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search</a> <div id="mw-content-text" lang="en" dir="ltr" class="mw-content-ltr"><div class="mw-parser-output"><div id="toc" class="toc" role="navigation" aria-labelledby="mw-toc-heading"><input type="checkbox" role="button" id="toctogglecheckbox" class="toctogglecheckbox" style="display:none" /><div class="toctitle" lang="en" dir="ltr"><h2 id="mw-toc-heading">Contents</h2><span class="toctogglespan"><label class="toctogglelabel" for="toctogglecheckbox"></label></span></div> <ul> <li class="toclevel-1 tocsection-1"><a href="#About"><span class="tocnumber">1</span> <span class="toctext">About</span></a></li> <li class="toclevel-1 tocsection-2"><a href="#Meanings_of_terms_used_in_NCBO"><span class="tocnumber">2</span> <span class="toctext">Meanings of terms used in NCBO</span></a></li> <li class="toclevel-1 tocsection-3"><a href="#Definitions"><span class="tocnumber">3</span> <span class="toctext">Definitions</span></a> <ul> <li class="toclevel-2 tocsection-4"><a href="#Entity"><span class="tocnumber">3.1</span> <span class="toctext">Entity</span></a></li> <li class="toclevel-2 tocsection-5"><a href="#Domain"><span class="tocnumber">3.2</span> <span class="toctext">Domain</span></a></li> <li class="toclevel-2 tocsection-6"><a href="#Representation"><span class="tocnumber">3.3</span> <span class="toctext">Representation</span></a></li> <li class="toclevel-2 tocsection-7"><a href="#Representational_Units"><span class="tocnumber">3.4</span> <span class="toctext">Representational Units</span></a></li> <li class="toclevel-2 tocsection-8"><a href="#Ontology"><span class="tocnumber">3.5</span> <span class="toctext">Ontology</span></a> <ul> <li class="toclevel-3 tocsection-9"><a href="#Application_vs_Reference_Ontology"><span class="tocnumber">3.5.1</span> <span class="toctext">Application vs Reference Ontology</span></a></li> </ul> </li> <li class="toclevel-2 tocsection-10"><a href="#Mapping_vs._Alignment"><span class="tocnumber">3.6</span> <span class="toctext">Mapping vs. Alignment</span></a></li> <li class="toclevel-2 tocsection-11"><a href="#Universal_.28type.2C_natural_kind.29"><span class="tocnumber">3.7</span> <span class="toctext">Universal (type, natural kind)</span></a></li> <li class="toclevel-2 tocsection-12"><a href="#Particular_.28instance.29"><span class="tocnumber">3.8</span> <span class="toctext">Particular (instance)</span></a></li> <li class="toclevel-2 tocsection-13"><a href="#Aristotelian_Definition"><span class="tocnumber">3.9</span> <span class="toctext">Aristotelian Definition</span></a></li> </ul> </li> </ul> </div> <h2><span class="mw-headline" id="About">About</span></h2> <p>This glossary is to help communication within the NCBO by standardizing the terms we use internally </p><p>Many of the terms here are sourced from: <a href="/mediawiki/images/f/fc/SmithCeusters.pdf" class="internal" title="SmithCeusters.pdf">Media:SmithCeusters.pdf</a> </p> <h2><span class="mw-headline" id="Meanings_of_terms_used_in_NCBO">Meanings of terms used in NCBO</span></h2> <p><b>Levels of Reality:</b> </p><p>1 - Physical Reality </p><p>2 - Psychological Reality = our knowledge and beliefs about 1. </p><p>3 - Propositions, Theories, Texts = formalizations of those ideas and beliefs </p> <h2><span class="mw-headline" id="Definitions">Definitions</span></h2> <h3><span class="mw-headline" id="Entity">Entity</span></h3> <p>Anything which exists, including things and processes, functions and qualities, beliefs and actions, documents and software (Levels 1, 2 and 3) </p><p>Note that sometimes in software engineering the term "entity" refers solely to a the digital representation itself rather than the thing being represented. Within NCBO we use "entity" to mean anything that exists, but typically for level 1 entities. </p> <h3><span class="mw-headline" id="Domain">Domain</span></h3> <p>portion of reality that forms the subject-matter of a single science or technology or mode of study. </p> <h3><span class="mw-headline" id="Representation">Representation</span></h3> <p>An image, idea, map, picture, name or description ... of some entity or entities external to the representation. </p> <h3><span class="mw-headline" id="Representational_Units">Representational Units</span></h3> <p>Terms, icons, alphanumeric identifiers ... which refer, or are intended to refer, to entities in a representational artifact. Daniel S: Should we add 'representations of universals', 'definitions' and 'properties' to the examples of RUs above ? </p> <h3><span class="mw-headline" id="Ontology">Ontology</span></h3> <p>A representational artifact whose representational units (which may be drawn from a natural or from some formalized language) are intended to represent types in reality and those relations between these types which obtain universally (universally = for all instances) </p><p>From Reference Terminology Paper: An ONTOLOGY is a representational artifact, comprising a taxonomy as proper part, whose representational units are intended to designate some combination of universals, defined classes, and certain relations between them. </p><p>Comment: In ontologies nodes from a CV (each of which is associated with an identifier, term, definition, and an optional set of synonyms.) are linked by directed edges, thus forming a graph. This graph represents a counterpart structure on the side of entities (classes, universals) in reality, and its edges represent the relations (e.g. is-a or part-of) which hold between these entities. If a node has a parent node in the is-a hierarchy, then we say that the corresponding class is subsumed by this parent node. </p> <h4><span class="mw-headline" id="Application_vs_Reference_Ontology">Application vs Reference Ontology</span></h4> <p>There is a good summary here: </p> <pre> Reference Ontologies - Application Ontologies: Either/Or or Both/And? Christopher Menzel Texas AM University </pre> <p><a href="/mediawiki/images/d/d9/MenzelOntology.pdf" class="internal" title="MenzelOntology.pdf">Media:MenzelOntology.pdf</a> </p> <h3><span class="mw-headline" id="Mapping_vs._Alignment">Mapping vs. Alignment</span></h3> <p>Mapping = Refers to the process of creation of a relationship b/w terms in separate ontologies </p><p>Alignment = Refers to the process of creation of a near-synonymy relation b/w terms in separate ontologies </p><p><br /> </p> <h3><span id="Universal_(type,_natural_kind)"></span><span class="mw-headline" id="Universal_.28type.2C_natural_kind.29">Universal (type, natural kind)</span></h3> <p>From Reference Terminology paper: </p><p>General terms such as ‘DNA’, ‘fracture’, ‘cat’, which represent structures or characteristics in reality which are exemplified – the very same structures or characteristics; over and over again – in an open-ended collection of particulars in arbitrarily disconnected regions of space and time, e.g. as a certain DNA structure is instantiated as a transcript (RNA-structure) over and over again in cells of our body. A universal is something that is shared in common by all those particulars which are its INSTANCES. The universal itself then exists in Level 1 reality as a result of existing in its particular instances. It is overwhelmingly universals which are the entities represented in scientific texts and which are used for classifications. Comment: Universals in a taxonomy stand in an is_a relation </p> <h3><span id="Particular_(instance)"></span><span class="mw-headline" id="Particular_.28instance.29">Particular (instance)</span></h3> <p>From Reference Terminology paper: </p><p>No def, Examples: individual patients, their lesions, diseases, and bodily reactions, some of which receive PROPER NAMES. In the paper 'individuals' and 'tokens' were called synonyms also. This should be reslved more clearly I guess. </p> <h3><span class="mw-headline" id="Aristotelian_Definition">Aristotelian Definition</span></h3> <p>Also known as genus-differentia definition (but not limited to species taxonomies). </p><p><a rel="nofollow" class="external free" href="https://en.wikipedia.org/wiki/Genus-differentia_definition">http://en.wikipedia.org/wiki/Genus-differentia_definition</a> </p>    </div></div><div class="printfooter">Retrieved from "<a dir="ltr" href="https://www.bioontology.org//mediawiki/index.php?title=Glossary&oldid=10937">https://www.bioontology.org//mediawiki/index.php?title=Glossary&oldid=10937</a>"</div> <div id="catlinks" class="catlinks catlinks-allhidden" data-mw="interface"></div> </div> </div> <div id="mw-navigation"> <h2>Navigation menu</h2> <div id="mw-head">  <nav id="p-personal" class="vector-menu" aria-labelledby="p-personal-label" role="navigation" > <h3 id="p-personal-label"> <span>Personal tools</span> </h3>  <div class="body vector-menu-content">  <ul class="vector-menu-content-list"><li id="pt-login"><a href="/mediawiki/index.php?title=Special:UserLogin&returnto=Glossary" title="You are encouraged to log in; however, it is not mandatory [o]" accesskey="o">Log in</a></li></ul> </div> </nav> <div id="left-navigation">  <nav id="p-namespaces" class="vector-menu vector-menu-tabs vectorTabs" aria-labelledby="p-namespaces-label" role="navigation" > <h3 id="p-namespaces-label"> <span>Namespaces</span> </h3>  <div class="body vector-menu-content">  <ul class="vector-menu-content-list"><li id="ca-nstab-main" class="selected"><a href="/wiki/Glossary" title="View the content page [c]" accesskey="c">Page</a></li><li id="ca-talk" class="new"><a href="/mediawiki/index.php?title=Talk:Glossary&action=edit&redlink=1" rel="discussion" title="Discussion about the content page (page does not exist) [t]" accesskey="t">Discussion</a></li></ul> </div> </nav>  <nav id="p-variants" class="vector-menu-empty emptyPortlet vector-menu vector-menu-dropdown vectorMenu" aria-labelledby="p-variants-label" role="navigation" > <input type="checkbox" class="vector-menu-checkbox vectorMenuCheckbox" aria-labelledby="p-variants-label" /> <h3 id="p-variants-label"> <span>Variants</span> </h3>  <div class="body vector-menu-content">  <ul class="menu vector-menu-content-list"></ul> </div> </nav> </div> <div id="right-navigation">  <nav id="p-views" class="vector-menu vector-menu-tabs vectorTabs" aria-labelledby="p-views-label" role="navigation" > <h3 id="p-views-label"> <span>Views</span> </h3>  <div class="body vector-menu-content">  <ul class="vector-menu-content-list"><li id="ca-view" class="collapsible selected"><a href="/wiki/Glossary">Read</a></li><li id="ca-viewsource" class="collapsible"><a href="/mediawiki/index.php?title=Glossary&action=edit" title="This page is protected.
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