YGD is designed to be a simple database offering concise records of
yeast gene information. While other databases exist which are much more
comprehensive and complete, often what I'm looking for when sorting through
array data are simple concise records that I can always have access to.
- General Info
- Blast Map
- With each gene record there's a link to a graphic representation
of that gene blasted against all other yeast genes with default blast
parameters. The graphic is itself an imagemap with links to gene records
of the blast hits.
- Genetic and Biochemical interactions are listed by default.
This option can be turned off. The notation (L) means there's literature to support the interaction claim.
- Expression Information
- If gene expression profiles from certain fundamental experiments
can be miniaturized such that they quickly convey the behavior of a gene
then why not incorporate those empirical observtions into a database as a mini
expression browser? The little expression graphics that appear are images
made from the data sets of certain initial fundamental microarray
experiments. I'll post references when i get a chance. Otherwise it should
be pretty obvious what they are.
- Linking to Records
- To link to gene records from web pages you can construct a
simple URL with the orf name as an argument. For instance:
Thus a link constructed with that URL can bring up the database record for a
given gene, such as YGL043W
- The Genelist link is a utility for
returning gene information about a list of orfs or gene names. Sometimes papers
just list a bunch of orfs, this can help to map information onto a list of names. It's also a good way to see how a list of your favorite genes behaved in several experiments at once. Sample Output
YGD can be curated by those who choose to use it. If you want to add
something to a record there's a form for editing the database. Often when I'm sitting in a seminar I'll learn a whole bunch of things about a gene. One way to help me remember it is to enter the info into my database so it's there when I look up those gen
es in the future. Why not have a community curated database? One way to learn about a lot of genes is to build a database about them and update it.
YGD was constructed with freely available tools such as linux, Perl, php
The things I'm looking to add are:
- Linking to other databases. When you want more information, or different information, or to see what the latest information is you should be able to get there with a mouseclick to SGD, MIPS, or YPD.
- Searchability on any field.
- Blast of yeast genes against other organisms and better synonym support.
- The ability to display information about groups of genes, i.e. all essential genes, all genes with introns, all genes involved in glycolysis, etc.
- I'd like to have some way of displaying visually (and in a very simple fashion) what pathway a gene is involved in. There must be some simple map-like description language, just like is used for displaying Yahoo! driving maps that could be used to sh
ow a map of a gene's place in the cell.
- This may be related to the element directly above, but I'm thinking of incorporating information from geneontology.org.
- Why haven't I added these things yet?
- I don't have any time
- Why YGD?
- Often when I'm hunting around an array I don't need comprehensive information about a gene, I simply need concise information to remind me about what a gene does, or give me hints or clue
s to a gene's function. So simple information is sufficient,
and I can look up more details later with better resources.
I need access to yeast gene information regardless of
what computer I'm on. Commercial databases are often free to .edu computers
but if I'm at home I can't have access. YPD charges several tens of thousands of dollars per year for a license to it's database from a non .edu computer. I can't afford it.
Chris Seidel Fall 1999