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#10 Application and Biological ontologies
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.
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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