Use Cases for GeneNetwork

Note: We are trying to use this document to figure out how people are using GeneNetwork right now. We welcome potential use cases that require new features; please post them in FutureIdeas.

Right now, we have the following users. The headers below link to more detailed descriptions of the functionality that each user expects.

General Use Cases

• Gene search. A user searches a gene to find its gene expression data, genomic and functional data, all kinds of QTL analyses, and correlated genes. It seems to be the main use of genenetwork, and the tutorial tour written by Rob has described in detail how to use it.
• Scriptable interface. A programmer can use URLs to retrieve data sets/subsets, or do queries. Its documentation can be found from the search menu bar of genenetwork. I wonder if it makes more sense to put this document into help menu bar.
• Download data sets. Some users might be interested in getting a copy of some of our data sets to do analysis. This can be implemented by setting up a ftp site, or a data dump functionality. I don't know if we have any plan on this. It looks like our scriptable interface is doing part of this job.
• Data submission. Outside users might want to submit data for deposition. I think currently this is being done by individual emails, not by genenetwork. The prerequisite to automate this is to define a data format for the input data.
• Simply calculate QTLs. This is just my imagination. Some people may just want to calculate QTLs from their external data. I understand that webQTL does not mean to be a computing provider, so it may not be what we want to do. I heard that QTL caculation is computing-intensive, especially when the large amount of SNP data is involved. People may want some high-performance online computing service for QTLs somewhere.

More details about each case will be described:

BiologistUser

This user is a biology researcher who seeks to use GeneNetwork directly as a research tool. He or she would like to study the relationships and functions of genes and their transcripts as well as phenotypes.

BioinformaticistUser?

This user is a bioinformatician with training in biology and computer science and seeks to integrate Gene Network into a larger system.

GnAdministrator?

This user is connected with GeneNetwork and wants to edit the pages or contribute data.

-- ZhaohuiSun - 03 Aug 2006