Animal QTL

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Blair and Corinne's Database Information

General information about the database

What is the name of the database?

What type (or types) of database is it?

  • Animal QTL is a Biological Database that contains trait maps for animals. Animal QTLdb
  • This database is a secondary data source that provides "user/curator accounts for direct data submission, and supply users with a data summary link to facilitate the manuscript review process." Animal QTLdb
  • Animal QTL is a manual and community curated database that allows users to create accounts in order to submit and review data. Animal QTLdb

What individual or organization maintains the database?

What is their funding source(s)?

Scientific quality of the database

Does the content appear to completely cover its content domain? How many records does the database contain? What claims do the database owners make about coverage in the corresponding paper?

What species are covered in the database?

Is the database content useful? I.e., what biological questions can it be used to answer?

Is the database content timely?

Is there a need in the scientific community for such a database at this time? Is the content covered by other databases already? When did the database first go online? How often is the database updated? When was the last update?

General utility of the database to the scientific community

Are there links to other databases? Which ones?

Is it convenient to browse the data?

  • This website is very organized with their data giving titles to each animal subject they have on trait mapping. Each title links to a page where a summary of the animals current data numbers are held, data can be downloaded easily (in a variety of formats) and search/browse tools are suggested to make data easily readable.

Is it convenient to download the data?

  • Yes:
    1. The file formats include:
      1. On UMD_3.1 in GFF3 format
      2. On UMD_3.1 in SAM format
      3. On UMD_3.1 in BED format
      4. On Btau_4.6 in GFF3 format
      5. On Btau_4.6 in SAM format
      6. On Btau_4.6 in BED format
    2. This database included non-standard formats, as appose to PDF, DOC, or etc. standard formats.
    3. Animal QTL Data Download

Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?

Access: Is there a license agreement or any restrictions on access to the database?

  • No, this data is made freely available to anyone, and is also available on other database sites, such as NCBI or Ensembl.
    1. Frequently Asked Questions for NAGRP Information on licensing can be found under question 32.

Summary judgment

Would you direct a colleague unfamiliar with the field to use it?

Is this a professional or hobby database?

Acknowledgments

  1. Corinne Wong and Blair Hamilton worked on this homework assignment together by meeting in person outside of class, as well as through text messaging.

References

Animal QTL Database. (2017). Animal QTLdb. Retrieved September 28, 2017, from https://www.animalgenome.org/cgi-bin/QTLdb/index

Hu, Z.-L., Park, C. A., Wu, X.-L., & Reecy, J. M. (2013). Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Research, 41(Database issue), D871–D879. http://doi.org/10.1093/nar/gks1150

LMU BioDB 2017. (2017). Week 5. Retrieved September 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_5

U.S NAGRP Bioinformatics. (2017). Genome Informatics Resources. Retrieved October 1, 2017, from https://www.animalgenome.org/bioinfo/

Links

Blair

Category Links
User Page Blair Hamilton
Weekly Assignments Bhamilton18 Week 2   Bhamilton18 Week 3   Bhamilton18 Week 4  Animal QTL  Bhamilton18 Week 6  Bhamilton18 Week 7  Bhamilton18 Week 8  Bhamilton18 Week 9  Bhamilton18 Week 10  Bhamilton18 Week 11  Bhamilton18 Week 12  Bhamilton18 Week 14  Bhamilton18 Week 15
Weekly Assignment
Instructions		 Week 1   Week 2   Week 3   Week 4   Week 5   Week 6   Week 7   Week 8   Week 9   Week 10   Week 11   Week 12   Week 14   Week 15
Class Journals Class Journal Week 1   Class Journal Week 2   Class Journal Week 3   Class Journal Week 4   Class Journal Week 5   Class Journal Week 6   Class Journal Week 7   Class Journal Week 8   Class Journal Week 9   Class Journal Week 10
Final Project Lights, Camera, InterACTION!  Lights, Camera, InterACTION! Deliverables

Corinne

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Journal Entries:

Shared Journals:

Group Project

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