chemical information ontology (cheminf) - information entities about chemical entities

A chemical entity is any molecular entity or chemical substance.

Is this equivalent to IAO 'source code module' (IAO_0000096) on the same level as 'software'? From the textual definition in IAO it seems fairly close. (JH)

A software method (also called subroutine, subprogram, procedure, method, function, or routine) is a programming language implementation of a plan specification which is capable of realizing some objective specification when part of a software application.

A software library is a collection of programming language mplementations (e.g. modules, methods) capable of realizing some objective specification when linked to a application software.

A software application is a programming language implementation of a plan specification capable of realizing some objective specification.

Octanol-water distribution coefficient calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01.

Hydrogen bond acceptor count that has been calculated by ACD/Labs PhysChem software library version 12.01.

Hydrogen bond donor count that has been calculated by ACD/Labs PhysChem software library version 12.01.

The boiling point of a substance at 760 mmHg pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.

Number of freely rotating bonds that has been calculated by ACD/Labs PhysChem software library version 12.01.

Polar surface area that has been calculated by ACD/Labs PhysChem software library version 12.01.

The molecular weight for the free base chemical structure matching this chemical structure.

Molar refractivity that has been calculated by ACD/Labs PhysChem software library version 12.01.

Index of refraction that has been calculated by ACD/Labs PhysChem software library version 12.01.

Polarizability that has been calculated by ACD/Labs PhysChem software library version 12.01.

A parameterized software execution of ACD/Labs PhysChem software library version 12.01. This refers to a particular run of the software.

A parameterized software execution of Pipeline Pilot. This refers to a particular run of the software.

A parameterized software execution of GGA Indigo. This refers to a particular run of the software.

Molar volume that has been calculated by ACD/Labs PhysChem software library version 12.01.

Density that has been calculated by ACD/Labs PhysChem software library version 12.01.

Flash point that has been calculated by ACD/Labs PhysChem software library version 12.01.

Enthalpy of vaporization that has been calculated by ACD/Labs PhysChem software library version 12.01.

Vapour pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.

Organic carbon adsorption coefficient at pH 5.5 that has been calculated by ACD/Labs PhysChem software library version 12.01.

Organic carbon adsorption coefficient at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.

Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.

Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.

Number of rule of five violations for a chemical structure that has been calculated by ACD/Labs PhysChem software library version 12.01.

Surface tension, in dyne per centimetre, that has been calculated by ACD/Labs PhysChem software library version 12.01.

A descriptor that indicates the temperature at which a chemical substance undergoes a state transition from gas or liquid to solid, under standard conditions.

Henry's law, formulated by William Henry in 1803, states "At a constant temperature, the amount of a given gas that dissolves in a given type and volume of liquid is directly proportional to the partial pressure of that gas in equilibrium with that liquid." Henry's law can be put into mathematical terms (at constant temperature) as p = kHc where p is the partial pressure of the solute in the gas above the solution, c is the concentration of the solute and kH is a constant with the dimensions of pressure divided by concentration. The constant, known as the Henry's law constant, depends on the solute, the solvent and the temperature.

A physical descriptor for the rate constant of a reaction of a chemical entity with OH. This is used to describe the atmospheric behaviour (i.e. stability) of the entity.

A physical descriptor for the upper explosive limit of the entity in air as a percentage by volume at room temperature.

A physical descriptor for the lower explosive limit in air as a percentage by volume at room temperature

A physical descriptor for the minimum explosive concentration.

A physical descriptor of the ratio of the density of chemical substance to the density of a reference substance. The reference substance is usually water for liquids or air for gases.

A descriptor of the relative density of gases referenced to air as 1, which indicates how many times a gas is heavier than air at the same temperature.

A descriptor of the density of a vapour in relation in that of hydrogen, defined as the mass of a certain volume of the given substance divided by the mass of the same volume of hydrogen.

A physical descriptor for the lowest concentration of an odorant chemical entity that is perceivable by the human sense of smell.

A physical descriptor which gives a measure of the acidity or basicity of an aqueous solution, defined as the decimal logarithm of the reciprocal of the hydrogen ion activity in a solution.

A physical descriptor of the rate of evaporation of a liquid under standard conditions.

A physical descriptor of the lowest temperature at a substance will spontaneously ignite in a normal atmosphere without an external source of ignition.

A physical descriptor for the time it takes for half of a portion of substance of a given type to decompose in soil under standard conditions.

A software module to calculate a molecular descriptor is software module that implements an algorithm which calculates a descriptor value for a molecular entity.

This can be done automatically; it does not need a person bearing a curator role.

Molecular formula for a chemical structure as calculated by ACD/Labs PhysChem software library version 12.01.

Descriptor that returns the group in the periodic table of a given atom.

This may of course not be successful!

An error message produced in the execution of a structural standardiation algorithm.

A software message data item which is merely intended to convey information and not a warning or an error.

Identifier used by the USA Food and Drug Administration.

Identifier used by the LipidMaps database, http://www.lipidmaps.org/.

Identifier used by the Cancer Chemotherapy National Service Center.

Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/).

Eigenvalue based descriptor noted for its utility in chemical diversity.

Descriptor that calculates bond-pi Partial charge of a bond by determining the difference the Partial Pi Charge on atoms A and B of a bond (based in Gasteiger Charge).

Descriptor that calculates bond-sigma Partial charge of a bond.

Descriptor that calculates bond-total Partial charge of a bond.

Descriptor that calculates of bond-Polarizability of a bond by determining the difference the Sigma electronegativity on atoms A and B of a bond.

This is the shortest distance between a pair of atoms in a graph, defined as the number of edges in the shortest path between the atom pair in the molecular graph.

It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

Descriptor characterizing the mass distribution of the molecule.

Descriptor characterizing the mass distribution of the molecule as the square or cube root of the gravitational index.

Counts the number of acceptor field atoms for a carbonyl oxygen probe using force field based definition.

SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)

Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe.

Counts the number of donor field atoms for an amino hydrogen probe.

SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)

Descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions.

Descriptor returns true if the protons is directly bonded to a pi system.

Counts the number of occurrences of the E-state fragments.

Evaluate molecular distance edge descriptors for C, N and O.

Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration.

Descriptor that calculates total partial charges of an heavy atom.

Descriptor that returns the period in the periodic table of an atom belonging to an atom container.

Descriptor that check if two atoms have pi-contact (this is true when there is one and the same conjugated pi-system which contains both atoms, or directly linked neighboors of the atoms).

Descriptor that calculates partial charges of an heavy atom and its protons based on Gasteiger Marsili (PEOE).

This is a mixed descriptor: topological, geometrical and electronic descriptor.

{@cdk.cite BREN1995} {@cdk.cite BREN1997} {@cdk.cite WHITE2003}

The weighted path (molecular ID) descriptors were described by Randic and they characterize molecular branching.

Todeschini, R. and Gramatica, P.. New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design. 1998, pp. 355-380. Mixed descriptors: molecular size, shape, symmetry, and atom distribution and density. Uses 3D coordinates, PCA and it calculates 10 descriptors.

ATSc1 - ATSc5

ATSm1 - ATSm5

ATSp1 - ATSp5

C1SP1, C2SP1, C1SP2, C2SP2, C3SP2, C1SP3, C2SP3, C3SP3, C4SP3

Descriptor that calculates the carbon connectivity index (order 0).

Descriptor that calculates atomic valence connectivity index (order 0).

Descriptor that calculates carbon valence connectivity index (order 0).

Descriptor that calculates carbon connectivity index (order 1).

Descriptor that calculates atomic valence connectivity index (order 1).

Descriptor that calculates carbon valence connectivity index (order 1).

Descriptor that calculates the 3D distance between two atoms.

EffectiveAtomPolarizabilityDescriptor, effAtomPol

It reports the fraction of sp3 carbons to sp2 carbons as Nsp3/ (Nsp3 + Nsp2). The original form of the descriptor (i.e., simple ratio) has been used to characterize molecular complexity, especially in the are of natural products , which usually have a high value of the sp3 to sp2 ratio. Other short names: HybridizationRatio, HybRatio.

Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs. First kappa shape index is given by n ( n - 1 ) 2 m 2 , second kappa shape index is given by ( n - 1 ) ( n - 2 ) 2 p 2 2 and third kappa shape index is given by ( n - 1 ) ( n - 3 ) 2 p 3 2 for odd n and ( n - 3 ) ( n - 2 ) 2 p 3 2 for enev n, where n denotes the number of atoms in the hydrogen suppressed graph, m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2 and let p3 denote the number of paths of length 3. Other short names: KappaShapeIndices, Kier1, Kier2, Kier3.

Other short_name: pepe.

Descriptor that calculates sigma partial charges in sigma-bonded systems (PEOE) of an heavy atom based on Gasteiger Marsili.

Pi electronegativity is given by X = a + b q + c ( q 2 ) , where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge. Other short_name: elecPiA.