]> 2009/04/07 OpenCyc Knowledge Base Copyright© 2001-2009 Cycorp, Inc., http://www.cyc.com/, Austin, TX, USA This file contains an OWL representation of information contained in the OpenCyc Knowledge Base. The content of this OWL file is licensed under the Creative Commons Attribution 3.0 license whose text can be found at http://creativecommons.org/licenses/by/3.0/legalcode. The content of this OWL file, including the OpenCyc content it represents, constitutes the "Work" referred to in the Creative Commons license. The terms of this license equally apply to, without limitation, renamings and other logically equivalent reformulations of the content of this OWL file (or portions thereof) in any natural or formal language, as well as to derivations of this content or inclusion of it in other ontologies. Mappings between OpenCyc terms and Wikipedia article names provided by Olena Medelyan and Catherine Legg, University of Waikato, NZ under a Creative Commons Attribution 3.0 license. externalID A unique, language-neutral, variable-sized identifier for a concept that can be used to refer unambiguously to that concept across OWL exports or across Cyc inference engines. label A natural-language representation for a concept that is both human readable and readable by the Cyc inference engine. These terms are not guaranteed to refer to the same concept across time but are guaranteed to be consistent within a particular OWL export. Use 'cycAnnot:externalID' for unambiguously referring to a concept across OWL exports or across Cyc inference engines. protein molecule ProteinMolecule The collection of molecules of proteins. Instances are defined chemically as polymers made up of amino acids. Compare with <a href="http://sw.opencyc.org/concept/Mx4rvVjM3pwpEbGdrcN5Y29ycA" class="cyc_term">ProteinStuff</a>. molecule of protein protein molecules molecules of protein

Protein

http://en.wikipedia.org/wiki/Protein http://www.w3.org/2006/03/wn/wn20/instances/synset-protein_molecule-noun-1 protein molecule that is an internal part of some bacterium (SubcollectionOfWithRelationFromTypeFn ProteinMolecule internalParts Bacterium) A specialization of <a href="http://sw.opencyc.org/concept/Mx4rv0ARKpwpEbGdrcN5Y29ycA" class="cyc_term">ProteinMolecule</a>. Each instance of <a href="http://sw.opencyc.org/concept/Mx4rge1oQJyKEd2AAABQjYGu0g" class="cyc_term">FibrousProteinMolecule</a> is a protein molecule that is not water-soluble. Contrast this class with <a href="http://sw.opencyc.org/concept/Mx4rgAGASJyKEd2AAABQjYGu0g" class="cyc_term">GlobularProteinMolecule</a>, which is the collection of relatively water-soluble protein molecules. fibrous protein molecule FibrousProteinMolecule ReceptorMolecule receptor A subcollection of <a href="http://sw.opencyc.org/concept/Mx4rv0ARKpwpEbGdrcN5Y29ycA" class="cyc_term">ProteinMolecule</a>. Receptors reside in the plasma membrane of a cell and can bind with other molecules, called "ligands" to evoke a cellular response. The ability to so bind is a function of the chemical structures of the type of receptor and type of ligand. Ligands that have an appropriate structure to evoke a cellular response are considered agonists with respect to the class of receptors in question. Ligands that can bind without evoking a response are considered antagonists. GlobularProteinMolecule A specialization of <a href="http://sw.opencyc.org/concept/Mx4rv0ARKpwpEbGdrcN5Y29ycA" class="cyc_term">ProteinMolecule</a>. Each instance of <a href="http://sw.opencyc.org/concept/Mx4rgAGASJyKEd2AAABQjYGu0g" class="cyc_term">GlobularProteinMolecule</a> is a protein molecule that is water-soluble. Contrast this class with <a href="http://sw.opencyc.org/concept/Mx4rge1oQJyKEd2AAABQjYGu0g" class="cyc_term">FibrousProteinMolecule</a>, which is the collection of relatively non-soluble protein molecules. globular protein molecule BloodProteinMolecule A specialization of <a href="http://sw.opencyc.org/concept/Mx4rv0ARKpwpEbGdrcN5Y29ycA" class="cyc_term">ProteinMolecule</a>. Each instance of <a href="http://sw.opencyc.org/concept/Mx4rtnLyWJyIEd2AAABQjYGu0g" class="cyc_term">BloodProteinMolecule</a> is a molecule of a protein that naturally occurs in the blood of a living animal. Important specializations include immunoglobulins (see <a href="http://sw.opencyc.org/concept/Mx4rImDPUpx2Ed2AAABQjYGu0g" class="cyc_term">AntibodyMolecule</a>) and albumins (see #$AlbuminProteinMolecule). plasma protein molecule Pretty String (<a href="http://sw.opencyc.org/concept/Mx4rwLSVCpwpEbGdrcN5Y29ycA" class="cyc_term">prettyString</a> TERM STRING) means that STRING is the English word or expression (sequence of words) commonly used to refer to TERM. The predicate <a href="http://sw.opencyc.org/concept/Mx4rwLSVCpwpEbGdrcN5Y29ycA" class="cyc_term">prettyString</a> is used by the code which generates CycL to English paraphrases, but its applicability is not restricted to this use. prettyString Facets-Generic facets-Generic A <a href="http://sw.opencyc.org/concept/Mx4rvVkGXJwpEbGdrcN5Y29ycA" class="cyc_term">TaxonomicSlotForCollections</a> and a specialization (via <a href="http://sw.opencyc.org/concept/Mx4rvWHsNJwpEbGdrcN5Y29ycA" class="cyc_term">genlInverse</a>) of <a href="http://sw.opencyc.org/concept/Mx4rvhOImJwpEbGdrcN5Y29ycA" class="cyc_term">typeGenls</a> (q.v.). This is the most general of the "faceting" predicates. <code>(<a href="http://sw.opencyc.org/concept/Mx4rvjldVJwpEbGdrcN5Y29ycA" class="cyc_term">facets_Generic</a> COL COLTYPE)</code> means that <code>COLTYPE</code> corresponds to one way of dividing <code>COL</code> into subcollections. The instances of <code>COLTYPE</code> are all "the same sort" of subcollection of <code>COL</code>. For example, <a href="http://sw.opencyc.org/concept/Mx4rhz6DbnSwEdaAAACgyZzFrg" class="cyc_term">MovieTypeByGenre</a> facets <a href="http://sw.opencyc.org/concept/Mx4rv973YpwpEbGdrcN5Y29ycA" class="cyc_term">Movie_CW</a> according to movie-genre; the former's instances thus include such collections as <a href="http://sw.opencyc.org/concept/Mx4rv0pzgpwpEbGdrcN5Y29ycA" class="cyc_term">WesternMovie</a> and <a href="http://sw.opencyc.org/concept/Mx4rwFmUH5wpEbGdrcN5Y29ycA" class="cyc_term">HorrorMovie</a>. And <a href="http://sw.opencyc.org/concept/Mx4rYZUSFovbQdeY8PrkLdTqKA" class="cyc_term">FunctionTypeByRangeType</a> facets <a href="http://sw.opencyc.org/concept/Mx4rvVxAsJwpEbGdrcN5Y29ycA" class="cyc_term">Function_Denotational</a> according to the type of thing a given function returns as values; the former's instances thus include such collections as <a href="http://sw.opencyc.org/concept/Mx4rvVj62ZwpEbGdrcN5Y29ycA" class="cyc_term">IndividualDenotingFunction</a> and <a href="http://sw.opencyc.org/concept/Mx4rvViAapwpEbGdrcN5Y29ycA" class="cyc_term">CollectionDenotingFunction</a>. Note that generic faceting does not entail that the instances of <code>COLTYPE</code> are mutually disjoint. Thus, a given film might be an instance of both <a href="http://sw.opencyc.org/concept/Mx4rwCRfN5wpEbGdrcN5Y29ycA" class="cyc_term">ChildrensMovie</a> and <a href="http://sw.opencyc.org/concept/Mx4rv2VcW5wpEbGdrcN5Y29ycA" class="cyc_term">ActionMovie</a>. Note also that generic faceting does not entail that every instance of <code>COL</code> falls under some instance of <code>COLTYPE</code>. Thus, consider the universal identity function <a href="http://sw.opencyc.org/concept/Mx4rwSspMZwpEbGdrcN5Y29ycA" class="cyc_term">IdentityFn</a>. Its range of values is so broad that it does not fall under any instance of <a href="http://sw.opencyc.org/concept/Mx4rYZUSFovbQdeY8PrkLdTqKA" class="cyc_term">FunctionTypeByRangeType</a>. Specializations of <a href="http://sw.opencyc.org/concept/Mx4rvjldVJwpEbGdrcN5Y29ycA" class="cyc_term">facets_Generic</a> include <a href="http://sw.opencyc.org/concept/Mx4rv86JWpwpEbGdrcN5Y29ycA" class="cyc_term">facets_Covering</a>, <a href="http://sw.opencyc.org/concept/Mx4rvcZ1FpwpEbGdrcN5Y29ycA" class="cyc_term">facets_Strict</a>, and <a href="http://sw.opencyc.org/concept/Mx4rwA9k15wpEbGdrcN5Y29ycA" class="cyc_term">facets_Partition</a>, as well as <a href="http://sw.opencyc.org/concept/Mx4rgQmwRl2xEdif1wACs2IMlQ" class="cyc_term">facets_NearCovering</a>, <a href="http://sw.opencyc.org/concept/Mx4rRA9CIljCEdiRSAACs2IMlQ" class="cyc_term">facets_NearStrict</a>, and <a href="http://sw.opencyc.org/concept/Mx4rRA9CJFjCEdiRSAACs2IMlQ" class="cyc_term">facets_NearPartition</a>. Whenever possible, one of these more specific predicates should be used. The collection of all instances of <a href="http://sw.opencyc.org/concept/Mx4r_4bScKNtQdiVw7XtX-HN0Q" class="cyc_term">ClarifyingCollectionType</a> that are used by the #$KRAKEN application to resolve natural language ambiguities. KE clarifying collection type KEClarifyingCollectionType (ThePartition GlobularProteinMolecule FibrousProteinMolecule) either a globular protein molecule or a fibrous protein molecule molecule A subcollection of <a href="http://sw.opencyc.org/concept/Mx4rvViRapwpEbGdrcN5Y29ycA" class="cyc_term">ChemicalObject</a>. Each instance of <a href="http://sw.opencyc.org/concept/Mx4rvVjwspwpEbGdrcN5Y29ycA" class="cyc_term">Molecule</a> is a microscopic-scale object whose component atoms are all chemically bonded to each other; typically, this means that the atoms are covalently bonded. Examples: some instances of <a href="http://sw.opencyc.org/concept/Mx4rvVjwspwpEbGdrcN5Y29ycA" class="cyc_term">Molecule</a>, including molecules of oxygen (O2), ozone (O3), water (H2O), carbon monoxide (CO), carbon dioxide (CO2), etc., contain covalently bonded atoms belonging to the collection <a href="http://sw.opencyc.org/concept/Mx4rvVjIyJwpEbGdrcN5Y29ycA" class="cyc_term">Oxygen</a>. Some highly complex examples of <a href="http://sw.opencyc.org/concept/Mx4rvVjwspwpEbGdrcN5Y29ycA" class="cyc_term">Molecule</a> are those belonging to the collection <a href="http://sw.opencyc.org/concept/Mx4rvpIyn5wpEbGdrcN5Y29ycA" class="cyc_term">DNAMolecule</a>. See also <a href="http://sw.opencyc.org/concept/Mx4rwPzt4pwpEbGdrcN5Y29ycA" class="cyc_term">MoleculeFn</a>. Note: <a href="http://sw.opencyc.org/concept/Mx4rvgC2UJwpEbGdrcN5Y29ycA" class="cyc_term">Diamond</a> and other macroscopic covalent solids are excluded from belonging to <a href="http://sw.opencyc.org/concept/Mx4rvVjwspwpEbGdrcN5Y29ycA" class="cyc_term">Molecule</a> by the constraint that instances of <a href="http://sw.opencyc.org/concept/Mx4rvVjwspwpEbGdrcN5Y29ycA" class="cyc_term">Molecule</a> are microscopic. Molecule Wikipedia Article URL (<a href="http://sw.opencyc.org/concept/Mx4rNv0nbm4TTjOp7yhmnzOyqg" class="cyc_term">wikipediaArticleURL</a> THING URL) means that in <a href="http://sw.opencyc.org/concept/Mx4rtqXA6OC8QdiWC72DuLJdUw" class="cyc_term">Wikipedia_WebSite</a> THING is described by an article located at URL wikipediaArticleURL seeAlsoURI <code>(<a href="http://sw.opencyc.org/concept/Mx4riWVFR6HJSpaEaHrcWS3MSA" class="cyc_term">seeAlsoURI</a> THING URI)</code> means that a description of the resource identified by URI is likely to contain information pertinent to THING. This predicate is roughly equivalent to rdfs:seeAlso. See Also URI Partitioned Into partitionedInto (<a href="http://sw.opencyc.org/concept/Mx4rvVj1MJwpEbGdrcN5Y29ycA" class="cyc_term">partitionedInto</a> SETORCOL PART) means that the mathematical set or collection PART is a partition of the mathematical set or collection SETORCOL; that is, the elements of PART are themselves mathematical sets or collections, and every element of SETORCOL is an element of exactly one element of PART, and every element of PART is a subset of SETORCOL. In other words, PART is a set or collection of pairwise disjoint sets or collections whose union is co-extensional with SETORCOL. Typically, the <a href="http://sw.opencyc.org/concept/Mx4rk8dxOVcGEdaLwgACs0uFOQ" class="cyc_term">DisjointSetOrCollectionType</a> that plays the role of PART in an assertion about partitioning will be a set specified by enumerating its elements, using the function <a href="http://sw.opencyc.org/concept/Mx4rvcUeB5wpEbGdrcN5Y29ycA" class="cyc_term">ThePartition</a>. A specialization of <a href="http://sw.opencyc.org/concept/Mx4rvViAyZwpEbGdrcN5Y29ycA" class="cyc_term">equals</a> and a <a href="http://sw.opencyc.org/concept/Mx4rvWKHbpwpEbGdrcN5Y29ycA" class="cyc_term">CycLReformulatorConstant</a> that relates pairs of <a href="http://sw.opencyc.org/concept/Mx4rwE2kWpwpEbGdrcN5Y29ycA" class="cyc_term">CycLClosedDenotationalTerm</a>s. <a href="http://sw.opencyc.org/concept/Mx4rwTvAxJwpEbGdrcN5Y29ycA" class="cyc_term">rewriteOf</a> is, in a sense, a "directional" version of <a href="http://sw.opencyc.org/concept/Mx4rvViAyZwpEbGdrcN5Y29ycA" class="cyc_term">equals</a>. <code>(<a href="http://sw.opencyc.org/concept/Mx4rwTvAxJwpEbGdrcN5Y29ycA" class="cyc_term">rewriteOf</a> FAVORED-TERM DISFAVORED-TERM)</code> means that (1) <code>FAVORED-TERM</code> and <code>DISFAVORED-TERM</code> denote the same thing, and (2) <code>FAVORED-TERM</code> is deemed worthy of being privileged over <code>DISFAVORED-TERM</code> in the following senses: assertions made on <code>DISFAVORED-TERM</code> will be propagated to <code>FAVORED-TERM</code>, and whenever possible attempts to reason about <code>DISFAVORED-TERM</code> will be transformed into attempts to reason about <code>FAVORED-TERM</code>. The propagated assertions will differ from the original assertions only in that the propagated assertions will be the result of substituting <code>FAVORED-TERM</code> for <code>DISFAVORED-TERM</code> wherever <code>DISFAVORED-TERM</code> occurs in the original assertions. Note that substitution does not happen in the opposite direction. That is, assertions containing <code>FAVORED-TERM</code> will not propagate to <code>DISFAVORED-TERM</code>. One common use of <a href="http://sw.opencyc.org/concept/Mx4rwTvAxJwpEbGdrcN5Y29ycA" class="cyc_term">rewriteOf</a> is that in which <code>FAVORED-TERM</code> is a syntactically simpler term than <code>DISFAVORED-TERM</code>. For example, <code>FAVORED-TERM</code> may contain fewer nested terms that denote <a href="http://sw.opencyc.org/concept/Mx4rvVxAsJwpEbGdrcN5Y29ycA" class="cyc_term">Function_Denotational</a>s than does <code>DISFAVORED-TERM</code>. (<a href="http://sw.opencyc.org/concept/Mx4rwTvAxJwpEbGdrcN5Y29ycA" class="cyc_term">rewriteOf</a> <a href="http://sw.opencyc.org/concept/Mx4rvVjxdJwpEbGdrcN5Y29ycA" class="cyc_term">UnitedStatesNavy</a> (<a href="http://sw.opencyc.org/concept/Mx4rwGGrfpwpEbGdrcN5Y29ycA" class="cyc_term">NavyFn</a> <a href="http://sw.opencyc.org/concept/Mx4rvVikKpwpEbGdrcN5Y29ycA" class="cyc_term">UnitedStatesOfAmerica</a>)) is a good example of this common sort of use. Note that <a href="http://sw.opencyc.org/concept/Mx4rwTvAxJwpEbGdrcN5Y29ycA" class="cyc_term">rewriteOf</a> expresses a strictly conventional notion of "directional" equality. Pragmatic considerations, not ontology, will dictate which term is chosen to occur as the privileged (left-hand side) term in a <a href="http://sw.opencyc.org/concept/Mx4rwTvAxJwpEbGdrcN5Y29ycA" class="cyc_term">rewriteOf</a> assertion. Thus, in the example the fact that simpler terms are generally easier to use (remember, manipulate, etc.) dictates that <a href="http://sw.opencyc.org/concept/Mx4rvVjxdJwpEbGdrcN5Y29ycA" class="cyc_term">UnitedStatesNavy</a> should be a rewrite of (<a href="http://sw.opencyc.org/concept/Mx4rwGGrfpwpEbGdrcN5Y29ycA" class="cyc_term">NavyFn</a> <a href="http://sw.opencyc.org/concept/Mx4rvVikKpwpEbGdrcN5Y29ycA" class="cyc_term">UnitedStatesOfAmerica</a>), and not vice versa. Rewrite Of rewriteOf The collection of all instances of <a href="http://sw.opencyc.org/concept/Mx4rvt8DM5wpEbGdrcN5Y29ycA" class="cyc_term">MoleculeTypeByChemicalSpecies</a> whose instances are protein molecules (see <a href="http://sw.opencyc.org/concept/Mx4rv0ARKpwpEbGdrcN5Y29ycA" class="cyc_term">ProteinMolecule</a>). type of protein molecule ProteinMoleculeTypeByChemicalSpecies protein molecule The collection of molecules of proteins. Instances are defined chemically as polymers made up of amino acids. Compare with <a href="http://sw.opencyc.org/concept/Mx4rvVjM3pwpEbGdrcN5Y29ycA" class="cyc_term">ProteinStuff</a>. ProteinMolecule protein molecule The collection of all protein molecules. A type of <a href="http://sw.opencyc.org/concept/Mx4rvVjwspwpEbGdrcN5Y29ycA" class="cyc_term">Molecule</a>. (MoleculeFn ProteinStuff) A collection of collections. Each instance of <a href="http://sw.opencyc.org/concept/Mx4rvWXYgJwpEbGdrcN5Y29ycA" class="cyc_term">ExistingObjectType</a> is a specialization of <a href="http://sw.opencyc.org/concept/Mx4rvVj27ZwpEbGdrcN5Y29ycA" class="cyc_term">PartiallyTangible</a> (q.v.). Moreover, each instance of <a href="http://sw.opencyc.org/concept/Mx4rvWXYgJwpEbGdrcN5Y29ycA" class="cyc_term">ExistingObjectType</a> is a collection that is temporally stuff-like (see <a href="http://sw.opencyc.org/concept/Mx4rvVitN5wpEbGdrcN5Y29ycA" class="cyc_term">TemporalStuffType</a>) but physically-spatially object-like (see <a href="http://sw.opencyc.org/concept/Mx4rvVirnZwpEbGdrcN5Y29ycA" class="cyc_term">ObjectType</a>) -- i.e. object-like with respect to some physical-spatial part-whole predicate (e.g. some specialization of <a href="http://sw.opencyc.org/concept/Mx4r8a2smPXcQdiEoJhcx65EiQ" class="cyc_term">properPhysicalDecompositions</a>). Consider the collection <a href="http://sw.opencyc.org/concept/Mx4rwJaXepwpEbGdrcN5Y29ycA" class="cyc_term">BookCopy</a>. <a href="http://sw.opencyc.org/concept/Mx4rwJaXepwpEbGdrcN5Y29ycA" class="cyc_term">BookCopy</a> is a specialization of <a href="http://sw.opencyc.org/concept/Mx4rvVj27ZwpEbGdrcN5Y29ycA" class="cyc_term">PartiallyTangible</a>. Further, <a href="http://sw.opencyc.org/concept/Mx4rwJaXepwpEbGdrcN5Y29ycA" class="cyc_term">BookCopy</a> is temporally stuff-like: any one of the <a href="http://sw.opencyc.org/concept/Mx4rvWn4OZwpEbGdrcN5Y29ycA" class="cyc_term">timeSlices</a> of a given copy <code>COPY</code> of (say) "Moby Dick" is still a copy of "Moby Dick". (Most collections of tangible objects are temporally stuff-like in this way.) But <a href="http://sw.opencyc.org/concept/Mx4rwJaXepwpEbGdrcN5Y29ycA" class="cyc_term">BookCopy</a> is spatially object-like: if we take a scalpel and slice <code>COPY</code> into ten pieces, each piece is not a copy of "Moby Dick". So <a href="http://sw.opencyc.org/concept/Mx4rwJaXepwpEbGdrcN5Y29ycA" class="cyc_term">BookCopy</a> is an instance of <a href="http://sw.opencyc.org/concept/Mx4rvWXYgJwpEbGdrcN5Y29ycA" class="cyc_term">ExistingObjectType</a>. See also <a href="http://sw.opencyc.org/concept/Mx4rvVir35wpEbGdrcN5Y29ycA" class="cyc_term">StuffType</a> and <a href="http://sw.opencyc.org/concept/Mx4rvVny6pwpEbGdrcN5Y29ycA" class="cyc_term">ExistingStuffType</a>. ExistingObjectType type of object protein molecule The collection of molecules of proteins. Instances are defined chemically as polymers made up of amino acids. Compare with <a href="http://sw.opencyc.org/concept/Mx4rvVjM3pwpEbGdrcN5Y29ycA" class="cyc_term">ProteinStuff</a>. ProteinMolecule biopolymer BiopolymerMolecule The collection of macromolecules which are produced by and can be found within living things, such as proteins (essentially polymers of amino acids), nucleic acids (such as DNA or RNA), and polysaccharides (polymers of simple sugars). protein molecule The collection of molecules of proteins. Instances are defined chemically as polymers made up of amino acids. Compare with <a href="http://sw.opencyc.org/concept/Mx4rvVjM3pwpEbGdrcN5Y29ycA" class="cyc_term">ProteinStuff</a>. ProteinMolecule heteropolymer HeteroPolymer The collection of all #$Polymers whose instances are characterized by having more than one type of <a href="http://sw.opencyc.org/concept/Mx4rv0l_WZwpEbGdrcN5Y29ycA" class="cyc_term">Monomer</a> as <a href="http://sw.opencyc.org/concept/Mx4rvagtsZwpEbGdrcN5Y29ycA" class="cyc_term">polymericSubComponents</a>. More specifically, if HET is an instance of <a href="http://sw.opencyc.org/concept/Mx4rwPljEJwpEbGdrcN5Y29ycA" class="cyc_term">HeteroPolymer</a>, then there are least two different <a href="http://sw.opencyc.org/concept/Mx4rv0l_WZwpEbGdrcN5Y29ycA" class="cyc_term">Monomer</a>s such that both are <a href="http://sw.opencyc.org/concept/Mx4rvagtsZwpEbGdrcN5Y29ycA" class="cyc_term">polymericSubComponents</a> of HET and each is an instance of a different spec of <a href="http://sw.opencyc.org/concept/Mx4rv0l_WZwpEbGdrcN5Y29ycA" class="cyc_term">Monomer</a>. wikipediaArticleName (<a href="http://sw.opencyc.org/concept/Mx4rTv-jk9SPTXa991kk5mAvHg" class="cyc_term">wikipediaArticleName</a> THING NAME) means that in <a href="http://sw.opencyc.org/concept/Mx4rtqXA6OC8QdiWC72DuLJdUw" class="cyc_term">Wikipedia_WebSite</a> THING is described by an article with the title NAME Wikipedia Article Name peptide PeptideMolecule A collection of any group of compounds formed from two or more <a href="http://sw.opencyc.org/concept/Mx4rvVibZJwpEbGdrcN5Y29ycA" class="cyc_term">AminoAcid</a>s by the linkage of amino groups of some of the acids with carboxyl groups of others.