(define-ontology reagent-antibody-domain (:base "http://www.w3.org/2001/sw/hcls/ontologies/reagent.owl") (class !Database "Databases (not necessarily relational) that are collections of entries that describe things" :partial) (class !DatabaseEntry "Entries in databases. Close to a foaf:Document, but I don't want to commit because I'm not sure of their exact intention for the term" :partial) (class !AntibodyReagentDatabase "A database that describes antibody reagents" :partial !Database) (class !PhysicalEntity "Probably #$SpatialThing-Localized" :partial) (class !Reagent "A substance used in an assay. Mass versus count noun." :partial !PhysicalEntity) (class !AntibodyReagent "A reagent composed of antibodies. The antibodies can be monoclonal(all of the same type), or polyclonal(inhomogeneous). This term is intended to refer to e.g. bottles of reagant that can get purchased/shipped, decanted and used in some experiment." :partial !Reagent) (class !Antibody "An immune system protein which binds to some antigen" :partial !Protein) (class !Protein "A polymer composed of amino acids and chemical modifications of those, produced by cells, initially constructed based on a gene template" :partial !PhysicalEntity) (class !Gene "A Dna sequence which forms a template for producing gene products such as proteins." :partial !PhysicalEntity) (class !GeneProduct "Something that is produced by a cell, based on the pattern of amino acids in a gene" :partial !PhysicalEntity) (class !Protein :partial !GeneProduct) (class !LivingThing "Something that is alive. A carbon based life form - life as we know it" :partial !PhysicalEntity) (class !LivingThingDatabase "A database that describes living things" :partial !Database) (individual !WikiPedia "The wikipedia, at http://www.wikipedia.com, which, among other things, has many pages that describe living things" (type !LivingThingDatabase) ) ;; antibody clonality (value-partition '(!AntibodyClonality !PolyclonalAntibody !MonoclonalAntibody)) (object-property !hasClonality "Describing whether an antibody reagent is monoclonal, i.e. all the same, derived from a single clone, or polyclonal, derived from multiple clones" :functional (domain !AntibodyReagent) (range !AntibodyClonality)) (object-property !definedByDatabaseEntry "If the database uniquely identifies the thing" :inverse-functional) (object-property !describedInDatabase "relating an object to a database it is part of") (object-property !describedByDatabaseEntry "If the database entry describes, but doesn't uniquely identify the thing" ) (object-property !describedByDatabaseEntry "Relating a biological entity to a database that describes it" (inverse-of !reagent:describesBiologicalEntity) ) (object-property !canBeAcquiredFrom "where the reagent can be acquired from, usually a reagent vendor") ;; isotype (value-partition '(!Antibody (!IgG !IgG1 (!IgG2 !IgG2a !IgG2b !IgG2c) !IgG3) !IgM !IgY)) (class !Antibody :complete (restriction !describedByDatabaseEntry (has-value !wikipedia:Antibody))) (class !ImmunoglobulinHeavyChain :partial !PhysicalEntity) (object-property !hasAntibodyHeavyChain "Antibodies can be classified by the type of their heavy chain." (domain !Antibody) (range !ImmunoglobulinHeavyChain )) (value-partition '(!ImmunoglobulinHeavyChain !KappaChain !LambaChain)) (class !ImmunoAssaySample "cells or tissues" :partial !PhysicalEntity) (value-partition '(!ImmunoAssaySample !CellSmearSample !CellsSample !VibratomeSectionsSample !ParaffinSectionsSample !FrozenSectionsSample)) (object-property !reactiveInOrganism (range !LivingThing)) (individual !SNOMED (type !Database)) (class !SNOMEDTerm :partial !DatabaseEntry) (individual ! (annotation !rdfs:label "Alzheimer's disease") (type !SNOMEDTerm)) (object-property !associatedWithDiseaseTerm "Used to associate something with a disease term, probably from SNOMED") ) (defun import-foaf () ; (ontology-annotation !owl:imports !) (list (class !foaf:Document :partial) (class !foaf:Organization :partial) (class !foaf:Person :partial) (object-property !foaf:homepage) (object-property !foaf:mbox) (object-property !foaf:page) (object-property !foaf:member) (datatype-property !foaf:name))) (define-ontology alzheimer-forum-organization (:base "http://www.alzforum.org/res/com/ant") (import-foaf) ; (individual ! (type !foaf:Document)) ; (individual ! (type !foaf:Document)) ; (individual !) (individual !alz:AlzheimerResearchForum (type !foaf:Organization) (value !foaf:name "Alzheimer Research Forum") (value !foaf:mbox !) (value !foaf:homepage !) (value !foaf:member !alz:JuneKinoshita) (value !foaf:member !alz:GabrielleStrobel) (value !foaf:member !alz:TomFagan) (value !foaf:member !alz:HakonHeimer) (value !foaf:member !alz:ElizabethWu) (value !foaf:member !alz:DonHatfield) (value !foaf:member !alz:NicoStanculescu) (value !foaf:member !alz:SandyKirley) (value !foaf:member !alz:PaulaNoyes) (value !foaf:member !alz:ColinKnep) (value !foaf:member !alz:ElaineAlibrandi) ) (individual !alz:JuneKinoshita (type !foaf:Person) (value !foaf:name "June Kinoshita") (value !foaf:page !)) (individual !alz:GabrielleStrobel (type !foaf:Person) (value !foaf:name "Gabrielle Strobel") (value !foaf:page !)) (individual !alz:TomFagan (type !foaf:Person) (value !foaf:name "Tom Fagan") (value !foaf:page !)) (individual !alz:HakonHeimer (type !foaf:Person) (value !foaf:name "Hakon Heimer") (value !foaf:page !)) (individual !alz:ElizabethWu (type !foaf:Person) (value !foaf:name "Elizabeth Wu") (value !foaf:page !)) (individual !alz:DonHatfield (type !foaf:Person) (value !foaf:name "Don Hatfield") (value !foaf:page !)) (individual !alz:NicoStanculescu (type !foaf:Person) (value !foaf:name "Nico Stanculescu") (value !foaf:page !)) (individual !alz:SandyKirley (type !foaf:Person) (value !foaf:name "Sandy Kirley") (value !foaf:page !)) (individual !alz:PaulaNoyes (type !foaf:Person) (value !foaf:name "Paula Noyes") (value !foaf:page !)) (individual !alz:ColinKnep (type !foaf:Person) (value !foaf:name "Colin Knep") (value !foaf:page !)) (individual !alz:ElaineAlibrandi (type !foaf:Person) (value !foaf:name "Elaine Alibrandi") (value !foaf:page !)) ) (define-ontology alzheimer-antibody-compendium (:base "http://www.alzforum.org/res/com/ant") (import-foaf) (annotation-property !alz:hasAntibodyId) (annotation-property !alz:hasAntigenClass) ;; database fields (annotation-property !hasEpitopeDescription) (annotation-property !hasSpecificityDescription) (annotation-property !hasHostDescription) (annotation-property !hasReactivityDescription) (annotation-property !hasCompanyDescription) (annotation-property !dcterms:issued) (annotation-property !dcterms:provenance) (annotation-property !dcterms:rightsHolder) (annotation-property !dcterms:accessRights) (annotation-property !dcterms:license) (annotation-property !dcterms:temporal) (annotation-property !dc:coverage) (annotation-property !dc:source) (Object-Property !reagent:associatedWithDiseaseTerm) (individual !alz:AntibodyCompendium (annotation !rdfs:label "The Alzheimer Research Foundation's Antibody Compendium") (annotation !dcterms:issued "2006-04-16") (annotation !dcterms:provenance "Translated to RDF by Alan Ruttenberg and AJ Chen from database dump supplied from the Alzheimer Research Forum") (annotation !dcterms:rightsHolder !alz:AlzheimerResearchForum) (annotation !dcterms:license !) (annotation !dcterms:accessRights !) (annotation !dcterms:accessRights !) (annotation !dcterms:accessRights !) (annotation !dcterms:temporal "Content valid as of 2006-04-16. Source database continues to be updated and so may differ from this version.") (annotation !dc:source !) (annotation !dc:source !) (annotation !dc:coverage "A selection of approximately 10% of the full database, for evaluation purposes") (type !reagent:AntibodyReagentDatabase) (value !reagent:associatedWithDiseaseTerm !) ) (class !AntibodyCompendiumDatabaseEntry :partial !reagent:DatabaseEntry) ) (define-ontology reagent-vendors (:base "http://www.w3.org/2001/sw/hcls/ontologies/reagent.owl") (import-foaf) (individual ! (type !foaf:Organization) (value !foaf:name "Accurate Chemical and Scientific Corporation") (value !foaf:mbox !) (value !foaf:mbox !) (value !foaf:mbox !) (value !foaf:homepage !)) (individual ! (type !foaf:Organization) (value !foaf:name "BioMOL") (value !foaf:homepage !)) (individual ! (type !foaf:Organization) (value !foaf:name "Panomics") (value !foaf:homepage !)) (individual ! (type !foaf:Organization) (value !foaf:name "R&D Systems") (value !foaf:homepage !)) (individual ! (type !foaf:Organization) (value !foaf:name "Invitrogen") (value !foaf:homepage !)) (individual ! (type !foaf:Organization) (value !foaf:name "Santa Cruz") (value !foaf:homepage !))) (define-ontology alzforum-database (:base "http://www.w3.org/2001/sw/hcls/ontologies/reagent.owl" :includes (reagent-antibody-domain reagent-vendors alzheimer-antibody-compendium alzheimer-forum-organization )) (individual !alz:antibody-compendium-entry-383 (annotation !alz:hasAntibodyId "383") (annotation !hasHostDescription "monoclonal (ascites)") (annotation !hasReactivityDescription "human (not-mouse)") (annotation !alz:hasAntigenClass "Bcl") (type !alz:AntibodyCompendiumDatabaseEntry) (value !associatedWithDiseaseTerm !) (value !describedInDatabase !alz:AntibodyCompendium) (value !canBeAcquiredFrom !)) (class !alz:antibody-383 :partial (restriction !describedByDatabaseEntry (has-value !alz:antibody-compendium-entry-383)) ) (object-property !geneProduct (inverse-of !geneProductOf)); (domain !Gene) (range !GeneProduct)) ; (object-property !geneProductOf (domain !GeneProduct) (range !Gene)) (object-property !proteinGeneProduct (super !geneProduct) (range !Protein)) (object-property !targetsProtein (range !Protein)) (class !alz:Human :partial !LivingThing) (class !foaf:Person :partial !alz:Human) (class !alz:Human :complete (intersection-of !LivingThing (restriction !describedByDatabaseEntry (has-value !)))) (class !alz:antibody-383 :partial (intersection-of !IgG1 (classprops !hasClonality !MonoclonalAntibody !hasAntibodyHeavyChain !KappaChain !targetsProtein !alz:antibody-383 !reactiveInOrganism !alz:Human ))) (class !Protein-bcl2-383 :complete (intersection-of !Protein (classprops !geneProductOf !Gene-Bcl2-383))) (class !Gene-Bcl2-383 :partial !Gene) (class !Gene-Bcl2-383 :complete (restriction !definedByDatabaseEntry (has-value !entrezgene:596))) (class !Gene-Bcl2-383 :complete (restriction !proteinGeneProduct (all-values-from (union-of (restriction !describedByDatabaseEntry (has-value !refseqp:NP_000648)) (restriction !describedByDatabaseEntry (has-value !refseqp:NP_000624)))) )))