Monarch Initiative Week 4

To User Page: User: Asandle1, User: Kmill104

To Assignment Page: Week 4

https://academic.oup.com/nar/article/52/D1/D938/7449493

Database Evaluation

Andrew doing 1 and 3, Katie 2 and 4 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.

• The name of your page should be "Database name Week 4".

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? Monarch Initiative Monarch Initiative
  2. What type (or types) of database is it? The Monarch Initiative integrates gene, disease, and phenotype data. The database combines knowledge from across sources to reveal how they are connected. The database intends to show how these connections can tell us the causes and mechanisms of human disease. Nucleic Acids Research Article
     1. What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
     2. What type of data source does it have?
        • primary versus secondary ("meta")?
        • curated versus non-curated?
          • if curated, is it electronic versus human curation?
            • if human curation, is it in-house staff versus community curation?
  3. What individual or organization maintains the database?
     • public versus private
     • large national or multinational entity or small lab group
  4. What is their funding source(s)?

Scientific quality of the database

• 1. Does the content appear to completely cover its content domain?
     • How many records does the database contain?

It is not completely clear how many databases the database contains. This is something that could be better communicated. That being said when opening the search bar it shows 845539 results. It is possible that this is the total number of entries in the database. Search Page

• 1. • What claims do the database owners make about coverage in the corresponding paper?
  2. What species are covered in the database? (If it is a very long list, summarize.)

The database covers and connects "phenotypes to genotypes across species". About

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

It could be useful, it helps merge data from different scientific research fields onto one platform to help inform research and improve data organization to make more informed clinical decisions. About

• 1. Is the database content timely?

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

They are no very forthcoming or clear about which species/model organisms they are using other than humans.

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, or 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.