https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=GaryBader 2026-06-07T10:50:16Z User contributions MediaWiki 1.35.9 https://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Main_Page&diff=3827 2006-08-20T22:12:58Z

<p>GaryBader: /* Request tracker */ Fix link</p> <hr /> <div>=PATO - Phenotype and Trait Ontology=<br /> <br /> Welcome to the PATO wiki.<br /> <br /> PATO was originally devised for the purposes of post-coordinating phenotype annotations using terms from ontologies such as GO and fly anatomy combined with *attribute* and *value* terms. The scope of PATO has been widened, and it is now intended to serve as a reference ontology of biological qualities in general.<br /> <br /> =Resources=<br /> <br /> ==Ontology==<br /> <br /> Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net<br /> <br /> ==Request tracker==<br /> <br /> You can use the tracker (currently hosted on sourceforge) to request new terms or suggest modifications<br /> <br /> - http://sourceforge.net/tracker/?group_id=76834&amp;atid=595654 [PATO Request tracker]<br /> <br /> When submitting term requests, please remember to include definition according to PATO definition guidelines (below)<br /> <br /> ==Mail list==<br /> <br /> You can subscribe or browse the archives here:<br /> <br /> - https://lists.sourceforge.net/lists/listinfo/obo-phenotype [OBO-Phenotype Mail List]<br /> <br /> The mail list is for discussion of PATO and phenotype annotation in general<br /> <br /> =Content=<br /> <br /> ==Definition guidelines==<br /> <br /> Definitions will be specified in accord with [[OBO Foundry]] principles. Each term definition should refine it's parent (genus) term by providing differentiating characteristics that are both necessary and sufficient to discriminate instances of this term from siblings terms. These definitions are of the form &quot;An X is a G which D&quot;<br /> <br /> =Annotation=<br /> <br /> ==OBD==<br /> <br /> [http://www.fruitfly.org/~cjm/obd OBD] (temporary page)<br /> <br /> ==Formats==<br /> <br /> http://www.fruitfly.org/~cjm/obd/formats.html<br /> <br /> ==Chado==<br /> <br /> Chado has a module for representing phenotypic data (under revision)<br /> <br /> See the [http://www.gmod.org/chado GMOD/Chado page]<br /> <br /> =Related ontologies=<br /> <br /> PATO is intended to be used with post-coordinated annotations. There are various ontologies containing pre-coordinated phenotype terms. See for example the plant_trait ontology or the mammaliam phenotype [[MP:Main_Page]] ontology<br /> <br /> =Old Material=<br /> <br /> Primarily for internal NCBO software team reference<br /> <br /> *[[Phenotype Reading List]]<br /> <br /> <br /> [[Media:Pre-coordination.ppt]]</div>

GaryBader https://www.bioontology.org//mediawiki/index.php?title=Special:Badtitle/NS200:Main_Page&diff=3826 2006-08-20T22:12:44Z

<p>GaryBader: /* Mail list */ Fix link</p> <hr /> <div>=PATO - Phenotype and Trait Ontology=<br /> <br /> Welcome to the PATO wiki.<br /> <br /> PATO was originally devised for the purposes of post-coordinating phenotype annotations using terms from ontologies such as GO and fly anatomy combined with *attribute* and *value* terms. The scope of PATO has been widened, and it is now intended to serve as a reference ontology of biological qualities in general.<br /> <br /> =Resources=<br /> <br /> ==Ontology==<br /> <br /> Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net<br /> <br /> ==Request tracker==<br /> <br /> You can use the tracker (currently hosted on sourceforge) to request new terms or suggest modifications<br /> <br /> - http://sourceforge.net/tracker/?group_id=76834&amp;atid=595654[PATO Request tracker]<br /> <br /> When submitting term requests, please remember to include definition according to PATO definition guidelines (below)<br /> <br /> ==Mail list==<br /> <br /> You can subscribe or browse the archives here:<br /> <br /> - https://lists.sourceforge.net/lists/listinfo/obo-phenotype [OBO-Phenotype Mail List]<br /> <br /> The mail list is for discussion of PATO and phenotype annotation in general<br /> <br /> =Content=<br /> <br /> ==Definition guidelines==<br /> <br /> Definitions will be specified in accord with [[OBO Foundry]] principles. Each term definition should refine it's parent (genus) term by providing differentiating characteristics that are both necessary and sufficient to discriminate instances of this term from siblings terms. These definitions are of the form &quot;An X is a G which D&quot;<br /> <br /> =Annotation=<br /> <br /> ==OBD==<br /> <br /> [http://www.fruitfly.org/~cjm/obd OBD] (temporary page)<br /> <br /> ==Formats==<br /> <br /> http://www.fruitfly.org/~cjm/obd/formats.html<br /> <br /> ==Chado==<br /> <br /> Chado has a module for representing phenotypic data (under revision)<br /> <br /> See the [http://www.gmod.org/chado GMOD/Chado page]<br /> <br /> =Related ontologies=<br /> <br /> PATO is intended to be used with post-coordinated annotations. There are various ontologies containing pre-coordinated phenotype terms. See for example the plant_trait ontology or the mammaliam phenotype [[MP:Main_Page]] ontology<br /> <br /> =Old Material=<br /> <br /> Primarily for internal NCBO software team reference<br /> <br /> *[[Phenotype Reading List]]<br /> <br /> <br /> [[Media:Pre-coordination.ppt]]</div>

GaryBader