The Galter Library teaches a related class called Bioinformatics Hubs on the Web. See our Classes schedule for the next available offering. If this class is not on our upcoming schedule, it is still available to you or your group by request.
There are hundreds of tools and databases available on the Web for identifying and analyzing biomolecules. These bioinformatics resources have diverse and specific uses. Some tools and databases are more reliable, more current, or more accepted by the research community than others. With this abundance of resources available, it is hard for users to find the best tools and databases for their research needs.
There are some sites on the Web that organize and link to many of these bioinformatics resources. These sites are named "hubs" because they provide centralized points of access.
This guide provides descriptions on the location and use of a few of the most useful bioinformatics hubs. This guide is not intended to be exhaustive in its inclusion of sites, and users are encouraged to explore tools and databases and discover which sites work best for their research and information needs.
The NCBI was founded in 1988 as a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). The NCBI website contains several free computerized information-processing methods of biological information.
NCBI conducts research on biomedical problems at the molecular level using mathematical and computational methods, and also provides numerous free databases and molecular search tools, with extensive support documentation for these resources.
Why use NCBI?
The Galter Library teaches a class entitled Introduction to NCBI's Bioinformatics Resources. The class is taught approximately twice a year, but users can schedule sessions of this class by request for individuals or groups. There is also a Galter guide to the NCBI on our website. The NCBI class and guide provide more detail on individual NCBI databases than you will find in this guide on bioinformatics hubs.
There are shortcuts and menus on all NCBI database pages:
Using the features available in MyNCBI is a good practice to save PubMed searches, nucleotide sequences, even BLAST queries. This is especially useful if you have created a complex search with multiple search terms.
Start with a General Search
Search terms can be entered just as in PubMed:
Refining Searches with Limits and Indexing
Within individual NCBI databases, you can refine searches with limits and indexing. The types of limits and fields are dependent on the database you are searching in.
The Limits Tab (Entrez Gene)
Navigating Using Links
NCBI updates pages and database record displays quite frequently. Links to related records will link from features within the record entry itself, but links to related records can also be found on the right side of the page. Links may look different in different NCBI databases.
Left: Links from Entrez Gene Right: Links from Entrez Nucleotide
Accessing Limits from other NCBI Databases
In some NCBI databases, such as PubMed, Entrez Nucleotide, Protein and many others, the limits and indexes have been updated and are now accessible from small text links next to the search box in those databases,
and the limits page looks much different, with pull-down menus for many of the choices (instead of checkboxes).
To access the indexing function from these databases, click the Advanced Search text link.
Now you can use the Search Builder to add terms and specify fields in which these terms are searched. Click the Show index link to view the index of suggested terms for your field search.
Pay careful attention to where NCBI places parentheses after you add terms to your search. You may have to do some adjusting of parentheses to get the best search results.
Saving or Downloading Records
After you have run your search, you can change the Display Settings and save records using drop-down menus at the top of the record.
Summary of Searching NCBI Databases
The EBI was founded in 1992 as the result of an effort to integrate the EMBL Nucleotide Sequence Data Library (now known as EMBL-Bank), with the major sequencing efforts at the Sanger Institute. The EMBL-EBI is located in Hinxton, U.K.
EBI conducts research in sequencing and computational methods, and the website serves as a node for major European molecular databases such as EMBL-Bank, the Ensembl Genome pages, PDB, UniProt, Interpro and Array Express. EBI also provides education and training in the use of their resources.
Why use EBI?
The Galter Library teaches a class entitled EBI's Bioinformatics Resources for Researchers. The class is taught approximately twice a year, but users can schedule sessions of this class by request for individuals or groups. The EBI class provides more detail on individual NCBI databases than you will find in this guide on bioinformatics hubs.
Accessing EBI’s Cross-Database Search Page, EB-eye
Go to http://www.ebi.ac.uk/
Navigating Hints & Tips
There are shortcuts and menus on EBI database pages:
Start with a General Search
Unlike NCBI databases, not all of the databases linked through EBI searches are based at EMBL-EBI, so they all have different appearances and thus may have different linking or navigating features.Click the link for a database or category in your results to see other EBI record links.
Links in Ensembl
The OBRC is managed by the Health Sciences Library System at the University of Pittsburgh. It provides a searchable interface to databases and tools featured in the Nucleic Acids databases and Web server editions, with convenient clustering functionality.
Access the OBRC at:
Refining Search Results
Benefits and Limitations of OBRC
For users who prefer to browse databases and tools by category, two sites provide categorized listings of resources.
The Bioinformatics Links Directory
The Bioinformatics Links Directory is located at:
BioMed Central Databases
For users who want databases with more of a clinical focus, the BioMed Central Databases may be a good choice. Databases are categorized by disease or condition, plus BMC maintains an online image catalog.
Access the catalog of BMC databases at:
Drawbacks of BioMed Central Databases