Difference between revisions of "Influenza Research Database"
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#::* [http://avibase.bsc-eoc.org/avibase.jsp?lang=EN Avibase] | #::* [http://avibase.bsc-eoc.org/avibase.jsp?lang=EN Avibase] | ||
# Is it convenient to browse the data? | # Is it convenient to browse the data? | ||
| + | #:: IRD has multiple ways to browse and search the data within their database. They also have a number of tools that make it convenient to refine and analyze the search as well as save the data you are working on to your "workbench" so you can come back to it later. | ||
| + | #::* You can use their quick search tool, to "search for sequence records using any text terms in key text fields and public IDs (e.g. accession numbers) of nucleotide and protein sequence records, strain data, surveillance data, and human clinical metadata." | ||
| + | #::* Or, you search using any of the following, focused, search tools: | ||
| + | #::** Sequences & Strains | ||
| + | #::** Animal Surveillance | ||
| + | #::** 3D Protein Structure Files | ||
| + | #::** Human Clinical Metadata | ||
| + | #::** Serology Experiments (Beta) | ||
| + | #::** Host Factor Data | ||
| + | #::** Antiviral Drugs | ||
| + | #::** Immune Epitopes | ||
| + | #::** Phenotypes | ||
| + | #::** PCR Primer Probe Data | ||
| + | #::** Sequence Feature Variant Types | ||
| + | #::** Human Clinical Studies and Lab Experiments (Beta) | ||
| + | #:: With all of these tools, you have many options to access any single piece of data. This provides a lot of convenience when it comes too trying to locate anything within their database. | ||
# Is it convenient to download the data? | # Is it convenient to download the data? | ||
#* In what file formats are the data provided? | #* In what file formats are the data provided? | ||
Revision as of 21:17, 4 October 2017
Contents
General information about the database
The database we chose is the Influenza Research Database
Type of Database
- Contains avian and non-human mammalian influenza surveillance data, human clinical data associated with virus extracts, phenotypic characteristics of viruses isolated from extracts, and all genomic and proteomic data available in public repositories for influenza viruses.
- Includes both primary and secondary data that appears to be curated by the community
Maintenance
- Maintained privately by a team of 29 individuals belonging to Northrop Grumman Health IT, Vecna Technologies, DMID/NIAID/NIH/DHHS, and J. Craig Venter Institute.
- Public is encouraged to submit their own data
Funding
- IRD is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, and Department of Health and Human Services.
- It is a collaboration between Northrop Grumman Health and Human Services, J. Craig Venter Institute, and Vecna Technologies
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?
- IRD has multiple ways to browse and search the data within their database. They also have a number of tools that make it convenient to refine and analyze the search as well as save the data you are working on to your "workbench" so you can come back to it later.
- You can use their quick search tool, to "search for sequence records using any text terms in key text fields and public IDs (e.g. accession numbers) of nucleotide and protein sequence records, strain data, surveillance data, and human clinical metadata."
- Or, you search using any of the following, focused, search tools:
- Sequences & Strains
- Animal Surveillance
- 3D Protein Structure Files
- Human Clinical Metadata
- Serology Experiments (Beta)
- Host Factor Data
- Antiviral Drugs
- Immune Epitopes
- Phenotypes
- PCR Primer Probe Data
- Sequence Feature Variant Types
- Human Clinical Studies and Lab Experiments (Beta)
- With all of these tools, you have many options to access any single piece of data. This provides a lot of convenience when it comes too trying to locate anything within their database.
- IRD has multiple ways to browse and search the data within their database. They also have a number of tools that make it convenient to refine and analyze the search as well as save the data you are working on to your "workbench" so you can come back to it later.
- 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.
