or base.
biological function ontology >> biological role
cuticular hydrocarbons (CHEBI:23416) ... suggest we delete this phytosterols (CHEBI:26125) ... suggest we delete this antibiotics (CHEBI:22582) > antibiotic ... add as an isa of CHEBI:33281 antimicrobial agent antifeedants (CHEBI:22583) > antifeedant ... as child of pesticide antioxidants (CHEBI:22586) > antioxidant antiviral agents (CHEBI:22587) > antiviral agent ... add as an isa of CHEBI:33281 antimicrobial agent chelators (CHEBI:23090) > chelator CHEBI:24028 ferric chelators > ferric chelator ... add: copper chelator & others chromophores (CHEBI:23240) > chromophore coenzymes (CHEBI:23354) > coenzyme ... move to isa of cofactor cofactors (CHEBI:23357) > cofactor enzyme inhibitors (CHEBI:23924) > enzyme inhibitor ... add as an isa child of enzyme substrate I think ??? CHEBI:20569 5-enolpyruvylshikimate-3-phosphate synthase inhibitors > 5-enolpyruvylshikimate-3-phosphate synthase inhibitor CHEBI:22180 acetohydroxyacid synthase inhibitors > acetohydroxyacid synthase inhibitor CHEBI:23018 carbonic anhydrase inhibitors > carbonic anhydrase inhibitor CHEBI:24319 glutamine synthetase inhibitors > glutamine synthetase inhibitor CHEBI:25355 mitochondrial electon transport chain inhibitors > mitochondrial electron transport chain inhibitor !! note spelling electon CHEBI:26087 photosynthetic electron transport chain inhibitors > mitochondrial electon transport chain inhibitor ionophores (CHEBI:24869) > ionophore CHEBI:22986 calcium ionophores > calcium ionophore CHEBI:24874 iron ionophores > calcium ionophore luciferins (CHEBI:25078) > luciferin ... add as an isa child of enzyme substrate metabolites (CHEBI:25212) > metabolite ... I am unsure about this ? CHEBI:26619 secondary metabolites ... I am unsure about this ? mutagens (CHEBI:25435) > mutagen CHEBI:22333 alkylating agents > alkylating agent CHEBI:24853 intercalating agents > intercalating agent nodulation factors (CHEBI:25573) > nodulation factor osmolytes (CHEBI:25728) > osmolyte CHEBI:23366 compatible osmolytes > compatible osmolyte phytoalexins (CHEBI:26115) > phytoalexin ... move to an isa of toxin pigments (CHEBI:26130) > pigment plant growth regulators (CHEBI:26155) > plant growth regulator CHEBI:22581 antiauxins > antiauxin CHEBI:23582 defoliants > defoliant CHEBI:24002 ethylene releasers > ethylene releaser CHEBI:26154 plant growth inhibitors > plant growth inhibitor CHEBI:26156 plant growth retardants > plant growth retardant ... how does this differ from a plant growth inhibitor ?? CHEBI:26157 plant growth stimulators > plant growth stimulator prosthetic groups (CHEBI:26348) > prosthetic group ... move to isa of cofactor toxins (CHEBI:27026) > toxin xenobiotic compounds (CHEBI:27333) > xenobiotic chemical messengers (CHEBI:33280) > chemical messenger CHEBI:24621 hormones > hormone CHEBI:24943 juvenile hormones > juvenile hormone CHEBI:26764 steroid hormones > steroid hormone CHEBI:25905 peptide hormones > peptide hormone CHEBI:26158 plant hormones > plant hormone ... also an isa of plant growth regulator CHEBI:25512 neurotransmitters > neurotransmitter (btw you have BOTH serotinin and 5hydroxytryptophan ... the same I think) CHEBI:26645 semiochemicals > semiochemical CHEBI:24850 insect attractants > insect attractant CHEBI:26013 pheromones > pheromone nutrients (CHEBI:33284) > nutrient
new enzyme substrate defn: A chemical that is chemically modified by enzymatic activity.
antifeedant defn: A chemical that reduces the propensity of an animal to feed.
antibiotic defn: A chemical that kills or slows the growth of bacteria.
chromophore defn: A part of a molecule that is responsible for its color.
antioxidant defn: A chemical that scavenges free radicals, thereby decreasing the damage that these may do to other substances.
chelator defn: A chemical that acts as a ligand, binding, perhaps ireverisbly, to metal ions, forming a chelate.
coenzyme defn: A low-molecular-weight, non-protein organic chemical (often a nucleotide) participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons. [http://www.chem.qmul.ac.uk/iupac/bioinorg/CD.html]
cofactor defn: An organic chemical or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). [http://www.chem.qmul.ac.uk/iupac/bioinorg/CD.html]
ionophore defn: A lipid-soluble chemical that transports ions across the lipid bilayer of the cell membrane.
luciferin defn: A chemical that can be acted upon by an enzyme and emit light.
mutagen defn: A chemical that increases the frequency of spontaenous mutation, usually by interacting directly with DNA and causing it damage, including base substitution.
nodulation factor defn: A chemical that increase the formation of nodules, typically on plant roots, that are a consequence of microbial action.
nutrient defn: An element or compound necessary for or contributing to an organism's metabolism, growth, or other functioning. [http://en.wikipedia.org/wiki/Nutrients]
pigment defn: A chemical that results in color as the consequence of the selective absorption of light.
osmolyte def: A neutral solute that reacts minimally with the contents of a cell while protecting it from drying out, or in a cells response to salinity changes.
phytoalexin defn: A toxin made by a plant that acts against an organism attacking it.
plant growth regulator defn: A chemical, natural or artificial, that can affect the rate of growth of a plant.
prosthetic group defn: A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity. [http://www.chem.qmul.ac.uk/iupac/bioinorg/PR.html]
toxin defn: A chemical produced by living cells or organisms that is poisonous to the same or other cells or organisms.
xenobiotic defn: A chemical substance that is foreign to a biological system. [MESH]
hormone defn: A chemical messenger from one cell (or group of cells) to another within an organism.
Reported by: kiri11