GeneDB

Database Analysis

1. What database did you access? (link to the home page of the database)
   • We accessed Gene DB Gene DB.
2. What is the purpose of the database?’’
   • The purpose of Gene DB, is to provide the public with reliably sequenced genomes as soon as they become available. Gene DB offers the sequences of a variety of different organisms in the pathogenic group.
3. What biological information does it contain?
   • Since Gene DB is concerned with pathogens, it includes information on the disease that each species is responsible for creating in different organisms. The database contains the seqeunces data of each pathogen as well and it includes articles relating to that specific organism. Descriptives of each pathogen consist of:
     1. protein length
        • maximum length
        • minimum length
     2. molecular mass
        • minimum mass
        • maximum mass
     3. gene type
        • protein-coding
        • pseudogene
        • rRNA
        • snoRNA
        • snRNA
        • tRNA
        • miscRNA
     4. date sequenced was last modified
     5. location
        • region
        • boundaries
     6. protein targeting
        • signal peptide
        • GPI anchor
        • Apicoplast
     7. transmembrane helices
        • minimum number of domains
        • maximum number of domains
4. What species are covered in the database?
   • Gene DB covers various species of bacteria (e.g. Apicomplexan and Plasmodium)
5. What biological questions can it be used to answer?
   • GeneDB can answer numerous questions about sequenced genomes of pathogens. Any off the above descriptives can be search for specifically among all the genomes present on the database.
6. What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
   • GeneDB is concerned with the sequenced genomes of different pathogens. The database is curated electronically in a community setting.
7. What individual or organization maintains the database?
   • The Sanger Institute appears to run the website, but the sequences are a product of the Pathogen Group.
8. What is their funding source(s)?
   • Gene DB is primarily funded by research grants to individual professors working on the datasets. The list of currently funded researchers consists of:
     1. Dr. Matt Berriman (The Welcome Trust Sanger Institute)
     2. Prof. David Roos (University of Pennsylvania)
     3. Prof. Deborah Smith (University of York)
     4. Dr. Mark Carrington (University of Cambridge)
9. Is there a license agreement or any restrictions on access to the database?
   • The license agreement is based on the user terms and conditions for using the website. The content provided by the Sanger institute is licensed under a creative commons license. “A Creative Commons license is used when an author wants to give people the right to share, use, and even build upon a work that they have created. Creative Commons provides an author flexibility (for example, they might choose to allow only non-commercial uses of their own work) and protects the people who use or redistribute an author's work, so they don’t have to worry about copyright infringement, as long as they abide by the conditions the author has specified.” (Wikipedia)
10. How often is the database updated? When was the last update?
    • The Sanger Institute strives to keep information as up to date and accurate as possible the moment that it becomes available. There was not a “latest update” search option available. As of January 2013, the database for all the genomes of Trypanosomes and Leishmanias in GeneDB was updated. The Sanger Institute is working on a Working with Parasite Database Resources Workshop that is set for 20-25 October 2013.
11. Are there links to other databases?
    • There are links to other databases based on which dataset is chosen. From that page, there are multiple links to other databases containing information on the dataset queried.
12. Can the information be downloaded?
    • The information cannot be downloaded into files, but has an option to view the history of datasets that were queried on the database.
13. Evaluate the “user-friendliness” of the database.
    • The website itself is organized by the datasets of the species contained within the database. It does not have a help section or a tutorial.

Laurmagee (talk) 01:42, 22 October 2013 (PDT)