Difference between revisions of "Influenza Research Database"
From LMU BioDB 2017
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=General utility of the database to the scientific community= | =General utility of the database to the scientific community= | ||
# Are there links to other databases? Which ones? | # Are there links to other databases? Which ones? | ||
| + | #:: Although most of the data is generated by the IRD team, the database also imports data from the following databases: | ||
| + | #::* [https://www.ncbi.nlm.nih.gov/genbank/ NCBI - GenBank] | ||
| + | #::* [https://www.ncbi.nlm.nih.gov/refseq/ NCBI - RefSeq | ||
| + | #::* [http://www.iedb.org/ Immune Epitope Database (IEDB)] | ||
| + | #::* [http://www.uniprot.org/ UniProt] | ||
| + | #::* [http://www.rcsb.org/pdb/home/home.do RCSB Protein Data Bank (PDB)] | ||
| + | #::* [https://www.ebi.ac.uk/thornton-srv/databases/CSA/ Catalytic Site Atlas] | ||
| + | #::* [http://avibase.bsc-eoc.org/avibase.jsp?lang=EN Avibase] | ||
# Is it convenient to browse the data? | # Is it convenient to browse the data? | ||
# Is it convenient to download the data? | # Is it convenient to download the data? | ||
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#* Are the search options sensible? | #* Are the search options sensible? | ||
#* Run a sample query. Do the results make sense? | #* Run a sample query. Do the results make sense? | ||
| − | # Access: Is there a license agreement or any restrictions on access to the database? | + | # Access: Is there a license agreement or any restrictions on access to the database? |
| + | |||
=Summary judgment= | =Summary judgment= | ||
# Would you direct a colleague unfamiliar with the field to use it? | # Would you direct a colleague unfamiliar with the field to use it? | ||
Revision as of 20:23, 4 October 2017
Contents
General information about the database
The database we chose is the Influenza Research Database
Type of Database
- What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
- What type of data source does it have?
- primary versus secondary ("meta")
- curated versus non-curated
- electronic versus human curation
- in-house staff versus community curation
Maintenance
- What individual or organization maintains the database?
- public versus private
- large national or multinational entity or small lab group
Funding
Scientific quality of the database
- 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?
- What species are covered in the database?
- Is the database content useful? I.e., what biological questions can it be used to answer?
- 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?
- 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
- Are there links to other databases? Which ones?
- Although most of the data is generated by the IRD team, the database also imports data from the following databases:
- Is it convenient to browse the data?
- Is it convenient to download the data?
- In what file formats are the data provided?
- Are they standard or non-standard formats?
- 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?
- Access: Is there a license agreement or any restrictions on access to the database?
Summary judgment
- Would you direct a colleague unfamiliar with the field to use it?
- Is this a professional or hobby database?
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.
