Bioinformatics Hubs on the Web

Background

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 National Center for Biotechnology Information (NCBI)

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 Entrez search of NCBI allows a search across all databases:  Genome, Gene, Protein, Nucleotide, even PubMed
• NCBI gives you real-time results for all searches
• NCBI’s multi-database management allows you to go from one database to another without having to re-enter your search terms

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.

Go to http://www.ncbi.nlm.nih.gov/

Navigation Hints

There are shortcuts and menus on all NCBI database pages:

• Top-of-page menu bar shortcuts will take you to other major NCBI tools
• Right-side menus and links from records will take you to related records
• To get back to the NCBI home page at any time, just click the NCBI logo in the upper left of any screen

Using MyNCBI

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.

• Find the MyNCBI link in the upper right corner of any NCBI page.  Click this link.
• If you have a MyNCBI account, sign in.  If you don't have an account, register for one.  It is free.
  • As of May 2010, you can now log in to MyNCBI with your NU NetID and password, eRA ID and password or even your Google ID and password using the Sign in via Partner Organization feature
• Use My Collections to save records from different databases and share them with collaborators

Start with a General Search

Search terms can be entered just as in PubMed: 

• You can use Boolean terms (AND, OR, NOT)
• Use quotation marks to define a phrase
• You can supply qualifiers in square brackets [au] = author, [organism], etc.

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)

• Add additional search terms
• Limit current search terms by field names
• View the square bracketed field name operators used in specific NCBI databases
• Limit using checkboxes to species, cellular structures or entry dates

• Add terms to your query
• Use the pull-down menu to view fields available to search
• Use the Index feature to see suggested terms matching your query
• Use Preview to see numbers of results before running the search

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.

• If you want to save a particular record, use MyNCBI features to save the record to My Collections
• Or download a sequence file to your computer
  • You can change the format to FASTA and save to MyCollections
  • Or, for mRNA records, you can choose Coding Sequences from the Send menu and download to your computer

Summary of Searching NCBI Databases

• Use the general cross-database search when you want to see results in multiple databases for your molecule of interest
• Use one database and apply limits to find specific information more efficiently
• Use links to related records in other databases from right-side links menus
• Use MyNCBI to save records or sequences

The European Bioinformatics Institute (EBI)

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 EB-eye search allows a search across all databases linked through the EBI 
• EBI's website contains links to some of the most-used sequence tools in the world (CLUSTAL, MUSCLE, BLAST, etc.)
• EBI’s multi-database management, like NCBI's allows you to go from one database to another without having to re-enter your search terms

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:

• Top-of-page menu bar shortcuts will take you to other major EBI tools
• To get back to the EMBL-EBI home page at any time, just click the EMBL-EBI logo in the upper left of any screen
• When clicking links to specific records in search results, it is recommended that you use right-click on your mouse (or COMMAND-click on a Mac) to open specific records in a new tab or window.  This will save you from hitting the “Back” button on your browser multiple times to get back to your search results

Start with a General Search   

• Enter search terms in the search box
• You can search the website or all databases from the EB-eye search box.
  • Alternately, you can use the pull-down menus or blue-green text links to go to specific types of database searches.
• Clicking on each category heading will take you to a summary page for results in those databases
• Expand or collapse any category by clicking on the red triangles next to category names
• Refine your results by typing more keywords to add to your search in the Refine your search: box

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.

• Light gray links at the top of results summary listings will take you to other results for your search term
• Click the entry number (or database accession number) to link to the record in that database
• Click the References links to see EBI listings for results in those databases for your terms

• Like NCBI, you can create a user account with Ensembl.  Look for the Log In/Register links at the upper right of Ensembl pages.
• Links to features in Ensembl entries are on the LEFT of the page, and these link menus are context-sensitive, so if you click on a transcript record in the main window, the links menu on the left will change
• Note the tabs at the top of the page to flip between chromosome and gene views
• You can export sequences using the Export Data menu on the left

Online Bioinformatics Resources Collection (OBRC)

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:
http://www.hsls.pitt.edu/guides/genetics/obrc/

• Search by phrase or by single keyword
• Use tabs to select searches of Databases/Tools, Articles or Web
  • The Databases/Tools search is the default and is the most useful search
• You can suggest new resources using links on the left of the page

Refining Search Results

• Choose to narrow a search by selecting a clustered subset of results or by using the text box to search within results
• Find citations for entries using Google Scholar (do not use Scopus button, since Northwestern does not subscribe to Scopus)
• Clicking on the link to the entry's title will take you to an information page for the entry

Benefits and Limitations of OBRC

• OBRC's clustering provides an extra level of easy search refinement
• OBRC's information pages are manually curated to provide extra keyword entry points
• Drawback:  some links to databases or tools may have expired, but curators work to remove "dead" links 

Bioinformatics Links Directory and BioMed Central Databases

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:
http://www.bioinformatics.ca/links_directory/index.php

• Hover your mouse over a category to see subcategories
• Links are based on expert recommendations, plus all listings in Nucleic Acids Research
• Includes computer (programming and scripting languages) and educational resources as well as molecular resources

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:

http://databases.biomedcentral.com/browsecatalog

Drawbacks of BioMed Central Databases

• The BMC site is a commercial site, so advertising appears on results pages
• Many "dead" links exist in the results