chemical information ontology (cheminf) - information entities about chemical entities
type: Ontology
version info: 2.1.0
contributor: Egon Willighagen
contributor: Janna Hastings
contributor: Michel Dumontier
comment: The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.
format: application/rdf+xml
language: en
comment: 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_
license: http://creativecommons.org/publicdomain/zero/1.0/
contributor: Cristian Munteanu
contributor: Gang Fu
contributor: Leonid Chepelev
contributor: Mark Davies
contributor: Evan Bolton
contributor: Colin Batchelor
imports: iao.owl
imports: cdk.owl
imports: cheminf-algorithms.owl
imports: cheminf-core.owl
imports: cheminf-external.owl

is enantiomer of
type: ObjectProperty
description: 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.
range: CHEBI_23367
domain: CHEBI_23367
sub property of: is_stereoisomer_of
property disjoint with: is_diastereomer_of

is tautomer of
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
description: 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.
range: CHEBI_23367
domain: CHEBI_23367
sub property of: topObjectProperty

has output
type: ObjectProperty
domain: BFO_0000015
sub property of: RO_0000057

has input
type: ObjectProperty
domain: BFO_0000015
sub property of: RO_0000057
range: Thing

has attribute
type: ObjectProperty
range: IAO_0000027
inverse of: is attribute of

is attribute of
type: ObjectProperty
domain: IAO_0000027

is variant of
type: ObjectProperty
type: SymmetricProperty

has_protein_binding_participant
type: ObjectProperty
domain: GO_0005515
sub property of: RO_0000057

participates_in_protein_binding
type: ObjectProperty
range: GO_0005515
inverse of: has_protein_binding_participant
sub property of: RO_0000056

ligates
type: ObjectProperty
domain: CHEBI_23367
range: PR_000000001
property chain axiom: participates_in_protein_binding
property chain axiom: has_protein_binding_participant

is_isotopologue_of
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
description: An isotopologue is a molecular entity that differs only in isotopic composition from another molecular entity. (AU:I03351)
range: CHEBI_23367
domain: CHEBI_23367
sub property of: has_same_connectivity_as

has_stereoundefined_parent
type: ObjectProperty
description: Subclass relation between a class that has stereochemistry defined and an otherwise identical class that does not.
range: CHEBI_23367
domain: CHEBI_23367
sub property of: subClassOf

has_normalized_counterpart
type: ObjectProperty
description: Connects a molecule to a normalized counterpart of the same molecule according to an algorithm.
comment: Caution: The number of moieties in the first molecule may be greater than in the second molecule. Example: salts.
comment: Caution: this is not a subclass relation and should not be thought of as such for reasoning purposes.
domain: CHEBI_23367
range: CHEBI_23367
sub property of: has counterpart molecular entity

has OPS normalized counterpart
type: ObjectProperty
description: This connects a molecule to its normalized counterpart according to the OPS specification.
range: CHEBI_23367
domain: CHEBI_23367
sub property of: has_normalized_counterpart

has_isotopically_unspecified_parent
type: ObjectProperty
description: 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.
domain: CHEBI_23367
range: CHEBI_23367
sub property of: subClassOf

has_uncharged_counterpart
type: ObjectProperty
description: Connects a molecule to molecule with identical heavy-atom connectivity which is neutral. It is not a subclass relation.
range: CHEBI_23367
domain: CHEBI_23367
sub property of: has counterpart molecular entity

is_stereoisomer_of
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
description: Connects a molecule to an isomer with identical constitution but differing in its arrangement of atoms in space. (AU:S05984)
domain: CHEBI_23367
range: CHEBI_23367
sub property of: has_same_connectivity_as

has_same_connectivity_as
type: ObjectProperty
description: Connects a molecule to an isomer with identical constitution.
domain: CHEBI_23367
range: CHEBI_23367

is_diastereomer_of
type: ObjectProperty
description: Connects a molecule to a stereoisomer which is not its enantiomer.
domain: CHEBI_23367
range: CHEBI_23367
sub property of: is_stereoisomer_of

has PubChem normalized counterpart
type: ObjectProperty
IAO_0000115: This connects a molecule to its normalized counterpart according to the PubChem specification.
sub property of: has_normalized_counterpart

has component
type: ObjectProperty
comment: This connects entities at different granularities.
IAO_0000115: Has as member parts (see BFO 2 Graz for more on this) many molecular entities.
range: CHEBI_23367
domain: CHEMINF_000266
sub property of: BFO_0000051

has counterpart molecular entity
type: ObjectProperty
comment: This is intended to capture the case where a database has ad hoc relations between molecules that are not necessarily subclass relations.
IAO_0000115: Connects a molecular entity to another molecular entity according to some specification.

has component with uncharged counterpart
type: ObjectProperty
IAO_0000115: Connects a molecular substance, say a mixture containing ions, with a neutral form of one of the ions.
range: CHEBI_23367
domain: CHEMINF_000266
property chain axiom: has component
property chain axiom: has_uncharged_counterpart

similar to
type: ObjectProperty
comment: not transitive, obviously
IAO_0000115: Connects a molecular entity that is deemed similar to another according to some algorithm.
sub property of: has counterpart molecular entity

similar to by PubChem 2D similarity algorithm
type: ObjectProperty
comment: http://pubchem.ncbi.nlm.nih.gov/help.html#tanimoto
IAO_0000115: Has a Tanimoto score with the counterpart molecular entity of more than 0.9, based on the PubChem fingerprint specification.
sub property of: similar to

similar to by PubChem 3D similarity algorithm
type: ObjectProperty
comment: http://dx.doi.org/10.1186/1758-2946-3-32
IAO_0000115: 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.
sub property of: similar to

has major tautomer at pH 7.4
type: ObjectProperty
IAO_0000115: A exists in an equilibrium with B at pH 7.4 and physiological temperature and B is the dominant isomer.
sub property of: is tautomer of

is_isotopically_unspecified_parent_of
type: ObjectProperty
description: 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.
IAO_0000117: Colin Batchelor
domain: CHEBI_23367
range: CHEBI_23367
inverse of: has_isotopically_unspecified_parent

is_stereoundefined_parent_of
type: ObjectProperty
IAO_0000117: Colin Batchelor
description: Superclass relation between a class that does not have stereochemistry defined and another otherwise identical one that does.
range: CHEBI_23367
domain: CHEBI_23367
inverse of: has_stereoundefined_parent

is component with uncharged counterpart of
type: ObjectProperty
comment: This is here because Open PHACTS has requested an inverse. Use with caution!
IAO_0000115: Connects a neutral molecule with a salt.
inverse of: has component with uncharged counterpart

is major tautomer at pH 7.4 of
type: ObjectProperty
IAO_0000115: A exists in an equilibrium with B at pH 7.4 and physiological temperature and A is the dominant isomer.
sub property of: is tautomer of
inverse of: has major tautomer at pH 7.4

is OPS normalized counterpart of
type: ObjectProperty
IAO_0000115: 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.
inverse of: has OPS normalized counterpart
sub property of: has counterpart molecular entity

is uncharged counterpart of
type: ObjectProperty
IAO_0000115: If A 'is uncharged counterpart of' B, then A is the neutral species corresponding to B. B may itself of course be neutral.
inverse of: has_uncharged_counterpart
sub property of: has counterpart molecular entity

is counterpart with different charge of
type: ObjectProperty
IAO_0000117: Colin Batchelor
IAO_0000115: If A 'is a counterpart with different charge of' B, then A is an otherwise identical species to B but for charge.
domain: CHEBI_23367
range: CHEBI_23367
sub property of: has_same_connectivity_as

shares OPS normalized parent with
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
IAO_0000115: If A 'shares OPS normalized parent with' B, then A 'has OPS normalized counterpart' C and B 'has OPS normalized counterpart' C.
IAO_0000117: Colin Batchelor
domain: CHEBI_23367
range: CHEBI_23367
sub property of: has counterpart molecular entity

has ChemAxon canonicalised tautomer
type: ObjectProperty
comment: A and B can be identical.
IAO_0000117: Colin Batchelor
IAO_0000115: 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.
sub property of: is tautomer of
range: CHEBI_23367
domain: CHEBI_23367

is ChemAxon canonicalised tautomer of
type: ObjectProperty
IAO_0000115: 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.
IAO_0000117: Colin Batchelor
comment: A and B can be identical.
sub property of: is tautomer of
domain: CHEBI_23367
range: CHEBI_23367
inverse of: has ChemAxon canonicalised tautomer

is output of
type: ObjectProperty
inverse of: has output
sub property of: RO_0000056

has uncertainty value
type: DatatypeProperty
type: FunctionalProperty
domain: IAO_0000030
sub property of: has value
range: float

has value
type: DatatypeProperty
domain: IAO_0000027

IAO_0000064
type: Class
has alternative id: BODO:Algorithm
IAO_0000114: IAO_0000120

chemical entity
type: Class
subclass of: BFO_0000040
description: A chemical entity is any molecular entity or chemical substance.
has alternative id: obo:24431

file
type: Class
subclass of: IAO_0000310

software implementation
type: Class
subclass of: IAO_0000010

PubChem compound identifier (CID)
type: Class
subclass of: CHEMINF_000302

PubChem substance identifier (SID)
type: Class
subclass of: CHEMINF_000302

Pipeline Pilot library
type: Class
subclass of: software library
IAO_0000115: http://accelrys.com/products/pipeline-pilot/

molecular weight calculated by pipeline pilot
type: Class
subclass of: CHEMINF_000216
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction
IAO_0000115: A molecular weight descriptor calculated by a relevant module of the Pipeline Pilot software tool.

Ghose/Crippen ALogP calculation algorithm
type: Class
subclass of: CHEMINF_000450
IAO_0000115: 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.

CHEMINF_000238
subclass of: CHEMINF_000404
has synonym: fusibility

ALogP calculated by Pipeline Pilot
type: Class
subclass of: CHEMINF_000295
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

Ertl polar surface area calculation algorithm
type: Class
subclass of: CHEMINF_000450
IAO_0000115: 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
type: Class
subclass of: CHEMINF_000229

polar surface area descriptor calculated by Pipeline Pilot
type: Class
subclass of: polar surface area descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

hydrogen bond acceptor count calculated by pipeline pilot
type: Class
subclass of: CHEMINF_000245
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

hydrogen bond donor count calculated by pipeline pilot
type: Class
subclass of: CHEMINF_000244
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

rotatable bond count calculated by pipeline pilot
type: Class
subclass of: CHEMINF_000254
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

rule of five violations descriptor
type: Class
subclass of: CHEMINF_000025
IAO_0000115: 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
type: Class
subclass of: CHEMINF_000450
IAO_0000115: 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
type: Class
subclass of: rule of five violations descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

rule of three passes descriptor
type: Class
subclass of: CHEMINF_000025
IAO_0000115: 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
type: Class
subclass of: CHEMINF_000450
IAO_0000115: 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
type: Class
subclass of: rule of three passes descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

medchem friendly descriptor
type: Class
subclass of: CHEMINF_000025
IAO_0000115: 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
type: Class
subclass of: medchem friendly descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

ACD/Labs PhysChem software library
type: Class
subclass of: software library
IAO_0000115: http://www.acdlabs.com/resources/knowledgebase/app_notes/physchem/

logP calculated by ACD/Labs PhysChem software
type: Class
subclass of: CHEMINF_000251
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01

logD descriptor
type: Class
subclass of: CHEMINF_000025
IAO_0000115: octanol-water distribution coefficient calculated at a given pH.

logD calculated at pH 7.4 by ACD/Labs PhysChem software
type: Class
subclass of: logD descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
IAO_0000115: ACD_LogD(pH7.4) Distribution Coefficient calculated at pH7.4

most acidic pKa calculated by ACD/Labs PhysChem software library
type: Class
subclass of: CHEMINF_000195
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0002218
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction
IAO_0000115: Most acidic pKa of the molecule

most basic pKa calculated by ACD/Labs PhysChem software library
type: Class
subclass of: CHEMINF_000195
IAO_0000115: Most basic pKa of the molecule

molecular species at pH 7.4 descriptor
type: Class
subclass of: CHEMINF_000025
IAO_0000115: 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
type: Class
subclass of: molecular species at pH 7.4 descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
IAO_0000115: 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
type: Class
subclass of: ACD/Labs PhysChem software library

Pipeline Pilot Server Version 8.5.0
type: Class
subclass of: Pipeline Pilot library

PubChem software library
type: Class
subclass of: software library
IAO_0000115: http://pubchem.ncbi.nlm.nih.gov/help.html

RDKit software library
type: Class
subclass of: software library
IAO_0000115: http://www.rdkit.org/

RDKit software library version 2015_09_2
type: Class
subclass of: RDKit software library
IAO_0000115: http://www.rdkit.org/

number of rule of five violations calculated by RDKit software library version 2015_09_2
type: Class
subclass of: rule of five violations descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

hydrogen bond acceptor count calculated by RDKit software library version 2015_09_2
type: Class
subclass of: CHEMINF_000245
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

hydrogen bond donor count calculated by RDKit software library version 2015_09_2
type: Class
subclass of: CHEMINF_000244
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

logP descriptor calculated by RDKit software library version 2015_09_2
type: Class
subclass of: CHEMINF_000251
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

molecular formula calculated by RDKit software library version 2015_09_2
type: Class
subclass of: CHEMINF_000042
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

average molecular weight calculated by RDKit software library version 2015_09_2
type: Class
subclass of: CHEMINF_000216
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

total polar surface area calculated by RDKit software library version 2015_09_2
type: Class
subclass of: polar surface area descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

PubChem software library version 2.1
type: Class
subclass of: PubChem software library

molecular weight calculated by the pubchem software library
type: Class
subclass of: CHEMINF_000216
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

molecular formula calculated by the pubchem software library
type: Class
subclass of: CHEMINF_000042
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

total formal charge calculated by the pubchem software library
type: Class
subclass of: CHEMINF_000268
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

monoisotopic mass calculated by the pubchem software library
type: Class
subclass of: CHEMINF_000218
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

exact mass calculated by pubchem software library
type: Class
subclass of: CHEMINF_000217
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

pubchem depositor-supplied molecular entity name
type: Class
subclass of: CHEMINF_000043
IAO_0000115: 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
type: Class
subclass of: software implementation
subclass of: Restriction
  on property: BFO_0000051
  some values from: software method
description: A software module is a collection of software methods.
comment: 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
type: Class
subclass of: software implementation
subclass of: Restriction
  on property: CHEMINF_000330
  some values from: parameter data item
subclass of: Restriction
  on property: CHEMINF_000331
  some values from: parameter data item
subclass of: Restriction
  on property: CHEMINF_000331
  some values from: CHEMINF_000505
description: 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
type: Class
subclass of: software application
subclass of: Restriction
  on property: BFO_0000051
  some values from: Class
    union of: software module
    union of: software method
description: 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
type: Class
subclass of: software implementation
description: 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
type: Class
subclass of: logD descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000245
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000244
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000257
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000254
description: 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
type: Class
subclass of: polar surface area descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Polar surface area that has been calculated by ACD/Labs PhysChem software library version 12.01.

molecular weight of the corresponding free base
type: Class
subclass of: CHEMINF_000216
description: 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
type: Class
subclass of: CHEMINF_000001
description: 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
type: Class
subclass of: CHEMINF_000253
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000089
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Polarizability that has been calculated by ACD/Labs PhysChem software library version 12.01.

execution of ACD/Labs PhysChem software library version 12.01
type: Class
equivalent class: Class
  intersection of: CHEMINF_000138
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: CHEMINF_000103
      intersection of: Restriction
        on property: BFO_0000050
        some values from: Pipeline Pilot library
description: 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
type: Class
equivalent class: Class
  intersection of: CHEMINF_000138
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: CHEMINF_000103
      intersection of: Restriction
        on property: BFO_0000050
        some values from: ACD/Labs PhysChem software library version 12.01
description: A parameterized software execution of Pipeline Pilot. This refers to a particular run of the software.

GGA Indigo
type: Class
subclass of: software library
IAO_0000115: http://ggasoftware.com/opensource/indigo

execution of GGA Indigo
type: Class
equivalent class: Class
  intersection of: CHEMINF_000138
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: CHEMINF_000103
      intersection of: Restriction
        on property: BFO_0000050
        some values from: GGA Indigo
description: 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
type: Class
subclass of: CHEMINF_000415
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000416
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000417
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000418
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000419
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000413
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000413
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000414
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000414
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: rule of five violations descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000420
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: 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
type: Class
subclass of: CHEMINF_000280
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

defined atom stereocenter count generated by the pubchem software library
type: Class
subclass of: CHEMINF_000206
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

defined bond stereocenter count generated by pubchem software library
type: Class
subclass of: CHEMINF_000214
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

isotope atom count generated by pubchem software library
type: Class
subclass of: CHEMINF_000301
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

heavy atom count generated by pubchem software library
type: Class
subclass of: CHEMINF_000300
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

undefined atom stereocenter count generated by the pubchem software library
type: Class
subclass of: CHEMINF_000212
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

undefined bond stereocenter count generated by the pubchem software library
type: Class
subclass of: CHEMINF_000215
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

canonical smiles generated by OEChem
type: Class
subclass of: CHEMINF_000007
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

OEChem software library
type: Class
subclass of: software library
IAO_0000115: http://www.eyesopen.com/oechem-tk

OEChem software library version 1.9.0
type: Class
subclass of: OEChem software library

isomeric SMILES generated by OEChem
type: Class
subclass of: CHEMINF_000032
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

cycle count
type: Class
subclass of: CHEMINF_000209
IAO_0000115: A descriptor that specifies the integer count of cycles in a given molecular entity.

aromatic cycle count
type: Class
subclass of: cycle count
IAO_0000115: A descriptor that specifies the integer count of aromatic cycles in a given molecular entity.
IAO_0000118: aromatic rings

IUPAC Name generated by LexiChem
type: Class
subclass of: CHEMINF_000107
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

LexiChem
type: Class
subclass of: software library
IAO_0000115: http://www.eyesopen.com/news/lexichem-v210-released

LexiChem version 2.2.0
type: Class
subclass of: LexiChem

Cactvs software library
type: Class
subclass of: software library
IAO_0000115: http://www2.ccc.uni-erlangen.de/software/cactvs/tools.html

Cactvs software library version 3.408
type: Class
subclass of: Cactvs software library

hydrogen bond donor count calculated by cactvs
type: Class
subclass of: CHEMINF_000244
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

hydrogen bond acceptor count calculated by cactvs
type: Class
subclass of: CHEMINF_000245
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

rotatable bond count calculated by cactvs
type: Class
subclass of: CHEMINF_000254
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

structure complexity calculated by cactvs
type: Class
subclass of: CHEMINF_000219
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

tautomer count calculated by cactvs
type: Class
subclass of: CHEMINF_000202
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

TPSA calculated by cactvs
type: Class
subclass of: CHEMINF_000174
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

XLogP3 software library
type: Class
subclass of: software library
IAO_0000115: http://www.sioc-ccbg.ac.cn/skins/ccbgwebsite/software/xlogp3/manual/XLOGP3_Manual.pdf

XLogP3 software library version 3.0
type: Class
subclass of: XLogP3 software library

xlogp3 calculated by the xlogp3 software
type: Class
subclass of: CHEMINF_000186
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

InChI calculated by library version 1.0.4
type: Class
subclass of: CHEMINF_000113
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

InChI software library
type: Class
subclass of: software library
IAO_0000115: http://old.iupac.org/inchi/download/index.html

InChI software library version 1.0.4
type: Class
subclass of: InChI software library

InChIKey generated by software version 1.0.4
type: Class
subclass of: CHEMINF_000059
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: CHEMINF_000138
    intersection of: Restriction
      on property: RO_0000057
      some values from: Class
        intersection of: CHEMINF_000103
        intersection of: Restriction

OEChem software library version 1.7.6
type: Class
subclass of: OEChem software library

structural alert count
type: Class
subclass of: CHEMINF_000209
IAO_0000115: 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
type: Class
subclass of: CHEMINF_000025
IAO_0000118: QED weighted
IAO_0000115: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: A physical descriptor for the lower explosive limit in air as a percentage by volume at room temperature

minimum explosive concentration descriptor
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: A physical descriptor for the minimum explosive concentration.

specific gravity descriptor
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: A physical descriptor for the lowest concentration of an odorant chemical entity that is perceivable by the human sense of smell.

pH descriptor
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: A physical descriptor of the rate of evaporation of a liquid under standard conditions.

autoignition temperature descriptor
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: A physical descriptor of the lowest temperature at a substance will spontaneously ignite in a normal atmosphere without an external source of ignition.
IAO_0000118: kindling point

soil half-life descriptor
type: Class
subclass of: CHEMINF_000025
subclass of: Restriction
  on property: IAO_0000136
  some values from: CHEMINF_000266
description: 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
type: Class
subclass of: CHEMINF_000263
IAO_0000115: A descriptor that specifies the integer count of metal atoms in a given chemical entity.

oxygen atom count
type: Class
subclass of: CHEMINF_000263
IAO_0000115: A descriptor that specifies the integer count of oxygen atoms in a given chemical entity.

software module to calculate a molecular descriptor
type: Class
equivalent class: Class
  intersection of: CHEMINF_000103
  intersection of: Restriction
    on property: CHEMINF_000331
    some values from: CHEMINF_000065
subclass of: Restriction
  on property: CHEMINF_000047
  some values from: CHEMINF_000450
description: 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
type: Class
subclass of: IAO_0000577
subclass of: CHEMINF_000061
IAO_0000117: Person: Colin Batchelor
IAO_0000115: An identifying descriptor which is used within a particular database system to identify a chemical system.

ChemSpider validated synonym
type: Class
subclass of: CHEMINF_000044
IAO_0000117: Person: Colin Batchelor
IAO_0000115: A preferred name in ChemSpider by virtue of having been validated by a curator.

ChemSpider unvalidated synonym
type: Class
subclass of: CHEMINF_000043
IAO_0000115: A molecular entity name in the ChemSpider database which has not been validated by a curator.
IAO_0000117: Person: Colin Batchelor

validated chemical database identifier
type: Class
subclass of: chemical database identifier
subclass of: Restriction
  on property: OBI_0000312
  some values from: CRID validation
IAO_0000117: Person: Colin Batchelor
IAO_0000115: A chemical database identifier which has been validated by a curator.

curator role
type: Class
subclass of: BFO_0000023
IAO_0000115: A role inhering in a person which is realized when they perform a curation task.

CRID validation
type: Class
subclass of: CRID registry curation
subclass of: Restriction
  on property: RO_0000057
  some values from: IAO_0000577
IAO_0000115: A planned process in which a person bearing a curator role confirms an association between a CRID and an information content entity.
IAO_0000117: Person: Colin Batchelor

chemical name devalidation
type: Class
subclass of: CRID registry curation
subclass of: Restriction
  on property: RO_0000057
  some values from: CHEMINF_000043
IAO_0000115: 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.
IAO_0000117: Person: Colin Batchelor

CRID registry curation
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: RO_0000057
  some values from: IAO_0000579
IAO_0000115: A planned process in which a person bearing a curator role modifies a CRID registry.
IAO_0000117: Person: Colin Batchelor

chemical name validation
type: Class
subclass of: CRID registry curation
subclass of: Restriction
  on property: RO_0000057
  some values from: CHEMINF_000043
IAO_0000117: Person: Colin Batchelor
IAO_0000115: 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
type: Class
subclass of: CRID registry curation
subclass of: Restriction
  on property: RO_0000057
  some values from: CHEMINF_000043
IAO_0000117: Person: Colin Batchelor
IAO_0000115: 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
type: Class
subclass of: CRID registry curation
subclass of: Restriction
  on property: RO_0000057
  some values from: IAO_0000577
IAO_0000115: A planned process in which an association between a CRID and an information content entity is deprecated.
comment: This can be done automatically; it does not need a person bearing a curator role.
IAO_0000117: Person: Colin Batchelor

CRID devalidation
type: Class
subclass of: CRID registry curation
subclass of: Restriction
  on property: RO_0000057
  some values from: IAO_0000577
IAO_0000115: A planned process in which an association between a CRID and an information content entity is marked as unconfirmed.
IAO_0000117: Person: Colin Batchelor

ChemSpider title
type: Class
subclass of: ChemSpider validated synonym
IAO_0000115: 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
type: Class
subclass of: CHEMINF_000216
IAO_0000117: Person: Colin Batchelor

monoisotopic molecular weight descriptor calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: CHEMINF_000218
IAO_0000117: Person: Colin Batchelor

energy band gap
type: Class
subclass of: CHEMINF_000016
IAO_0000118: energy gap
IAO_0000118: band gap
IAO_0000115: 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
type: Class
subclass of: CHEMINF_000083
IAO_0000115: A descriptor describing the mass of the metal element component of a composite substance.
IAO_0000118: metal element mass

molecular formula calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: CHEMINF_000042
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Molecular formula for a chemical structure as calculated by ACD/Labs PhysChem software library version 12.01.

partition coefficient
type: Class
subclass of: CHEMINF_000025
IAO_0000115: 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
type: Class
subclass of: IAO_0000027
IAO_0000115: A parameter data item is a data item that plays the role of a parameter to a software method.

numeric data item
type: Class
subclass of: IAO_0000027
subclass of: Restriction
  on property: CHEMINF_000047
  some values from: numeric data format specification
subclass of: Restriction
  on property: has value
  some values from: Datatype
    union of: decimal
    union of: float
    union of: integer
    union of: long
disjoint with: textual data item
IAO_0000115: A numeric data item is a data item which has a value which is numeric.

textual data item
type: Class
subclass of: IAO_0000027
subclass of: Restriction
  on property: CHEMINF_000047
  some values from: textual data format specification
subclass of: Restriction
  on property: has value
  some values from: string
IAO_0000115: 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
type: Class
equivalent class: Class
  intersection of: parameter data item
  intersection of: numeric data item
subclass of: parameter data item
subclass of: numeric data item

textual parameter
type: Class
equivalent class: Class
  intersection of: parameter data item
  intersection of: textual data item
subclass of: parameter data item
subclass of: textual data item

numeric data format specification
type: Class
subclass of: IAO_0000098
IAO_0000115: 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
type: Class
subclass of: IAO_0000098
IAO_0000115: 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
type: Class
equivalent class: Class
  intersection of: CHEMINF_000123
  intersection of: numeric data item
subclass of: CHEMINF_000123

textual chemical descriptor
type: Class
equivalent class: Class
  intersection of: CHEMINF_000123
  intersection of: textual data item
subclass of: CHEMINF_000123

specific surface area
type: Class
subclass of: CHEMINF_000101
IAO_0000115: 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
type: Class
subclass of: CHEMINF_000136
description: Descriptor that returns the group in the periodic table of a given atom.

ChEBI name
type: Class
subclass of: CHEMINF_000044
IAO_0000115: 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
type: Class
subclass of: IAO_0000064
description: An algorithm that specifies how to take a connection table and convert it into a representation of a molecule.
IAO_0000117: Colin Batchelor
comment: This may of course not be successful!

structural standardization error
type: Class
subclass of: CHEMINF_000507
subclass of: Restriction
  on property: CHEMINF_000606
  some values from: CHEMINF_000424
IAO_0000117: Colin Batchelor
description: An error message produced in the execution of a structural standardiation algorithm.

structural standardization warning
type: Class
subclass of: CHEMINF_000506
subclass of: Restriction
  on property: CHEMINF_000606
  some values from: CHEMINF_000423

connection table interpretation warning
type: Class
subclass of: CHEMINF_000506
subclass of: Restriction
  on property: CHEMINF_000606
  some values from: algorithm to interpret a connection table

connection table interpretation error
type: Class
subclass of: CHEMINF_000507
subclass of: Restriction
  on property: CHEMINF_000606
  some values from: algorithm to interpret a connection table

information data item
type: Class
subclass of: CHEMINF_000505
description: 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
type: Class
subclass of: information data item
subclass of: Restriction
  on property: CHEMINF_000606
  some values from: algorithm to interpret a connection table

structural standardization information data item
type: Class
subclass of: information data item
subclass of: Restriction
  on property: CHEMINF_000606
  some values from: CHEMINF_000424

structural validation information data item
type: Class
subclass of: information data item
subclass of: Restriction
  on property: CHEMINF_000606
  some values from: CHEMINF_000423

drug trade name
type: Class
subclass of: CHEMINF_000043
IAO_0000115: Trade name of a drug compound.

International Non-proprietary Name
type: Class
subclass of: CHEMINF_000043
short name: INN
IAO_0000115: International Non-proprietary Name, defined by the WHO.

Unique Ingredient Identifier
type: Class
subclass of: chemical database identifier
description: Identifier used by the USA Food and Drug Administration.
short name: UNII

LipidMaps identifier
type: Class
subclass of: chemical database identifier
description: Identifier used by the LipidMaps database, http://www.lipidmaps.org/.

National Service Center number
type: Class
subclass of: chemical database identifier
description: Identifier used by the Cancer Chemotherapy National Service Center.
short name: NSC number

RTECS identifier
type: Class
subclass of: chemical database identifier
description: Identifier used by the RTECS database (http://www.cdc.gov/niosh/rtecs/).

BCUT
type: Class
subclass of: CHEMINF_000092
doi: http://dx.doi.org/10.1021/ci980137x
short name: BCUT
description: Eigenvalue based descriptor noted for its utility in chemical diversity.

bond partial pi charge
type: Class
subclass of: CHEMINF_000087
short name: bondPartialPiCharge
description: 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
type: Class
subclass of: CHEMINF_000087
description: Descriptor that calculates bond-sigma Partial charge of a bond.
short name: bondPartialSigmaCharge

bond partial total charge
type: Class
subclass of: CHEMINF_000087
description: Descriptor that calculates bond-total Partial charge of a bond.
short name: bondPartialTCharge

bond sigma electronegativity
type: Class
subclass of: CHEMINF_000087
description: Descriptor that calculates of bond-Polarizability of a bond by determining the difference the Sigma electronegativity on atoms A and B of a bond.
short name: bondSigmaElectronegativity

bonds to Atom
type: Class
subclass of: CHEMINF_000092
description: Descriptor based on the number of bonds on the shortest path between two atoms (topological distance).
comment: 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.
short name: bondsToAtom

chi chain indices
type: Class
subclass of: CHEMINF_000092
description: Evluates the simple and valence chi chain descriptors (Kier and Hall) of orders 3, 4, 5, 6 and 7.
comment: It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
short name: chiChain

chi cluster indices
type: Class
subclass of: CHEMINF_000092
comment: It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
short name: chiCluster
description: Evluates the simple and valence chi cluster descriptors (Kier and Hall) of orders 3, 4,5 and 6.

chi path indices
type: Class
subclass of: CHEMINF_000092
short name: chiPath
description: Evaluates the Kier and Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7.
comment: 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
type: Class
subclass of: CHEMINF_000092
description: Evaluates the Kier and Hall Chi path cluster indices of orders 4,5 and 6.
comment: It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
short name: chiPathCluster

gravitational index
type: Class
subclass of: CHEMINF_000093
doi: http://dx.doi.org/10.1021/jp953224q
description: Descriptor characterizing the mass distribution of the molecule.
short name: gravitationalIndex

gravitational index (square and cube roots)
type: Class
subclass of: gravitational index
doi: http://dx.doi.org/10.1021/ci980029a
description: Descriptor characterizing the mass distribution of the molecule as the square or cube root of the gravitational index.
short name: gravitationalIndex_SquareAndCubeRoots

acceptor field atoms (Boehm,Klebe)
type: Class
subclass of: CHEMINF_000087
doi: http://dx.doi.org/10.1021/jm011039x
description: Counts the number of acceptor field atoms for a carbonyl oxygen probe using force field based definition.
short name: hBondAcceptorsBoehmKlebe

hydrogen bond acceptors (Daylight)
type: Class
subclass of: CHEMINF_000087
comment: SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)
short name: hBondacceptorsDaylight
description: Descriptor that calculates the number of hydrogen bond acceptors (by Daylight).

acceptors or donors field atoms (Boehm,Klebe)
type: Class
subclass of: CHEMINF_000087
doi: http://dx.doi.org/10.1021/jm011039x
description: Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe.
short name: hBondAcceptorsDonorsBoehmKlebe

donor field atoms (Boehm,Klebe)
type: Class
subclass of: CHEMINF_000087
doi: http://dx.doi.org/10.1021/jm011039x
short name: hBondDonorsBoehmKlebe
description: Counts the number of donor field atoms for an amino hydrogen probe.

hydrogen bond donors (Daylight)
type: Class
subclass of: CHEMINF_000087
short name: hBondDonorsDaylight
comment: SMILES on-line tutorial, http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html)
description: Descriptor that calculates the number of hydrogen bond donors (by Daylight).

proton belonging to an aromatic system
type: Class
subclass of: CHEMINF_000136
short name: isProtonInAromaticSystem
description: 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
type: Class
subclass of: CHEMINF_000136
short name: isProtonInConjugatedPiSystem
description: Descriptor returns true if the protons is directly bonded to a pi system.

Kier Hall SMARTS
type: Class
subclass of: CHEMINF_000092
doi: http://dx.doi.org/10.3390/91201004
description: Counts the number of occurrences of the E-state fragments.
short name: kierHallSmarts

molecular distance edge
type: Class
subclass of: CHEMINF_000092
doi: http://dx.doi.org/10.1021/ci970109z
description: Evaluate molecular distance edge descriptors for C, N and O.
short name: mde

moments of inertia
type: Class
subclass of: CHEMINF_000093
description: Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration.
short name: momentOfInertia

partial total charge (MMFF94)
type: Class
subclass of: CHEMINF_000087
short name: partialTChargeMMFF94
description: Descriptor that calculates total partial charges of an heavy atom.

period of an atom
type: Class
subclass of: CHEMINF_000136
short name: period
description: Descriptor that returns the period in the periodic table of an atom belonging to an atom container.

pi-contact of two atoms
type: Class
subclass of: CHEMINF_000136
description: 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).
short name: piContact

proton total partial charge
type: Class
subclass of: CHEMINF_000087
short name: protonPartialCharge
description: Descriptor that calculates partial charges of an heavy atom and its protons based on Gasteiger Marsili (PEOE).

RDF proton descriptor
type: Class
subclass of: CHEMINF_000092
doi: http://dx.doi.org/10.1021/ac010737m
description: Calculation of RDF proton descriptor.
short name: rdfProtonCalculatedValues
comment: This is a mixed descriptor: topological, geometrical and electronic descriptor.

TAE RECON descriptors for amino acid sequences
type: Class
subclass of: CHEMINF_000087
doi: http://dx.doi.org/10.1016/0097-8485(94)00052-G
short name: taeAminoAcid
description: 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.
comment: {@cdk.cite BREN1995} {@cdk.cite BREN1997} {@cdk.cite WHITE2003}

weighted path
type: Class
subclass of: CHEMINF_000092
short name: weightedPath
description: The weighted path (molecular ID) descriptors were described by Randic and they characterize molecular branching.

WHIM
type: Class
subclass of: CHEMINF_000092
comment: 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.
description: Holistic descriptors described by Todeschini et al.
short name: WHIM

Moreau-Broto Autocorrelation (charge) descriptors
type: Class
subclass of: CHEMINF_000092
comment: ATSc1 - ATSc5
description: The Moreau-Broto autocorrelation descriptors using partial charges.
short name: autoCorrelationCharge

Moreau-Broto autocorrelation (mass) descriptors
type: Class
subclass of: CHEMINF_000092
description: The Moreau-Broto autocorrelation descriptors using atomic weight.
short name: autoCorrelationMass
comment: ATSm1 - ATSm5

Moreau-Broto autocorrelation (polarizability) descriptors
type: Class
subclass of: CHEMINF_000092
comment: ATSp1 - ATSp5
short name: autoCorrelationPolarizability
description: The Moreau-Broto autocorrelation descriptors using polarizability.

carbon types
type: Class
subclass of: CHEMINF_000092
short name: carbonTypes
description: Characterizes the carbon connectivity in terms of hybridization
comment: C1SP1, C2SP1, C1SP2, C2SP2, C3SP2, C1SP3, C2SP3, C3SP3, C4SP3

carbon connectivity index (order 0)
type: Class
subclass of: CHEMINF_000092
short name: chi0C
description: Descriptor that calculates the carbon connectivity index (order 0).

valence connectivity index (order 0)
type: Class
subclass of: CHEMINF_000092
description: Descriptor that calculates atomic valence connectivity index (order 0).
short name: chi0v

valence carbon connectivity index (order 0)
type: Class
subclass of: CHEMINF_000092
short name: chi0vC
description: Descriptor that calculates carbon valence connectivity index (order 0).

carbon connectivity index (order 1)
type: Class
subclass of: CHEMINF_000092
short name: chi1C
description: Descriptor that calculates carbon connectivity index (order 1).

valence connectivity index (order 1)
type: Class
subclass of: CHEMINF_000092
short name: chi1v
description: Descriptor that calculates atomic valence connectivity index (order 1).

valence carbon connectivity index (order 1)
type: Class
subclass of: CHEMINF_000092
description: Descriptor that calculates carbon valence connectivity index (order 1).
short name: chi1vC

distance to atom
type: Class
subclass of: CHEMINF_000093
short name: distanceToAtom
description: Descriptor that calculates the 3D distance between two atoms.

effective polarizability
type: Class
subclass of: CHEMINF_000087
comment: EffectiveAtomPolarizabilityDescriptor, effAtomPol
short name: effectivePolarizability
description: Descriptor that calculates the effective polarizability of a given heavy atom.

hybridization ratio
type: Class
subclass of: CHEMINF_000092
description: Characterizes molecular complexity in terms of carbon hybridization states.
comment: 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.
short name: hybratio

Kier and Hall kappa molecular shape indices
type: Class
subclass of: CHEMINF_000092
description: Descriptor that calculates Kier and Hall kappa molecular shape indices.
short name: kierValues
comment: 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
type: Class
subclass of: CHEMINF_000087
doi: http://dx.doi.org/10.1002/ange.19850970818
description: Descriptor that calculates pi partial charges in pi-bonded systems of an heavy atom based on based on Gasteiger H.Saller (PEPE).
short name: partialPiCharge
comment: Other short_name: pepe.

partial sigma charge
type: Class
subclass of: CHEMINF_000087
doi: http://dx.doi.org/10.1016/0040-4020(80)80168-2
short name: partialSigmaCharge
description: Descriptor that calculates sigma partial charges in sigma-bonded systems (PEOE) of an heavy atom based on Gasteiger Marsili.

pi electronegativity
type: Class
subclass of: CHEMINF_000087
description: Descriptor that returns the pi electronegativity for a given atom.
short name: piElectronegativity
comment: 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
type: Class
subclass of: chemical database identifier

MolMeDB identifier
type: Class
subclass of: chemical database identifier

PDB ligand identifier
type: Class
subclass of: chemical database identifier

PDB structure identifier
type: Class
subclass of: chemical database identifier
short name: PDB identifier

CHEMINF_000064
comment: NOTE: QSAR descriptors are often just called 'chemical descriptor' or 'molecular descriptor' in the cheminformatics community.
has alternative id: BODO:Descriptor

CHEMINF_000191
IAO_0000118: ionization energy
IAO_0000118: ionization enthalpy
IAO_0000115: 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.
IAO_0000118: ionization potential

CHEMINF_000189
IAO_0000115: A descriptor characterizing the ratio of the length to the breadth of a given entity.

CHEMINF_000241
IAO_0000118: enthalpy of formation
IAO_0000118: heat of formation