Difference between revisions of "IMG/VR Week 5"

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(→‎1. What is the name of the database? (link to the home page): answer)
(→‎General information about the database: answer)
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1)What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
 
1)What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
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 +
IMG/M is a database of DNA fragments for sequencing and analysis. The site offers these viral fragments for sequencing and analysis, organizing each them according to which part of the human body the virus infects.
  
 
2)What type of data source does it have?
 
2)What type of data source does it have?
 
primary versus secondary ("meta")?
 
primary versus secondary ("meta")?
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IMG/M offers secondary source data, as the genomic information of this database was collected from outside sources that sequenced the DNA.
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curated versus non-curated?
 
curated versus non-curated?
 
if curated, is it electronic versus human curation?
 
if curated, is it electronic versus human curation?
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===3.What individual or organization maintains the database?===
 
===3.What individual or organization maintains the database?===
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*public versus private
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IMG/M is a public database maintained by The Regents of the University of California.
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*large national or multinational entity or small lab group
 
  
 
===4. What is their funding source(s)?===
 
===4. What is their funding source(s)?===
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Since it is a public database, IMG/VR is publically funded by the state of California.
  
 
==Scientific quality of the database==
 
==Scientific quality of the database==

Revision as of 16:28, 28 September 2019

General information about the database

1. What is the name of the database? (link to the home page)

IMG/VR [[1]]

2. What type (or types) of database is it?

1)What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])

IMG/M is a database of DNA fragments for sequencing and analysis. The site offers these viral fragments for sequencing and analysis, organizing each them according to which part of the human body the virus infects.

2)What type of data source does it have? primary versus secondary ("meta")?

IMG/M offers secondary source data, as the genomic information of this database was collected from outside sources that sequenced the DNA.

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?

IMG/M is a public database maintained by The Regents of the University of California.

4. What is their funding source(s)?

Since it is a public database, IMG/VR is publically funded by the state of California.

Scientific quality of the database

1. 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?

2. What species are covered in the database? (If it is a very long list, summarize.)

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

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?

5.How current is the database?

  • When did the database first go online?
  • How often is the database updated?
  • When was the last update?

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.

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