{"action":"created","issue":{"url":"https://api.github.com/repos/information-artifact-ontology/IAO/issues/103","labels_url":"https://api.github.com/repos/information-artifact-ontology/IAO/issues/103/labels{/name}","comments_url":"https://api.github.com/repos/information-artifact-ontology/IAO/issues/103/comments","events_url":"https://api.github.com/repos/information-artifact-ontology/IAO/issues/103/events","html_url":"https://github.com/information-artifact-ontology/IAO/issues/103","id":98475484,"number":103,"title":"synonym","user":{"login":"zhengj2007","id":6249284,"avatar_url":"https://avatars.githubusercontent.com/u/6249284?v=3","gravatar_id":"","url":"https://api.github.com/users/zhengj2007","html_url":"https://github.com/zhengj2007","followers_url":"https://api.github.com/users/zhengj2007/followers","following_url":"https://api.github.com/users/zhengj2007/following{/other_user}","gists_url":"https://api.github.com/users/zhengj2007/gists{/gist_id}","starred_url":"https://api.github.com/users/zhengj2007/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zhengj2007/subscriptions","organizations_url":"https://api.github.com/users/zhengj2007/orgs","repos_url":"https://api.github.com/users/zhengj2007/repos","events_url":"https://api.github.com/users/zhengj2007/events{/privacy}","received_events_url":"https://api.github.com/users/zhengj2007/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/information-artifact-ontology/IAO/labels/imported","name":"imported","color":"FFFFFF"},{"url":"https://api.github.com/repos/information-artifact-ontology/IAO/labels/Priority-Medium","name":"Priority-Medium","color":"FFFFFF"},{"url":"https://api.github.com/repos/information-artifact-ontology/IAO/labels/Type-Term","name":"Type-Term","color":"FFFFFF"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-07-31T21:39:25Z","updated_at":"2015-07-31T21:39:46Z","closed_at":null,"body":"_From [dosu...@gmail.com](https://code.google.com/u/102674886352087815907/) on March 10, 2011 09:53:44_\n\n*label for the new term*\r\n\r\nsynonym\r\n\r\n*Background*\r\n\r\nThis is intended as an IAO mapping for the OBO tag synonym. \r\n\r\nThis tag is used to relate ontology terms to the language that people use.  But that language is not always precise. Words do not come with necessary and sufficient conditions to specify their referents.  In regular language, and at least some scientific language, there is no way to define crisp boundaries for the referent of a word that will satisfy most users conception of what that word refers to. \r\n\r\nEven within a single scientific community there are often subtle distinctions of usage.   For a term used in anatomy, biologists often differ in how they define spatial and or temporal boundaries for the referents of a term. Or they might differ slightly in what subclasses they consider should be subsumed by a class.  Or they may use variants of a term to refer to the same thing, or some completely different term for identically or similarly defined structures . We can't possibly add terms for all such cases and deal with the resulting overlapping partonomies or fantastically detailed classifications. Such an ontology would be unmaintainable and probably unusable.\r\n\r\nSo, for a whole set of closely related terms we choose one definition and and one term and add the rest as synonyms.  That way, users can find candidate terms by searching with a term that is familiar to them.  It may be useful to further classify (scope) synonyms as having spatial, temporal boundaries or class referents that are broader, narrower, the same as or just slightly different from the referents of the ontology term.  But note that only where we can link to a particular usage can we be precise about this (in reference X Michael Ashburner uses term Y as an exact synonym of term Z).  The rest of the time, scoping synonyms in this way can only be a matter of judgment about usage by the community of users.  Given that, any definitions using quantifiers will be useless. Instead, we need qualitative terms like 'generally' or 'largely'.\r\n\r\nFinally, a note on definitions\r\n\r\nDefining these synonyms as ontology terms is far from trivial because it implicitly requires some stance on what words in regular language actually refer to. This is not exactly an uncontroversial subject.  I have neither the time nor inclination to get involved in a long debate on this matter before we can add this term to the IAO\r\n\r\n*Textual definition*\r\n\r\ndef: \"Information artifact that links an ontology term to a term in language that, within some specified discipline or publication, has referents that largely or completely correspond to the referents of the ontology term.\" \r\ncomment: \"Publication can be specified directly via a database cross reference, domain Please add an example of usage for that term Please see several 10s of thousands off instances of use in OBO ontologies.\n\n_Original issue: http://code.google.com/p/information-artifact-ontology/issues/detail?id=103_"},"comment":{"url":"https://api.github.com/repos/information-artifact-ontology/IAO/issues/comments/126818017","html_url":"https://github.com/information-artifact-ontology/IAO/issues/103#issuecomment-126818017","issue_url":"https://api.github.com/repos/information-artifact-ontology/IAO/issues/103","id":126818017,"user":{"login":"zhengj2007","id":6249284,"avatar_url":"https://avatars.githubusercontent.com/u/6249284?v=3","gravatar_id":"","url":"https://api.github.com/users/zhengj2007","html_url":"https://github.com/zhengj2007","followers_url":"https://api.github.com/users/zhengj2007/followers","following_url":"https://api.github.com/users/zhengj2007/following{/other_user}","gists_url":"https://api.github.com/users/zhengj2007/gists{/gist_id}","starred_url":"https://api.github.com/users/zhengj2007/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zhengj2007/subscriptions","organizations_url":"https://api.github.com/users/zhengj2007/orgs","repos_url":"https://api.github.com/users/zhengj2007/repos","events_url":"https://api.github.com/users/zhengj2007/events{/privacy}","received_events_url":"https://api.github.com/users/zhengj2007/received_events","type":"User","site_admin":false},"created_at":"2015-07-31T21:39:46Z","updated_at":"2015-07-31T21:39:46Z","body":"_From [dosu...@gmail.com](https://code.google.com/u/102674886352087815907/) on May 11, 2011 02:29:35_\n\nI’d argue that these annotation properties have two possible functions:\r\na.\tTo provide a bridge to language – in all its messiness. This is essential for the ontology to be easily searchable.\r\nb.\tTo provide alternative labels for classes/properties – suitable as an aid to display / querying in specific contexts.\r\n\r\nI think that ‘synonym’ works well for case ‘a’, and that dictionary definitions of synonym (see below) are consistent with the use of scoping (see clauses ‘or very similar to’ or ‘means exactly or nearly the same’).  Based on dictionary definitions / connotations for the word ‘term’, ‘alternative term’ might be better label for case b.  But note that some cases may have both functions.  So, I think the best way to deal with this is with this is to use annotate ‘synonym’ with some standard annotation property indicating suitability for use as an alternative term.\r\n\r\n*Dictionary definitions:*\r\n*synonym (wiktionary)*: A word or phrase with a meaning that is the same as or very similar to, another word or phrase\r\n*synonym (OED)*: 1. A word or phrase that means exactly or nearly the same as another in the same language (e.g. shut and close). 2. A word denoting the same thing as another but suitable for a different context (e.g. serpent for snake). 3. A word equivalent to another in some but not all senses (e.g. ship and vessel). \r\n*term (Wiktionary)*: A word or phrase, especially one from a specialized area of knowledge.\r\n*term (OED)*: A word used to express a definite concept, esp, in a particular branch of study etc. (a technical term). \r\n*terminology (Wiktionary)*: A system of specialized terms.\r\n*terminology (OED)*: 1. The system of terms used in a particular subject. 2. The science of the proper use of terms."}}