ASBMB Today, February 2003
Making Keyword Searches Work Better, KWIC-ly

[In early 2002, ASBMB Today introduced the new "portal" site from Stanford's HighWire Press, which allows you to search all of Medline plus 340 journals' full-text at once -- including the JBC, of course! We began a monthly series of short articles highlighting tools or features of this new site for researchers' sore eyes. The new site is at http://highwire.stanford.edu ]

We could pretend that keyword searches of full text are an excellent tool for finding the specific articles you need -- since keyword searches are just about the only tool most search systems give you! - but often a searcher is faced with thousands of search results in response to a keyword search because systems like PubMed index over 12 million article abstracts, and the HighWire Portal indexes all those abstracts plus the full text of over a million articles as well. But there is help for those who have to look for the needle in the haystack!

The HighWire Portal at http://highwire.stanford.edu has recently added some tools to help you spot the needles in the haystack of a large result. The new tools take advantage of the recognition ability we all have -- "I know it when I see it!" -- by augmenting the "recall" of the keywords to do a search, with the recognition of seeing just the right use of a term in the context of a sentence or phrase. These tools are helpful when a scientific term used in a keyword search is ambiguous or multi-faceted, or when you are interested in only one aspect of many uses of that term; the tools are also useful when you are doing broad subject searches and can't provide very specific keywords.

The new tools are called "KWIC" -- showing your search "keywords in context" -- and "Instant Index" -- which "clusters" items in your search results around major concepts. KWIC is shown in the first figure; here you see a search for the keywords "cytochrome oxidase" which returned over 13,000 citations. An Instant Index for a search on the term "mercury" is shown in the second figure.

KWIC

You can easily see from the example how KWIC can help you recognize articles that use your search terms in a relevant way in a sentence. Each citation in a search result will typically show you significant parts of the first two sentences in which your search terms are found in that citation. Not only can KWIC help you spot relevant results, but it can suggest additional terms or phrase-search criteria that you can use to narrow your result.

FIGURE 1

Instant Index

The Instant Index is a more subtle -- and potentially more helpful -- new feature. Each search that retrieves more than 50 items will have a hyperlink that will take you to the Instant Index built from the top 500 items in your search result. You can see the Instant Index hyperlink in the middle of the first figure; it is the last link in the box under the Search Results heading; click on that link, and a new window like the one in the second figure will open up. The left side of the new window shows the index to your results; like the index in the back of the book, it contains concepts and sub-concepts. To the right of each concept is the number of citations that match. If you click on the concept name, the right side of the window will change to display the citations for that concept; in the example, we've clicked on "Cell; Proteins" and are looking at a list of 36 citations for that concept that contain the keyword "mercury" from our search. If you click on the "+" sign, it will show you the concepts indexed under another concept.

FIGURE 2

The technology that brings you the Instant Index is still being tuned, and we'd appreciate your feedback on whether and where you find it most helpful, and where you find otherwise. You may also find some interesting tests and uses for it. For example: try a search for your own papers, and see whether the clusters of topics match what you think you've written about! Or, if you have to deliver a lecture (or a course!) on a topic, you might do a search for that topic as a keyword search - perhaps asking for "review articles only" -- and then see whether the resulting Instant Index suggests possible topics for your lecture outline.

The 2002 and 2003 issues of ASBMB Today covered topics about the new HighWire Portal. The articles are online at