Using the TAIR Keyword Search and Understanding the results and detail pages

These pages describe how to search TAIR database with keywords.Contents

Introduction

Keywords in TAIR are used to describe a variety of data such as genes, publications and microrarray experiments. The keywords are controlled vocabulary terms that are used by collaborating model organism databases to provide a uniform set of descriptive terms that can be used by all member groups. The keyword search allows you to find all types of data associated with a given phrase such as "leaf development' or "signal transduction".

A major use of keywords are for functional annotations of genes by association to Gene Ontology terms. The GO annotations describe gene products in terms of their molecular functions, sub cellular and roles in biological processes. GO ontologies are developed by the Gene Ontology Consortium.

Plant structure and developmental stage keywords are primarily used to describe patterns of gene expression and characteristics of biological materials such a germplasms. Plant structure and development terms are being developed in collaboration with the Plant Ontology Consortium.

Searching for Keywords

You can search for keywords using exact or inexact (starts with, contains, ends with) matching. If you are unsure of the phrasing of the term, choose a [contains] search. This will be slower but is likely to retrieve more results.

Choosing the type of keywords to search

You can choose to restrict your search to a subset of keywords by selecting the types of keywords to search. The default option searches all keywords regardless of type. Checking any of the boxes will limit your search to only keywords of the selected type; more than one keyword type can be searched.

Keyword search results

The keyword search results are displayed on a summary page which shows all of the keywords that were found in the query. From this summary page you can find information about the keywords, find data associated to keywords and keyword children terms, as well as perform a new keyword search.

The keyword details

Clicking on the keyword term will open a new window showing detailed information about the keyword. To see the definitions for any of the fields, click on the question mark icon.

Viewing associated data

Data types that are associated to each keyword are listed according to type. The number represents the total number of objects (e.g. genes, annotations) that are associated to either the term itself or its children terms. Click on the link for each data type to view a summary list.The current set of data types associated to keywords includes: genes, publications, annotations (functional annotations of genes) and expression sets(microarray experiments).For information about interpriting the annotation details see Annotation Detail Page help.