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<p><font size=+2><b>Plant Ontology and Controlled Vocabulary</b></font></center>

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<blockquote><font size=+1><b>Trait Ontology</b></font>
<p><font size=-1>Gramene is also a repository for rice functional mutations
and quantitative trait loci (QTL) curated from the literature. For each
mutation the genetic linkage data, phenotype, affected strains, gene sequence
and protein product and images are maintained when available. In order
to realize the full potential of this rich source of phenotypic information,
Gramene curators, in collaboration with <a href="http://www.irri.org/">IRRI</a>
(rice), <a href="http://www.cgiar.org/icis/">ICIS</a> (representing several
crops), <a href="http://www.agron.missouri.edu/index.html">MaizeDB</a>
(maize) and <a href="http://www.cimmyt.cgiar.org">CIMMYT</a> (maize and
wheat), have put intensive efforts into the development of structured controlled
vocabularies for traits, <i>viz.</i>, <b>Trait Ontology (TO)</b>. The trait
ontology (TO) is initially based on <a href="http://www.riceweb.org/ses/sesidx.htm">Standard Evaluation System for Rice (1996)</a> and provides the terms that
describe a trait as a distinguishable feature, characteristic, quality
of character, or a phenotypic feature of a developing or mature individual.&nbsp;
As it evolves, the TO will provide the basis for distributed curation of
phenotypic data associated with mutants and QTL in rice and other monocots.</font>
<p><font size=-1>The specific goal of Gramene will be to provide a trait
ontology that can be used across the grasses to facilitate phenotypic comparisons
both within and between genera and the common vocabulary will encourage
and enable interoperability between plant databases. Each assertion of
putative phenotypic homology will be supported by <a href="evidence_codes.html">evidence
codes</a>, that describes the basis for the assertion. Use of controlled
vocabularies will be increasingly important to systematically describe
the phenotypic consequences of both artificial and natural forms of genetic
variation.</font>
<p><font size=-1>Any suggestions for the addition, replacement or modification
of the TO can be made via a web <a href="http://brie2.cshl.org:8082/plant_ontology/submission/">submission
form</a>.</font>
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<p><b>Links to flat files</b>
<p><font size=-1>The flat files for the trait ontology (TO)&nbsp; and definitions
can be downloaded from the following sites and can be browsed by using
the stand-alone <a href="http://www.fruitfly.org/annot/go/editor.html">browser</a></font>
<p><font size=-1>Trait ontology terms&nbsp;&nbsp;&nbsp; <a href="cvs">CVS</a></font>
<p><font size=-1>Definitions of Trait Ontology terms&nbsp;&nbsp;&nbsp;
<a href="cvs">CVS</a></font></blockquote>
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<p><font size=-2>&copy;2001 Cold Spring Harbor Laboratory</font>
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