]> 2.1.0 Egon Willighagen Janna Hastings Michel Dumontier The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals. application/rdf+xml chemical information ontology (cheminf) - information entities about chemical entities en To develop the ontology, you must change the default auto-create settings in Protege 4. Go to file>preferences>New Entities. Change the following: specified URI = http://semanticscience.org/resource/ Followed by '/', End with : AutoID AutoID - digit count = 6, prefix = CHEMINF_ http://creativecommons.org/publicdomain/zero/1.0/ Cristian Munteanu Gang Fu Leonid Chepelev Mark Davies Evan Bolton Colin Batchelor A is_enantiomer_of B if and only if, given any a that instantiates A, has molecular graph ag, there is some b such that b instantiates B, is described by molecular graph bg, such that ca is equal to cb and ag is transformed into bg through a C2 symmetric transform. A is_tautomer_of B if and only if, given any a which instantiates A and has composition ca and is described by a molecular graph ag, there is some b that instantiates B, has composition cb and is described by a molecular graph bg, such that ca equals cb, ag is different from bg and a derives from b as the result of an intramolecular chemical transformation process (i.e. a chemical transformation process which has only one participant), in which only bonds to hydrogen are broken or formed. has output has input has attribute is attribute of is variant of has_protein_binding_participant participates_in_protein_binding ligates is_isotopologue_of An isotopologue is a molecular entity that differs only in isotopic composition from another molecular entity. (AU:I03351) has_stereoundefined_parent Subclass relation between a class that has stereochemistry defined and an otherwise identical class that does not. has_normalized_counterpart Connects a molecule to a normalized counterpart of the same molecule according to an algorithm. Caution: The number of moieties in the first molecule may be greater than in the second molecule. Example: salts. Caution: this is not a subclass relation and should not be thought of as such for reasoning purposes. has OPS normalized counterpart This connects a molecule to its normalized counterpart according to the OPS specification. has_isotopically_unspecified_parent Subclass relation between a class that has isotopes specified, for example D2O or 14C-urea, and an otherwise identical class that does not, for example water or urea. has_uncharged_counterpart Connects a molecule to molecule with identical heavy-atom connectivity which is neutral. It is not a subclass relation. is_stereoisomer_of Connects a molecule to an isomer with identical constitution but differing in its arrangement of atoms in space. (AU:S05984) has_same_connectivity_as Connects a molecule to an isomer with identical constitution. is_diastereomer_of Connects a molecule to a stereoisomer which is not its enantiomer. has PubChem normalized counterpart This connects a molecule to its normalized counterpart according to the PubChem specification. has component This connects entities at different granularities. Has as member parts (see BFO 2 Graz for more on this) many molecular entities. has counterpart molecular entity This is intended to capture the case where a database has ad hoc relations between molecules that are not necessarily subclass relations. Connects a molecular entity to another molecular entity according to some specification. has component with uncharged counterpart Connects a molecular substance, say a mixture containing ions, with a neutral form of one of the ions. similar to not transitive, obviously Connects a molecular entity that is deemed similar to another according to some algorithm. similar to by PubChem 2D similarity algorithm http://pubchem.ncbi.nlm.nih.gov/help.html#tanimoto Has a Tanimoto score with the counterpart molecular entity of more than 0.9, based on the PubChem fingerprint specification. similar to by PubChem 3D similarity algorithm http://dx.doi.org/10.1186/1758-2946-3-32 Has a 3D Tanimoto score with the counterpart molecule where the 3D shape similarity for the two is greater than 0.795 and the 3D feature score is greater than 0.495 or there are no features and the 3D shape similarity is greater than 0.925, where the shape similarity ST is calculated by ST=VAB/(VAA+VBB-VAB), where VAA and VBB are self-overlap volume of conformers A and B, and VAB is the common overlap volume between them and the feature score CT is calculated by CT=sum(VfAB)/(sum(VfAA)+sum(VfBB)-sum(VfAB)), where the superscript f indicates any of the six independent fictitious feature atom types, VfAA and VfBB are the respective self-overlap volumes of conformers A and B for feature atom type f, and VfAB is the overlap volume of conformers A and B for feature type f. has major tautomer at pH 7.4 A exists in an equilibrium with B at pH 7.4 and physiological temperature and B is the dominant isomer. is_isotopically_unspecified_parent_of Superclass relation between a class does not have isotopes specified, such as water or urea, and a class that does, such as D2O or 14C-urea. Colin Batchelor is_stereoundefined_parent_of Colin Batchelor Superclass relation between a class that does not have stereochemistry defined and another otherwise identical one that does. is component with uncharged counterpart of This is here because Open PHACTS has requested an inverse. Use with caution! Connects a neutral molecule with a salt. is major tautomer at pH 7.4 of A exists in an equilibrium with B at pH 7.4 and physiological temperature and A is the dominant isomer. is OPS normalized counterpart of If A 'is OPS normalized counterpart of' B, then A is the molecular entity corresponding to the connection table obtained by applying OPS normalization to the connection table of B. is uncharged counterpart of If A 'is uncharged counterpart of' B, then A is the neutral species corresponding to B. B may itself of course be neutral. is counterpart with different charge of Colin Batchelor If A 'is a counterpart with different charge of' B, then A is an otherwise identical species to B but for charge. shares OPS normalized parent with If A 'shares OPS normalized parent with' B, then A 'has OPS normalized counterpart' C and B 'has OPS normalized counterpart' C. Colin Batchelor has ChemAxon canonicalised tautomer A and B can be identical. Colin Batchelor If A 'has ChemAxon canonicalised tautomer' B then B is the molecular entity corresponding to the output of ChemAxon's canonical tautomer generation algorithm applied to the connection table of A. is ChemAxon canonicalised tautomer of If B 'has ChemAxon canonicalised tautomer' A then B is the molecular entity corresponding to the output of ChemAxon's canonical tautomer generation algorithm applied to the connection table of A. Colin Batchelor A and B can be identical. is output of has uncertainty value has value BODO:Algorithm chemical entity A chemical entity is any molecular entity or chemical substance. obo:24431 file software implementation PubChem compound identifier (CID) PubChem substance identifier (SID) Pipeline Pilot library http://accelrys.com/products/pipeline-pilot/ molecular weight calculated by pipeline pilot A molecular weight descriptor calculated by a relevant module of the Pipeline Pilot software tool. Ghose/Crippen ALogP calculation algorithm Fragment Method used for the calculation of ALogP as defined by Ghose and Crippen. Ghose, A.K., Viswanadhan V.N., and Wendoloski, J.J., Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragment Methods: An Analysis of AlogP and CLogP Methods. J. Phys. Chem. A, 1998, 102, 3762-3772. fusibility ALogP calculated by Pipeline Pilot Ertl polar surface area calculation algorithm Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties, Ertl, P., Rohde, B., Selzer, P., J. Med. Chem. 2000, 43, 3714-3717. polar surface area descriptor polar surface area descriptor calculated by Pipeline Pilot hydrogen bond acceptor count calculated by pipeline pilot hydrogen bond donor count calculated by pipeline pilot rotatable bond count calculated by pipeline pilot rule of five violations descriptor Number of properties defined in Lipinski’s Rule of 5 (RO5) that the compound fails. Conditions which violate the RO5 are: Molecular weight>=500 AlogP>=5 HBD>=5 HBA>=10 Lipinski rule of five violation calculation algorithm Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Deliv. Rev., 1997, 23, 3-25. rule of five violations calculated by pipeline pilot rule of three passes descriptor Rule of 3 passes. It is suggested that compounds that pass all these criteria are more likely to be hits in fragment screening. molecular weight <=300, number of hydrogen bond donors <=3, number of hydrogen bond acceptors <=3 AlogP <=3. RTB <=3 PSA<=60 rule of three passes calculation algorithm A ‘Rule of Three’ for fragment-based lead discovery? Miles Congreve, Robin Carr, Chris Murray and Harren Jhoti. Drug Discovery Today, 2003,8(19), 876-877 rule of three passes calculated by pipeline pilot medchem friendly descriptor MedChem Friendly These are functional groups that may not be desirable from a medicinal chemistry perspective. For example reactive groups will be flagged as “N” (not MedChem Friendly). Molecules which do not contain any of these groups will be flagged as “Y” (MedChem Friendly). The groups are defined by the following list of SMARTS: [N+]([O-])=O [C;!R](-[C;!R]=O)=[C;!R] C(-N)=S P O-N=C OS(=O)=O O1-CC-O-C-1 C(-N)=C [C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2] OC1OCC(O)C1 C=N-C(-O) [N;H]-[C;H]-[N;H] [C;!R]=[C;!R]-N-[C;D1&H3,D2&H2,D3&H1,D4] [S;!R]-[C;!R]-[O;!R] [O;D2]-[C;!H0](([F,Br,I,Cl])([F,Br,I,Cl])([!F,!Br,!I,!Cl])) CC([O;!R])([O;!R]) C1-C-O1 C(=O)-S-C(=S) [S;H] SC#N medchem friendly descriptor calculated by pipeline pilot ACD/Labs PhysChem software library http://www.acdlabs.com/resources/knowledgebase/app_notes/physchem/ logP calculated by ACD/Labs PhysChem software logD descriptor octanol-water distribution coefficient calculated at a given pH. logD calculated at pH 7.4 by ACD/Labs PhysChem software ACD_LogD(pH7.4) Distribution Coefficient calculated at pH7.4 most acidic pKa calculated by ACD/Labs PhysChem software library Most acidic pKa of the molecule most basic pKa calculated by ACD/Labs PhysChem software library Most basic pKa of the molecule molecular species at pH 7.4 descriptor Molecular Species is a description of the predominant form of the molecule at pH7.4. molecular species at pH 7.4 calculated by ACD/Labs PhysChem software These are defined according to the definitions: Acid(A) ACD_MOST_ApKa <6.5 and ACD_MOST_BpKa<8.5 Bas (B) ACD_MOST_ApKa >6.5 and ACD_MOST_BpKa>8.5 Neutral (N) ACD_MOST_ApKa >6.5 and ACD_MOST_BpKa<8.5 Zwitterion (ZW) ACD_MOST_ApKa <6.5 and ACD_MOST_BpKa>8.5 ACD/Labs PhysChem software library version 12.01 Pipeline Pilot Server Version 8.5.0 PubChem software library http://pubchem.ncbi.nlm.nih.gov/help.html RDKit software library http://www.rdkit.org/ RDKit software library version 2015_09_2 http://www.rdkit.org/ number of rule of five violations calculated by RDKit software library version 2015_09_2 hydrogen bond acceptor count calculated by RDKit software library version 2015_09_2 hydrogen bond donor count calculated by RDKit software library version 2015_09_2 logP descriptor calculated by RDKit software library version 2015_09_2 molecular formula calculated by RDKit software library version 2015_09_2 average molecular weight calculated by RDKit software library version 2015_09_2 total polar surface area calculated by RDKit software library version 2015_09_2 PubChem software library version 2.1 molecular weight calculated by the pubchem software library molecular formula calculated by the pubchem software library total formal charge calculated by the pubchem software library monoisotopic mass calculated by the pubchem software library exact mass calculated by pubchem software library pubchem depositor-supplied molecular entity name A molecular entity name that has been supplied by a depositor to the PubChem database. This is just a molecular entity name with additional provenance associated. software module A software module is a collection of software methods. 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) software method 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. software library 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. software application A software application is a programming language implementation of a plan specification capable of realizing some objective specification. logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01 Octanol-water distribution coefficient calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01. hydrogen bond acceptor count calculated 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 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. Boiling point at 760 mmHg pressure 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 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 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. molecular weight of the corresponding free base The molecular weight for the free base chemical structure matching this chemical structure. molar refractivity calculated by ACD/Labs PhysChem software library version 12.01 Molar refractivity that has been calculated by ACD/Labs PhysChem software library version 12.01. index of refraction 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 calculated by ACD/Labs PhysChem software library version 12.01 Polarizability that has been calculated by ACD/Labs PhysChem software library version 12.01. execution of 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. execution of Pipeline Pilot A parameterized software execution of Pipeline Pilot. This refers to a particular run of the software. GGA Indigo http://ggasoftware.com/opensource/indigo execution of GGA Indigo A parameterized software execution of GGA Indigo. This refers to a particular run of the software. molar volume calculated by ACD/Labs PhysChem software library version 12.01 Molar volume that has been calculated by ACD/Labs PhysChem software library version 12.01. density 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 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 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 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 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 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 5.5 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 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 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 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. covalent unit count generated by pubchem software library defined atom stereocenter count generated by the pubchem software library defined bond stereocenter count generated by pubchem software library isotope atom count generated by pubchem software library heavy atom count generated by pubchem software library undefined atom stereocenter count generated by the pubchem software library undefined bond stereocenter count generated by the pubchem software library canonical smiles generated by OEChem OEChem software library http://www.eyesopen.com/oechem-tk OEChem software library version 1.9.0 isomeric SMILES generated by OEChem cycle count A descriptor that specifies the integer count of cycles in a given molecular entity. aromatic cycle count A descriptor that specifies the integer count of aromatic cycles in a given molecular entity. aromatic rings IUPAC Name generated by LexiChem LexiChem http://www.eyesopen.com/news/lexichem-v210-released LexiChem version 2.2.0 Cactvs software library http://www2.ccc.uni-erlangen.de/software/cactvs/tools.html Cactvs software library version 3.408 hydrogen bond donor count calculated by cactvs hydrogen bond acceptor count calculated by cactvs rotatable bond count calculated by cactvs structure complexity calculated by cactvs tautomer count calculated by cactvs TPSA calculated by cactvs XLogP3 software library http://www.sioc-ccbg.ac.cn/skins/ccbgwebsite/software/xlogp3/manual/XLOGP3_Manual.pdf XLogP3 software library version 3.0 xlogp3 calculated by the xlogp3 software InChI calculated by library version 1.0.4 InChI software library http://old.iupac.org/inchi/download/index.html InChI software library version 1.0.4 InChIKey generated by software version 1.0.4 OEChem software library version 1.7.6 structural alert count The number of structural alerts, that is, unwanted features as defined according to the procedure followed in Brenk et al., 2008. Brenk R, et al. Lessons learnt from assembling screening libraries for drug discovery for neglected diseases. Chem Med Chem. 2008;3:435–444. weighted quantitative estimate of drug-likeness QED weighted A descriptor which gives a quantitative estimate of drug likeness according to the procedure outlined in Bickerton et al., 2012. http://www.ncbi.nlm.nih.gov/pubmed/22270643 Nat Chem. 2012 Jan 24;4(2):90-8. doi: 10.1038/nchem.1243. Quantifying the chemical beauty of drugs. Bickerton GR, Paolini GV, Besnard J, Muresan S, Hopkins AL. freezing point descriptor 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 constant 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. atmospheric OH rate constant 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. upper explosive limit descriptor A physical descriptor for the upper explosive limit of the entity in air as a percentage by volume at room temperature. lower explosive limit descriptor A physical descriptor for the lower explosive limit in air as a percentage by volume at room temperature minimum explosive concentration descriptor A physical descriptor for the minimum explosive concentration. specific gravity descriptor 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. relative density descriptor 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. vapor density descriptor 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. odor detection threshold descriptor A physical descriptor for the lowest concentration of an odorant chemical entity that is perceivable by the human sense of smell. pH descriptor 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. evaporation rate descriptor A physical descriptor of the rate of evaporation of a liquid under standard conditions. autoignition temperature descriptor A physical descriptor of the lowest temperature at a substance will spontaneously ignite in a normal atmosphere without an external source of ignition. kindling point soil half-life descriptor 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. metal atom count A descriptor that specifies the integer count of metal atoms in a given chemical entity. oxygen atom count A descriptor that specifies the integer count of oxygen atoms in a given chemical entity. software module to calculate a molecular descriptor A software module to calculate a molecular descriptor is software module that implements an algorithm which calculates a descriptor value for a molecular entity. chemical database identifier Person: Colin Batchelor An identifying descriptor which is used within a particular database system to identify a chemical system. ChemSpider validated synonym Person: Colin Batchelor A preferred name in ChemSpider by virtue of having been validated by a curator. ChemSpider unvalidated synonym A molecular entity name in the ChemSpider database which has not been validated by a curator. Person: Colin Batchelor validated chemical database identifier Person: Colin Batchelor A chemical database identifier which has been validated by a curator. curator role A role inhering in a person which is realized when they perform a curation task. CRID validation A planned process in which a person bearing a curator role confirms an association between a CRID and an information content entity. Person: Colin Batchelor chemical name devalidation A planned process in which a person bearing a curator role marks an association between a chemical name and an information content entity as unconfirmed. Person: Colin Batchelor CRID registry curation A planned process in which a person bearing a curator role modifies a CRID registry. Person: Colin Batchelor chemical name validation Person: Colin Batchelor A planned process in which a person bearing a curator role confirms an association between a chemical name and an information content entity. chemical name deprecation Person: Colin Batchelor A planned process in which a person bearing a curator role deprecates an association between a chemical name and an information content entity. CRID deprecation A planned process in which an association between a CRID and an information content entity is deprecated. This can be done automatically; it does not need a person bearing a curator role. Person: Colin Batchelor CRID devalidation A planned process in which an association between a CRID and an information content entity is marked as unconfirmed. Person: Colin Batchelor ChemSpider title A ChemSpider validated synonym that has been identified as a title by the ChemSpider software. average molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01 Person: Colin Batchelor monoisotopic molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01 Person: Colin Batchelor energy band gap energy gap band gap A descriptor that describes the energy range in a solid where no electron states can exist. In graphs of the electron band structure of solids, the band gap generally refers to the energy difference (in electron volts) between the top of the valence band and the bottom of the conduction band in insulators and semiconductors. [http://en.wikipedia.org/wiki/Band_gap] metal element mass descriptor A descriptor describing the mass of the metal element component of a composite substance. metal element mass molecular formula calculated by ACD/Labs PhysChem software library version 12.01 Molecular formula for a chemical structure as calculated by ACD/Labs PhysChem software library version 12.01. partition coefficient The ratio of a dissolved substance in a two-phase system, giving a measure of the difference in solubility of the substance in the two phases. parameter data item A parameter data item is a data item that plays the role of a parameter to a software method. numeric data item A numeric data item is a data item which has a value which is numeric. textual data item A textual data item is a data item which has a value that has at least some non-numeric characters included in it. numeric parameter textual parameter numeric data format specification A numeric data format specification is a data format specification for data items which are numeric, that is, they contain only numeric values. textual data format specification A textual data format specification is a specification of the format of data items which are textual, that is, they consist of character data. numeric chemical descriptor textual chemical descriptor specific surface area A property of solids which is the total surface area of a material per unit of mass, solid or bulk volume, or cross-sectional area. group of an atom Descriptor that returns the group in the periodic table of a given atom. ChEBI name A ChEBI name is a preferred name annotated by the ChEBI database. The ChEBI name has the additional feature that it is unique within the ChEBI dataset. algorithm to interpret a connection table An algorithm that specifies how to take a connection table and convert it into a representation of a molecule. Colin Batchelor This may of course not be successful! structural standardization error Colin Batchelor An error message produced in the execution of a structural standardiation algorithm. structural standardization warning connection table interpretation warning connection table interpretation error information data item A software message data item which is merely intended to convey information and not a warning or an error. connection table interpretation information data item structural standardization information data item structural validation information data item drug trade name Trade name of a drug compound. International Non-proprietary Name INN International Non-proprietary Name, defined by the WHO. Unique Ingredient Identifier Identifier used by the USA Food and Drug Administration. UNII LipidMaps identifier Identifier used by the LipidMaps database, http://www.lipidmaps.org/. National Service Center number Identifier used by the Cancer Chemotherapy National Service Center. NSC number RTECS identifier Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/). BCUT http://dx.doi.org/10.1021/ci980137x BCUT Eigenvalue based descriptor noted for its utility in chemical diversity. bond partial pi charge bondPartialPiCharge 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). bond partial sigma charge Descriptor that calculates bond-sigma Partial charge of a bond. bondPartialSigmaCharge bond partial total charge Descriptor that calculates bond-total Partial charge of a bond. bondPartialTCharge bond sigma electronegativity Descriptor that calculates of bond-Polarizability of a bond by determining the difference the Sigma electronegativity on atoms A and B of a bond. bondSigmaElectronegativity bonds to Atom Descriptor based on the number of bonds on the shortest path between two atoms (topological distance). 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. bondsToAtom chi chain indices Evluates the simple and valence chi chain descriptors (Kier and Hall) of orders 3, 4, 5, 6 and 7. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain. chiChain chi cluster indices It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain. chiCluster Evluates the simple and valence chi cluster descriptors (Kier and Hall) of orders 3, 4,5 and 6. chi path indices chiPath Evaluates the Kier and Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain. chi path-cluster indices Evaluates the Kier and Hall Chi path cluster indices of orders 4,5 and 6. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain. chiPathCluster gravitational index http://dx.doi.org/10.1021/jp953224q Descriptor characterizing the mass distribution of the molecule. gravitationalIndex gravitational index (square and cube roots) http://dx.doi.org/10.1021/ci980029a Descriptor characterizing the mass distribution of the molecule as the square or cube root of the gravitational index. gravitationalIndex_SquareAndCubeRoots acceptor field atoms (Boehm,Klebe) http://dx.doi.org/10.1021/jm011039x Counts the number of acceptor field atoms for a carbonyl oxygen probe using force field based definition. hBondAcceptorsBoehmKlebe hydrogen bond acceptors (Daylight) SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html) hBondacceptorsDaylight Descriptor that calculates the number of hydrogen bond acceptors (by Daylight). acceptors or donors field atoms (Boehm,Klebe) http://dx.doi.org/10.1021/jm011039x Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe. hBondAcceptorsDonorsBoehmKlebe donor field atoms (Boehm,Klebe) http://dx.doi.org/10.1021/jm011039x hBondDonorsBoehmKlebe Counts the number of donor field atoms for an amino hydrogen probe. hydrogen bond donors (Daylight) hBondDonorsDaylight SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html) Descriptor that calculates the number of hydrogen bond donors (by Daylight). proton belonging to an aromatic system isProtonInAromaticSystem 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. proton belonging to a pi-system isProtonInConjugatedPiSystem Descriptor returns true if the protons is directly bonded to a pi system. Kier Hall SMARTS http://dx.doi.org/10.3390/91201004 Counts the number of occurrences of the E-state fragments. kierHallSmarts molecular distance edge http://dx.doi.org/10.1021/ci970109z Evaluate molecular distance edge descriptors for C, N and O. mde moments of inertia Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration. momentOfInertia partial total charge (MMFF94) partialTChargeMMFF94 Descriptor that calculates total partial charges of an heavy atom. period of an atom period Descriptor that returns the period in the periodic table of an atom belonging to an atom container. pi-contact of two atoms 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). piContact proton total partial charge protonPartialCharge Descriptor that calculates partial charges of an heavy atom and its protons based on Gasteiger Marsili (PEOE). RDF proton descriptor http://dx.doi.org/10.1021/ac010737m Calculation of RDF proton descriptor. rdfProtonCalculatedValues This is a mixed descriptor: topological, geometrical and electronic descriptor. TAE RECON descriptors for amino acid sequences http://dx.doi.org/10.1016/0097-8485(94)00052-G taeAminoAcid Descriptors are derived from pre-calculated quantum mechanical parameters by using the paramaters for amino acids and evaluating a set of 147 descriptors for peptide sequences. {@cdk.cite BREN1995} {@cdk.cite BREN1997} {@cdk.cite WHITE2003} weighted path weightedPath The weighted path (molecular ID) descriptors were described by Randic and they characterize molecular branching. WHIM 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. Holistic descriptors described by Todeschini et al. WHIM Moreau-Broto Autocorrelation (charge) descriptors ATSc1 - ATSc5 The Moreau-Broto autocorrelation descriptors using partial charges. autoCorrelationCharge Moreau-Broto autocorrelation (mass) descriptors The Moreau-Broto autocorrelation descriptors using atomic weight. autoCorrelationMass ATSm1 - ATSm5 Moreau-Broto autocorrelation (polarizability) descriptors ATSp1 - ATSp5 autoCorrelationPolarizability The Moreau-Broto autocorrelation descriptors using polarizability. carbon types carbonTypes Characterizes the carbon connectivity in terms of hybridization C1SP1, C2SP1, C1SP2, C2SP2, C3SP2, C1SP3, C2SP3, C3SP3, C4SP3 carbon connectivity index (order 0) chi0C Descriptor that calculates the carbon connectivity index (order 0). valence connectivity index (order 0) Descriptor that calculates atomic valence connectivity index (order 0). chi0v valence carbon connectivity index (order 0) chi0vC Descriptor that calculates carbon valence connectivity index (order 0). carbon connectivity index (order 1) chi1C Descriptor that calculates carbon connectivity index (order 1). valence connectivity index (order 1) chi1v Descriptor that calculates atomic valence connectivity index (order 1). valence carbon connectivity index (order 1) Descriptor that calculates carbon valence connectivity index (order 1). chi1vC distance to atom distanceToAtom Descriptor that calculates the 3D distance between two atoms. effective polarizability EffectiveAtomPolarizabilityDescriptor, effAtomPol effectivePolarizability Descriptor that calculates the effective polarizability of a given heavy atom. hybridization ratio Characterizes molecular complexity in terms of carbon hybridization states. 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. hybratio Kier and Hall kappa molecular shape indices Descriptor that calculates Kier and Hall kappa molecular shape indices. kierValues 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. partial pi charge http://dx.doi.org/10.1002/ange.19850970818 Descriptor that calculates pi partial charges in pi-bonded systems of an heavy atom based on based on Gasteiger H.Saller (PEPE). partialPiCharge Other short_name: pepe. partial sigma charge http://dx.doi.org/10.1016/0040-4020(80)80168-2 partialSigmaCharge Descriptor that calculates sigma partial charges in sigma-bonded systems (PEOE) of an heavy atom based on Gasteiger Marsili. pi electronegativity Descriptor that returns the pi electronegativity for a given atom. piElectronegativity 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. SwissLipids identifier MolMeDB identifier PDB ligand identifier PDB structure identifier PDB identifier NOTE: QSAR descriptors are often just called 'chemical descriptor' or 'molecular descriptor' in the cheminformatics community. BODO:Descriptor ionization energy ionization enthalpy An ionization energy descriptor is a descriptor that describes the minimum amount of energy required to remove an electron (to an infinite distance) from an atom or molecule in a gaseous state. X + energy → X+ + e- The term 'ionization potential' has historically been used but is now no longer recommended. ionization potential A descriptor characterizing the ratio of the length to the breadth of a given entity. enthalpy of formation heat of formation