Difference between revisions of "Malverso Week 11"

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(answered some MOD questions)
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#For the genome paper (Coder and QA only): in addition to the journal article, please find and review the Model Organism Database (MOD) for your species similarly to what you did to review your assigned database for the NAR assignment. In particular, make sure to answer the following:
 
#For the genome paper (Coder and QA only): in addition to the journal article, please find and review the Model Organism Database (MOD) for your species similarly to what you did to review your assigned database for the NAR assignment. In particular, make sure to answer the following:
 
#*What types of data can be found in the database (sequence, structures, annotations, etc.)?
 
#*What types of data can be found in the database (sequence, structures, annotations, etc.)?
 +
#**You can search for genes, regions of the chromosome, or description such as enzymes or proteins, along with "Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs". You can download the DNA sequence, view a karyotype of the genome, and find other information such as the number of base pairs and the number of genes. [http://bacteria.ensembl.org/shewanella_oneidensis_mr_1/Info/Index]
 
#*Is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
 
#*Is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
−
#**
+
#**This is a meta database. I know this because it gets its information about S. oneidensis from a different database - the European Nucleotide Archive. Since "The goal of Ensembl was therefore to automatically annotate the genome" I would say that the database is curated electronically. However, Ensembl as a whole is updated every two months about, in releases. This implies that the curation is not automatic, which implies that curation is manual (in-house). The site also says that the database is "updated regularly with new data including new genomes, assemblies and gene models, and updates and additions to existing data sets" being included in each release.
 
#*What individual or organization maintains the database?
 
#*What individual or organization maintains the database?
 +
#**Ensembl is a joint project between European Bioinformatics Institute (EMBI-EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI).[http://uswest.ensembl.org/info/about/index.html]
 
#*What is their funding source(s)?
 
#*What is their funding source(s)?
 
#**"Ensembl Genomes is funded by the European Molecular Biology Laboratory and by grants from a variety of different funding sources."[http://ensemblgenomes.org/info/about/collaborations]
 
#**"Ensembl Genomes is funded by the European Molecular Biology Laboratory and by grants from a variety of different funding sources."[http://ensemblgenomes.org/info/about/collaborations]
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#**FASTA and GFF3 formats.  
 
#**FASTA and GFF3 formats.  
 
#*Evaluate the “user-friendliness” of the database.
 
#*Evaluate the “user-friendliness” of the database.
 +
#**This website is pretty user friendly. There are pictures and easy to understand labels to buttons. The search bar is at the top and it is clear that the search bar can be utilized in a few different ways.
 
#*Is the Web site well-organized?
 
#*Is the Web site well-organized?
 +
#**Yes, the resources available are clearly shown on the home screen, along with pictures, links to more information, and download buttons.
 
#*Does it have a help section or tutorial?
 
#*Does it have a help section or tutorial?
 +
#**Yes, there is a website help button, as well as FAQ pages and buttons to click if you want more information on a variety of items. There are also examples of searches to help out.
 
#*Run a sample query. Do the results make sense?
 
#*Run a sample query. Do the results make sense?
 +
#**I searched for SO_2097, which was mentioned in the genome paper. The results provided me with a chromosome location, a description of the gene, and a synonym for the gene. The description on the site matched the brief description in the genome paper, so the results made sense. 
 
#*What is the format (regular expression) of the main type of gene ID for this species (the "ordered locus name" ID)? (for example, for Vibrio cholerae it was VC#### or VC_####).
 
#*What is the format (regular expression) of the main type of gene ID for this species (the "ordered locus name" ID)? (for example, for Vibrio cholerae it was VC#### or VC_####).
 
#**SO_#### is the gene ID format.  
 
#**SO_#### is the gene ID format.  
  
 
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{{Template:Malverso}}

Revision as of 21:41, 16 November 2015

Personal Goals

  • Prepare for journal club presentations
  • Set up coding/testing environment
  • Determine the regular expression for the ordered locus ID for your species
  • Identify the appropriate model organism database for your species.
  • Perform an initial Gene Database export and Gene Database Testing Report

Electronic Journal

  • After struggling to find a Model Organism Gene Database for Shewanella oneidensis, I asked Dr.Dahlquist for assistance.
  • The only database link we could find was broken.
  • We decided that our next plan of action would be to use the website bacteria.ensembl.org as our MOD.

Journal Club Presentation

  1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own URL citation.
    1. bioremediation: When bacteria, plants, or other biological agents are used to get rid of pollutants in things such as soil or water.Found at this link.
    2. plasmid: DNA that can replicate itself without the chromosomal DNA.Found at this link.
    3. phage: Also known as bacteriophage. Viruses that usually cause the disintegration of a certain bacteria through infection. Found at this link.
    4. cytochromes: A protein whose main function is electron transport. Found at this link.
    5. redox: An abbreviation of reduction which is the loss of oxygen. Found at this link.
    6. heme: An iron compound that has oxygen carrying properties and is the non-protein part of hemoglobin. Found at this link.
    7. paralogous genes: Genes that are similar but at two different locations in the chromosome of the organism. This indicates that the sets came from an ancestral gene. Found at this link.
    8. hydrogenase: A catalyst for the formation/oxidation of H2. Found at this link.
    9. heterodimeric: An adjective that describes a protein which is comprised of two differing polyeptide chains. Found at this link.
    10. aquaporin: A channel that allows water to pass through the membrane (selectively), but not ions. Found at this link.
    11. efflux: The process of flowing/flowing out. Found at this link.
    12. biofilm: A colony of microorganisms that are encased in a protective coating of their own secretions. They can form on solid and liquid surfaces. Found at this link.
    13. virulence determinants: Factors that allow bacteria to cause disease. Found at this link.
  2. Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
    • What is the importance or significance of this work (i.e., your species)?
    • What were the methods used in the study?
    • Briefly state the result shown in each of the figures and tables.
    • How do the results of this study compare to the results of previous studies (See Discussion).
  3. For the genome paper (Coder and QA only): in addition to the journal article, please find and review the Model Organism Database (MOD) for your species similarly to what you did to review your assigned database for the NAR assignment. In particular, make sure to answer the following:
    • What types of data can be found in the database (sequence, structures, annotations, etc.)?
      • You can search for genes, regions of the chromosome, or description such as enzymes or proteins, along with "Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs". You can download the DNA sequence, view a karyotype of the genome, and find other information such as the number of base pairs and the number of genes. [1]
    • Is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
      • This is a meta database. I know this because it gets its information about S. oneidensis from a different database - the European Nucleotide Archive. Since "The goal of Ensembl was therefore to automatically annotate the genome" I would say that the database is curated electronically. However, Ensembl as a whole is updated every two months about, in releases. This implies that the curation is not automatic, which implies that curation is manual (in-house). The site also says that the database is "updated regularly with new data including new genomes, assemblies and gene models, and updates and additions to existing data sets" being included in each release.
    • What individual or organization maintains the database?
      • Ensembl is a joint project between European Bioinformatics Institute (EMBI-EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI).[2]
    • What is their funding source(s)?
      • "Ensembl Genomes is funded by the European Molecular Biology Laboratory and by grants from a variety of different funding sources."[3]
    • Is there a license agreement or any restrictions on access to the database?
      • No, and the data is also available for download through multiple routes. [4]
    • How often is the database updated?
      • The entire database website is updated every two months. [5] However, when I clicked on the link of the provider of the S. oneidensis information, it shows the last update of that specific information to be the 16th of November in 2012. [6]
    • Are there links to other databases?
    • Can the information be downloaded?
      • Yes!
    • In what file formats?
      • FASTA and GFF3 formats.
    • Evaluate the “user-friendliness” of the database.
      • This website is pretty user friendly. There are pictures and easy to understand labels to buttons. The search bar is at the top and it is clear that the search bar can be utilized in a few different ways.
    • Is the Web site well-organized?
      • Yes, the resources available are clearly shown on the home screen, along with pictures, links to more information, and download buttons.
    • Does it have a help section or tutorial?
      • Yes, there is a website help button, as well as FAQ pages and buttons to click if you want more information on a variety of items. There are also examples of searches to help out.
    • Run a sample query. Do the results make sense?
      • I searched for SO_2097, which was mentioned in the genome paper. The results provided me with a chromosome location, a description of the gene, and a synonym for the gene. The description on the site matched the brief description in the genome paper, so the results made sense.
    • What is the format (regular expression) of the main type of gene ID for this species (the "ordered locus name" ID)? (for example, for Vibrio cholerae it was VC#### or VC_####).
      • SO_#### is the gene ID format.


Team Page

Heavy Metal HaterZ

Assignments

Individual Journal Entries

Shared Journal Entries

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