Week 5 Individual Journal

Database Evaluation

For your assignment, create a new wiki page to profile your database. For this week, there will be one page per set of partners; both partners will contribute content and notes for their electronic lab notebook to the same page; you do not need to have separate individual journal entries for this week.

• Use the name of the database as the name of your page. [[1]]

Read the article about the database from the Nucleic Acids Research journal and then go online to the database itself. In keeping with Academic Honesty and citation practices, when you answer the questions below, provide a hyperlink to the page that you got the information from. There should be at least one hyperlink per answer.

General Information About the Database

1. What is the name of the database? (link to the home page)
   • We are utilizing the CRISPRInc Databse
2. What type (or types) of database is it?
   • CRISPR is a database of validated CRISPR/Cas9 sgRNAs "single guide RNA" for lncRNAs of model organisms "long non-coding RNA". From: Introduction to the 2019 NAR Database Issue: Rigden, D. J. & Fernández-Suárez, X. M. (2019). The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. Nucleic acids research, 47(D1): D1–D7. doi:10.1093/nar/gky1267 [2]
3. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
   • CRISPRlnc contains validated sgRNAs sequences and descriptions for model organisms lncRNAs.[3]
4. What type of data source does it have?
   • CRISPlnc utilizes specific literature information from PubMed, NCBI and Ensemble.
5. Primary versus secondary ("meta")?
   • CRISRlnc is a secondary source database. [4]
6. curated versus non-curated?
   • This database is manually curated. [5]
7. if curated, is it electronic versus human curation?
   • Human curation [6]
8. if human curation, is it in-house staff versus community curation?
   • In-house curation. [7]
9. What individual or organization maintains the database?
   • CRISPRlnc is maintained by Bioinformatics Group of XTBG [8]
10. public versus private
    • this database is public [9]
11. large national or multinational entity or small lab group
    • CRISPR is based in the Bioinformatics group of the Xishuangbanna Tropical Botanical Garden, of the Chinese Academy of Sciences. However, the tool created through this lab has gained international renown. [10]
12. What is their funding source(s)?
    • CRISPR is funded by The National Natural Science Foundation of China, Yunnan Province, The Scientific Research Fund of Hunan Provincial Education Department and The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province[11]

Scientific Quality of the Database

1. Does the content appear to completely cover its content domain?
   • How many records does the database contain?
     • The database contains 2089 records of collected sgRNA data.
   • What claims do the database owners make about coverage in the corresponding paper?
     • 7
2. What species are covered in the database? (If it is a very long list, summarize.)
   • This database covers:Homo sapiens(Humans), Mus musculus (Mouse), Drosophila melanogaster (Fly), Rattus norvegicus (Brown Rat), Oryctolagus cuniculus (European Rabbit), Sus scrofa (Wild Boar), danio rerio (Zebrafish), and solanum lycopersicum (Tomatoes)
3. Is the database content useful? I.e., what biological questions can it be used to answer?
4. Is the database content timely?
5. Is there a need in the scientific community for such a database at this time?
   • Is the content covered by other databases already?
6. How current is the database?
   • When did the database first go online?
     • May 18th, 2018
7. How often is the database updated?
   • When was the last update?
     • February 12th, 2019

General Utility of the Database to the Scientific Community

• 1. Are there links to other databases? Which ones?
  2. Is it convenient to browse the data?
  3. Is it convenient to download the data?
     • In what file formats are the data provided?
       • What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
       • Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
  4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
     • Is the website well-organized?
     • Does it have a help section or tutorial?
     • Are the search options sensible?
     • Run a sample query. Do the results make sense?
  5. Access: Is there a license agreement or any restrictions on access to the database?

Summary Judgment

• 1. Would you direct a colleague unfamiliar with the field to use it?
  2. Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, and seems amateur.

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.