Matthew R Allegretti Week 14: Difference between revisions
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==References== | ==References== | ||
*[[BIOL368/F16:Week | *[[BIOL368/F16:Week 13| Week 13 Instructions]] | ||
**Questions and references pulled from this page | **Questions and references pulled from this page | ||
*[http://nar.oxfordjournals.org/content/44/D1/D1.full Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6. doi: 10.1093/nar/gkv1356] | *[http://nar.oxfordjournals.org/content/44/D1/D1.full Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6. doi: 10.1093/nar/gkv1356] |
Revision as of 13:21, 4 December 2016
Week 14 Assignment
Purpose
To familiarize myself with the various aspects of biological databases.
Methods and Results
- What database did you access? (link to the home page of the database)
- MitoAge
- http://www.mitoage.info/
- What is the purpose of the database?
- It is a database for the storage of mitochondrial DNA sequences of various animals.
- http://www.mitoage.info/
- What biological information does it contain?
- "MitoAge contains calculated mtDNA compositional features of the entire mitochondrial genome, mtDNA coding (tRNA, rRNA, protein-coding genes) and non-coding (D-loop, insertions) regions, codon usage for each protein-coding gene, and longevity records for over 900 species from all taxa of the Kingdom Animalia."
- http://www.mitoage.info/
- What species are covered in the database?
- 922 species of animals, sorted by order, are covered including:
- 206 species of Actinopterygii
- 1 specie of Bivalvia
- 1 specie of Chromadorea
- 1 specie of Malacostraca
- 4 species of Sarcopterygii
- 29 species of Amphibia
- 6 species of Cephalaspidomorphi
- 1 species of Echinoidea
- 390 species of Mammalia
- 152 species of Aves
- 35 species of Chondrichthyes
- 2 species of Insecta
- 94 species of Reptilia
- http://www.mitoage.info/browse/taxonomy/
- 922 species of animals, sorted by order, are covered including:
- What biological questions can it be used to answer?
- How mitochondrial DNA plays a role in animal longevity, and other influences mtDNA has on the lifecycle of an animal.
- http://www.mitoage.info/
- 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])?
- Amino acid sequence database. "The MitoAge database was constructed using publicly available data, is being constantly updated through automatic tools and is manually curated for problematic issues."
- http://www.mitoage.info/view/18373/species/ under "codon usage". https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702847/#SEC3title
- What individual or organization maintains the database?
- Vadim E. Fraifeld, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- http://www.mitoage.info/about/
- What is their funding source(s)?
- Fund in Memory of Dr Amir Abramovich. Funding for open access charge: Ben-Gurion University of the Negev [to V.E.F.].
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702847/#SEC7title
- Is there a license agreement or any restrictions on access to the database?
- "The MitoAge database is free for all purposes, including commercial, educational, and research purposes, provided however that you cite the usage of MitoAge in subsequent presentations, publications, etc. Although referring to the URL might be enough in some cases (e.g., teaching and websites), for scientific publications we ask that you cite the paper describing MitoAge."
- http://www.mitoage.info/terms/
- How often is the database updated? When was the last update?
- The website is "being constantly updated through automatic tools and is manually curated for problematic issues"
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702847/#SEC3title
- Are there links to other databases?
- Yes, see below
- http://genomics.senescence.info/species/
- Can the information be downloaded? And in what file formats?
- "data export for a data set of interest [is available] (in a CSV format), without downloading the entire database"
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702847/#SEC2title
- Evaluate the “user-friendliness” of the database.
- Is the Web site well-organized?
- Yes. It is well organized with a number of easy to locate links.
- http://www.mitoage.info/ toolbar at the top, quick links in the bottom right
- Yes. It is well organized with a number of easy to locate links.
- Does it have a help section or tutorial?
- Yes. Help section in tool bar, as well as a user guide page.
- http://www.mitoage.info/user_guide/
- Run a sample query. Do the results make sense?
- Yes, I searched for an organism in plain English and it showed up.
- http://www.mitoage.info/search/?q=Human and http://www.mitoage.info/search/?q=snake
- Is the Web site well-organized?
- Some Definitions
- Electronic curation occurs when someone writes a program to add information to a database record from another database.
- Manual curation occurs when a human reviews the information being added to a record to validate it as true.
- In-house is when the human works for the database organization.
- Community is when the database allows members of the scientific community that don't work for the database organization to add information to the record.
Conclusion
References
- Week 13 Instructions
- Questions and references pulled from this page
- Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6. doi: 10.1093/nar/gkv1356
- Slides from DataONE.org
- DataONE: Data Sharing
- http://www.mitoage.info/
- Database used for the assignment
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702847/
- Provided information on the database
Acknowledgements
This individual journal entry was completed by me and not copied from another source.
- Dr. Dahlquist
- Author of the Week 14 Intructions
Useful links
- Stem Cell Overview
- Template
- Student Page
- Week 1 Instructions
- Journal Week 1
- Week 2 Instructions
- Week 2
- Journal Week 2
- Week 3 Instructions
- Week 3
- Journal Week 3
- Week 4 Instructions
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- Week 10
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- Week 11 Instructions
- Week 11
- Journal Week 11
- Week 12 Instructions
- Week 14 Instructions
- Week 14 Assignment Part 1 and 2
- Journal Week 14
- Week 15 Instructions
- Week 15
- Journal Week 15
- My user page