@@ -4,11 +4,10 @@ <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" > <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" > <!ENTITY owl "http://www.w3.org/2002/07/owl#" > - ]> -<rdf:RDF - xmlns="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#" + <!ENTITY me "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#" > +]> +<rdf:RDF xmlns="&me;" xml:base="&me;" xmlns:owl="&owl;" - xml:base="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#" xmlns:rdf="&rdf;" xmlns:rdfs="&rdfs;" xmlns:bibtex="http://bibtexml.sf.net/" @@ -22,38 +21,47 @@ <dc:date>$Date$</dc:date> <cvs:last-changed-by>$Author$</cvs:last-changed-by> <cvs:revision>$Revision$</cvs:revision> - <rdfs:comment rdf:parseType="Literal"> - Add some comment here. - </rdfs:comment> </owl:Ontology> <!-- classes and properties --> - <owl:Class rdf:ID="Category"/> + <owl:Class rdf:ID="Category"> + <rdfs:label>Category</rdfs:label> + </owl:Class> - <owl:Class rdf:ID="Algorithm"/> + <owl:Class rdf:ID="Algorithm"> + <rdfs:label>Algorithm</rdfs:label> + </owl:Class> <owl:Class rdf:ID="Descriptor"> + <rdfs:label>Descriptor</rdfs:label> <owl:subClassOf rdf:resource="#Algorithm"/> <rdfs:comment> - A descriptor is an algorithm that operates on a chemical + A feature (descriptor) is an algorithm that operates on a chemical entity (commonly atoms and molecules) - and returns a numerical (descriptor) value which described + and returns a numerical or nominal (descriptor) value which described certain information on that entity. </rdfs:comment> </owl:Class> <owl:Class rdf:ID="Reference"/> - <owl:Class rdf:ID="Contributor"/> +<owl:Class rdf:ID="Contributor"> + <rdfs:label>Contributor</rdfs:label> +</owl:Class> - <owl:Class rdf:ID="DataFeature"/> +<owl:Class rdf:ID="DataFeature"> + <rdfs:label>Data Feature</rdfs:label> +</owl:Class> - <owl:Class rdf:ID="DataRepresentation"> - <owl:subClassOf rdf:resource="#DataFeature"/> - </owl:Class> +<owl:Class rdf:ID="DataRepresentation"> + <rdfs:label>Data Representation</rdfs:label> + <owl:subClassOf rdf:resource="&me;DataFeature"/> +</owl:Class> - <owl:Class rdf:ID="Implementation"/> +<owl:Class rdf:ID="Implementation"> + <rdfs:label>Implementation</rdfs:label> +</owl:Class> <owl:Class rdf:ID="DescriptorValue"> <rdfs:label>Descriptor Value</rdfs:label> @@ -133,6 +141,10 @@ <!-- the facts: Contributors --> + <Contributor rdf:ID="jkw"> + <rdfs:label>Joerg Kurt Wegner</rdfs:label> + </Contributor> + <Contributor rdf:ID="elw"> <rdfs:label>Egon Willighagen</rdfs:label> </Contributor> @@ -1092,14 +1104,6 @@ <definition rdf:parseType='Literal'> Descriptor that calculates the number of hydrogen bond acceptors. </definition> - <description rdf:parseType='Literal'> - As defined by Daylight website, - <bibtex:cite ref="DAY01"/> - , a H-bond acceptor is a heteroatom with no positive charge, note that negatively - charged oxygen or sulphur are included. Excluded are halogens, including F, - heteroaromatic oxygen, sulphur and pyrrole N. Higher oxidation levels of N,P,S are excluded. - Note P(III) is currently included. Zeneca's work would imply that (O=S=O) shoud also be excluded. - </description> <isClassifiedAs rdf:resource="#electronicDescriptor"/> <isClassifiedAs rdf:resource="#molecularDescriptor"/> </Descriptor> @@ -1115,16 +1119,84 @@ <definition rdf:parseType='Literal'> Descriptor that calculates the number of hydrogen bond donors. </definition> - <description rdf:parseType='Literal'> - As defined by Daylight website, - <bibtex:cite ref="DAY01"/> - , a H-bond acceptor - must have an N-H bond, an O-H bond, or a F-H bond - </description> <isClassifiedAs rdf:resource="#electronicDescriptor"/> <isClassifiedAs rdf:resource="#molecularDescriptor"/> </Descriptor> +<Descriptor rdf:ID="hBondacceptorsDaylight"> + <rdfs:label>Hydrogen Bond Acceptors (Daylight)</rdfs:label> + <dc:contributor rdf:resource="mf"/> + <dc:contributor rdf:resource="elw"/> + <dc:date>2004-11-26</dc:date> + <definition> + Descriptor that calculates the number of hydrogen bond acceptors. + </definition> + <description rdf:parseType='Literal'> + As defined by Daylight website, <bibtex:cite ref="DAY01"/>, a H-bond acceptor is a heteroatom with no positive charge, note that negatively + charged oxygen or sulphur are included. Excluded are halogens, including F, + heteroaromatic oxygen, sulphur and pyrrole N. Higher oxidation levels of N,P,S are excluded. + Note P(III) is currently included. Zeneca's work would imply that (O=S=O) shoud also be excluded. + </description> + <isClassifiedAs rdf:resource="electronicDescriptor"/> + <isClassifiedAs rdf:resource="molecularDescriptor"/> +</Descriptor> + +<Descriptor rdf:ID="hBondDonorsDaylight"><rdfs:label>Hydrogen Bond Donors (Daylight)</rdfs:label> + <dc:contributor rdf:resource="mf"/> + <dc:date>2004-11-26</dc:date> + <definition> + Descriptor that calculates the number of hydrogen bond donors. + </definition> + <description rdf:parseType='Literal'> + As defined by Daylight website, <bibtex:cite ref="DAY01"/>, a H-bond acceptor + must have an N-H bond, an O-H bond, or a F-H bond + </description> + <isClassifiedAs rdf:resource="electronicDescriptor"/> + <isClassifiedAs rdf:resource="molecularDescriptor"/> +</Descriptor> + +<Descriptor rdf:ID="hBondAcceptorsBoehmKlebe"><rdfs:label>Acceptor Field Atoms (Boehm,Klebe)</rdfs:label> + <dc:contributor rdf:resource="jkw"/> + <dc:date>2006-09-08</dc:date> + <definition> + Counts the number of acceptor field atoms for a carbonyl oxygen probe. + </definition> + <description rdf:parseType='Literal'> + Force field based definition of hydrogen bond acceptors <bibtex:cite ref="BK02"/> + This rule covers nitril, carbonyl, ether, and amin nitrogens. + </description> + <isClassifiedAs rdf:resource="electronicDescriptor"/> + <isClassifiedAs rdf:resource="molecularDescriptor"/> +</Descriptor> + +<Descriptor rdf:ID="hBondDonorsBoehmKlebe"><rdfs:label>Donor Field Atoms (Boehm,Klebe)</rdfs:label> + <dc:contributor rdf:resource="jkw"/> + <dc:date>2006-09-08</dc:date> + <definition> + Counts the number of donor field atoms for an amino hydrogen probe. + </definition> + <description rdf:parseType='Literal'> + Force field based definition of hydrogen bond donors <bibtex:cite ref="BK02"/>. + This rule covers amino groups, chloro, bromo and iodo atoms <bibtex:cite ref="PL96"/>. + </description> + <isClassifiedAs rdf:resource="electronicDescriptor"/> + <isClassifiedAs rdf:resource="molecularDescriptor"/> +</Descriptor> + +<Descriptor rdf:ID="hBondAcceptorsDonorsBoehmKlebe"><rdfs:label>Acceptors or Donors Field Atoms (Boehm,Klebe)</rdfs:label> + <dc:contributor rdf:resource="jkw"/> + <dc:date>2006-09-08</dc:date> + <definition> + Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe. + </definition> + <description rdf:parseType='Literal'> + Force field based definition of hydrogen bond acceptors or donors <bibtex:cite ref="BK02"/>. + This rule covers amino and hydroxy groups. + </description> + <isClassifiedAs rdf:resource="electronicDescriptor"/> + <isClassifiedAs rdf:resource="molecularDescriptor"/> +</Descriptor> + <Descriptor rdf:ID="isProtonInAromaticSystem"> <rdfs:label>Proton belonging to an aromatic system</rdfs:label> <annotation> @@ -2470,6 +2542,19 @@ </bibtex:entry> </Reference> + <Reference rdf:ID="BK02"> + <bibtex:entry> + <bibtex:article> + <bibtex:author>Böhm, M. and Klebe, G.</bibtex:author> + <bibtex:title>Development of New Hydrogen-Bond Descriptors and Their {A}pplication to Comparative Molecular Field Analyses</bibtex:title> + <bibtex:journal>J. Med. Chem.</bibtex:journal> + <bibtex:year>2002</bibtex:year> + <bibtex:volume>45</bibtex:volume> + <bibtex:pages>1585-1597</bibtex:pages> + </bibtex:article> + </bibtex:entry> + </Reference> + <Reference rdf:ID="CHER2003"> <bibtex:entry> <bibtex:article> @@ -2529,6 +2614,19 @@ </bibtex:entry> </Reference> + <Reference rdf:ID="GWB98"> + <bibtex:entry> + <bibtex:article> + <bibtex:author>Gillet, J. and Willett, P. and Bradshaw, J.</bibtex:author> + <bibtex:title>Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms</bibtex:title> + <bibtex:journal>J. Chem. Inf. Comput. Sci.</bibtex:journal> + <bibtex:year>1998</bibtex:year> + <bibtex:volume>38</bibtex:volume> + <bibtex:pages>165-179</bibtex:pages> + </bibtex:article> + </bibtex:entry> + </Reference> + <Reference rdf:ID="KAT96"> <bibtex:entry> <bibtex:article> @@ -2622,7 +2720,19 @@ <bibtex:pages>331-337</bibtex:pages> </bibtex:article> </bibtex:entry> + </Reference> + <Reference rdf:ID="PL96"> + <bibtex:entry> + <bibtex:article> + <bibtex:author>Patani, G. A. and LaVoie, E. J.</bibtex:author> + <bibtex:title>Bioisosterism: A Rational Approach in Drug Design</bibtex:title> + <bibtex:journal>Chem. Rev.</bibtex:journal> + <bibtex:year>1996</bibtex:year> + <bibtex:volume>96</bibtex:volume> + <bibtex:pages>3147-3176</bibtex:pages> + </bibtex:article> + </bibtex:entry> </Reference> <Reference rdf:ID="RAN84"> @@ -2657,6 +2767,17 @@ </bibtex:entry> </Reference> + <Reference rdf:ID="TC00"> + <bibtex:entry> + <bibtex:article> + <bibtex:author>Todeschini, R. and Consonni, V.</bibtex:author> + <bibtex:title>Handbook of Molecular Descriptors</bibtex:title> + <bibtex:year>2000</bibtex:year> + <bibtex:isbn>3-52-29913-0</bibtex:isbn> + </bibtex:article> + </bibtex:entry> + </Reference> + <Reference rdf:ID="TOD98"> <bibtex:entry> <bibtex:article> src/main/org/openscience/cdk/dict/data/descriptor-algorithms.owl 46893ed070c10ae9abebc48cd5477c0517ed2e9f Egon Willighagen egonw@users.sourceforge.net http://github.com/egonw/cdk/commit/a91062b45475f0995b824cb5f7046197a5972098 a91062b45475f0995b824cb5f7046197a5972098 2009-11-01T07:10:14-08:00 2009-07-17T15:11:42-07:00 Synchronized with the Blue Obelisk version Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> d84bd0e1fad57990d00f3eda781eb2d52acf9cba Rajarshi Guha rajarshi.guha@gmail.com