]> 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 Colin Batchelor Leonid Chepelev http://creativecommons.org/licenses/by/3.0 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_ has output has input has attribute is attribute of is variant of is output of has uncertainty value has value BODO:Algorithm 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 chemical entity CHEBI:24431 A chemical entity is any molecular entity or chemical substance. molecular entity information format specification A molecular entity information format specification is an information content entity which specifies a format in which information about a molecular entity should be encoded. 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 software module 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 module is a collection of software methods. 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. 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. 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. BODO:Descriptor NOTE: QSAR descriptors are often just called 'chemical descriptor' or 'molecular descriptor' in the cheminformatics community.