FB2014_05, released September 9th, 2014
 
 

A Database of Drosophila Genes & Genomes

Introduction to TermLink

How do you find all the alleles that manifest a phenotype in the trachea? Or search for all the genes associated with a particular stage of development? All the alleles generated by ends-in gene targeting? How can you do all this in a controlled, accurate way, where it doesn't matter if you use US or UK-English spelling (behavior/behaviour), or if you call something a 'dorsal mesothoracic disc' as opposed to a 'wing disc'?

You can do all this using TermLink, our controlled vocabulary search tool.

This is all possible due to the use of controlled vocabularies. When we curate phenotypic, expression, or molecular data from the literature, we not only record free text descriptions but also annotate the data using controlled terms. These controlled terms are organised into hierarchical trees. This means that when you search using a controlled term, you can also find all the objects annotated with derivatives of that term, e.g. if you search for all the genes expressed in the larval head, you also get those genes that express in a part of the larval head, such as the cephalopharyngeal sclerites.

The controlled vocabulary trees used in TermLink encode for more than 'part_of' relationships. They also express relationships like 'develops from' or 'connects to'. This allows you to browse through terms to find exactly the term of interest. Once there, you can click through to lists of objects (such as cell lines, insertions, genes, alleles, images etc.) annotated with that term.

A powerful feature of controlled vocabularies is the addition of commonly used synonyms. This means that when you search with a term such as hypophysis, you not only get returned all the alleles with a phenotype in the hypophysis, but also those alleles annotated with the synonyms of hypophysis, such as hypophyseal sense organ, ventral pharyngeal sensilla, or labial sensory complex.

For these reasons we think TermLink makes for a far more meaningful search than simply searching the free text.

When to use TermLink instead of QuickSearch? While QuickSearch is very useful for getting to data fast, it can sometimes be less specific than required. If you're searching for genes annotated with a Gene Ontology term, or for expression or phenotype in a particular part of the anatomy or stage of development, TermLink will provide a quicker, more accurate search tool.