Animal QTL

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Blair and Corinne's Database Information

For this assignment, Corinne and Blair picked the Animal QTL database from the Nucleic Acids Research Database Issue Database List. Referencing the Week 5 Assignment page, we answered the guidelines/questions for database evaluation. We created a collaborative wiki page, as well as, google slides to work individually and together on the presentation. We split up questions and addition to pages/slides in order to be more efficient.

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)?

  • It is funded by the USDA NRSP-8 National Animal Genome Research Program, Bioinformatics Coordination Project, and the USDA-NRI. The funding for the open access charge is provided by USDA-NIFA Research Funds Research Funds to the National Research Service Program, NRSP-8, and the National Animal Genome Research Program. [1]

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?

  • Yes, the database provides sufficient information about animal trait mapping. Animal QTL contains 1881 publications in its collection. They claim to accumulate all the public data of trait mapping that they can to allow researchers to map genes across species. They also claim to have user/curator accounts that allow people to receive direct data submissions. [2]

What species are covered in the database?

  • They covered a variety of livestock, including cattle, catfish, chickens, horses, pigs, rainbow trout, and sheep. [3]

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

  • Yes, it is useful. It can be used to map out traits to figure out a species' genome and see how it converged or diverged from other species. Moreover, it shows the genetic information for the breeds, so people can look into how genes are inherited/acquired from parental genes or epistasis. [4]

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?

  • Yes, it is a very timely and useful tool. It is helpful in determining the genomes of various livestock, and it helps to see the connection between genes and traits. Moreover, the published data is frequently updated to provide the most current information. [5]
  • The content is not already covered by other databases. There is a similar one, but it covers more plants and crops instead of livestock.
  • The database first went online in 2003. It seems to be updated fairly frequently. They are on their 33rd release after 14 years, which means, on average, they must update it at least 2 times every year. The last update was August 26th, 2017. [6]

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.
  • Animal QTLdb

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?

  • The database allows the user to see the total database summary at the top of the page to gauge quantity of data.
  • Titles are bolded per species making navigation between animals convenient and organized.
  • Each section contains an icon deciphering between downloads, help, animals, references, and other useful links.
  • This database contains video tutorials as well as a frequently asked questions section for users to reference.
  • Within each animal there is a search option located at the top right of the page. This search field allows users to explore ore specific elements of an animals rapping traits.
    1. For example, we selected Cattle and typed "hoof" in the search field and received multiple relevant results pertaining to traits of cattle. The results were separate into various trait categories, like vertebrate trait ontology, clinical measurement ontology and trait distributions.
  • Cattle DTL Database

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?

  • Yes, we believe that this website clearly and effectively portrays animal traits of 7 species. Although this database does not contain every species, it is quite thorough in livestock animals. It provides multiple resources to other databases, help platforms, accessible data downloads and easy data addition/curation. As listed above in the user-friendliness section, our database provides easy browsing throughout the site.

Is this a professional or hobby database?

  • Both:
    1. Hobby- Since it is available to anyone who can create an account, and is interested in livestock mapping traits.
    2. Professional- Because it is funded and curated on a national basis, and routinely updated with the most recent livestock mapping trait data.

Powerpoint Presentation

Blair and Corinne's Powerpoint

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

  1. Animal QTL Database. (2017). Animal QTLdb. Retrieved September 28, 2017, from https://www.animalgenome.org/cgi-bin/QTLdb/index
  2. 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
  3. LMU BioDB 2017. (2017). Week 5. Retrieved September 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_5
  4. 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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