Review of BIND

Review of BIND

Title: BIND - The Biomolecular Interaction Network Database (version 2.0)

URL: http://www.binddb.org/

Date Reviewed:05/21/01

Description:

The Biomolecular Interaction Network Database (BIND) is a database designed to store full descriptions of interactions, molecular complexes and pathways. The website claims that it serves as a resource for identifying known interaction between proteins, chemicals, and physical processes. It also claims to be a useful resource for investigating taxonomic differences in molecular interactions. Basically, the BIND site is a portal to other databases, and is merely a different front end to information in the NCBI PUBMED and BLAST databases. BIND is not as usable or usefull as NCBI.

Strengths:
Search Engine on the front page is the first thing you see. Sometimes search engines can be hard to find. The tabs across the top are usefull in immediately seeing how the site is organized. The organization is again shown at the bottom in text format. This kind of redundancy enhances usability.
The site attempts to serve as a portal to many other databases. There are a huge list of related links.

Weaknesses:
It took me a long time to find the graphic visualiztion of interactions. The search of the database was useless, only the browse function was usefull. The browse function requires the user to manually search through thousands of links.

The visualizations don't work in some interaction citations.

Search Engine is text based and the advanced search is not any more advanced than the basic search, only adding 3 limits and still requiring a text input. The text input causes the user to guess the format of the entries in the database, ie not user friendly.

As the information comes in from high throughput screening, as they claim, they need to have different ways to access it and analyze it. I would rather use NCBI than this page.

The main page makes the site look like a gigantic portal with tons of information. However, this is not the case. The links on the left hand side of the page are useless and could be condensed into a single link called "about us" and then goes to a section with information about the organization, jobs, sponsors, publications by them, etc. In conclusion the site needs to decide what is its primary audience and purpose. Why not just use Pubmed?

The related links are too extensive, and should be catagorized not alphabetized. The other links section is sparse (1 link). This indicates to me that the site is not currated well.

Comprehensiveness:
STAT6 could not be found
JNK could not be found

JUN was found, however I got no information about specific interactions. Instead I got
8 links to the same reference in NCBI.

They describe their database format very well in several different locations, under the about link in the database section.

INTERACTIONS
5803
COMPLEXES
41
PATHWAYS
6

The search in a BIND BLAST is not user friendly. THe user has to have the protein sequence of the protein they are interested in. It would be better to have this as one of many optional input formats. I don't really understand why someone would want to use this program instead of NCBI blast.

Timeliness:
Newest Reference is this month due to the fact that this site links searches directly to NCBI.

Expired Links
Some of the add, change links in the database page don't work.
When you go to development and then database, you get an error.

Ease of Use:
The links are too complex on the front page and on the database page. They use words like "add and change" for links on the database page, which makes me feel like I have to learn something to use the page. They should stick to standard formats for search and retrieval.

Redundancy
The redundancy helps in the use, and the graphic interface with the side frame and top jump bar is good. The bad side of the redundancy is that the search applies to the database page only. There should be a site search. It's hard for me to tell if I have seen everything they have.

When you go to the Database page, you can get directly back to the homepage through a link or the back button, but you can when you go to the prebind page.

The download link is useless unless you are a computer programmer.

Responsiveness:
Server is Fast

Similar or Related Sites:
Too many to mention, see: Related Databases
This is actually the most useful part of the website.

Overall Evaluation: 2 stars

Reviewer: John Pratt

Email: jpratt01@tufts.edu