Search Engines, Genomics, Medical Literature: Tag Clouds come to PubMed via LigerCat

“… LigerCat is a search tool for NCBI’s PubMed that uses tag clouds to provide an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed, summing their MeSH descriptors and presenting them in a cloud, weighted by frequency “.

Except from:  http://ligercat.ubio.org/about#contact_us

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LigerCat is an abbreviation for Literature and Genomics Resource Catalog, which is a free PubMed search tool developed in 2009 as part of the Biology of Aging project at the MBLWHOI Library at the Woods Hole Marine Biological Laboratory.

LigerCat is great news for geneticists or anyone involved in translational research, a fairly effortless means of data mining for dynamic links to a very complex literature.

LigerCat can be used to search in several ways: 1) to locate and select a list of individual journal titles indexed in PubMed, 2) search using terms from the National Library of Medicine’s Medical Subject Heading (MeSH) list, 3) search using keywords, 4) search on Genes found in the NCBI databases.

Following is a screenshot of the LigerCat start page:

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A screenshot of the “in process” retrieval process using LigerCat for the MeSH term “pancreatic neoplasms” and keyword term, “pain“,  is shown below.

Notice that LigerCat provides the searcher two choices for getting the results, which could take a few minutes: the option of simply waiting a few moments for the search to execute, or save the shortened URL of the search-strategy to revisit the results at a later time.  That’s nice!

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.Here is a screenshot of the retrieval from LigerCat – which took about 20 seconds to execute:

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.Next:  I used LigerCat do a Gene Search for specific protein sequences.  This is how the site authors described the process of searching genes:

” LigerCat is performing a live BLAST to find similar sequences to your query. Once the sequences are identified, LigerCat will use its indices to map the genes into a set of PubMed articles that reference those genes, and extract all the MeSH terms for those articles. “

” When all the MeSH descriptors are gathered, LigerCat uses a statistical model to identify relevant descriptors, then sums them by frequency to create the MeSH tag clouds. “

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I went to NCBI to  find the Entrez Protein page and then searched FASTA for P53 and Homo Sapiens.  The search statement I found looked like this:

>gi|14993572|gb|AAK76358.1| P53 [Homo sapiens]
VGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDS

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This string was copied-and-pasted into the LigerCat Gene search box for the following result:

All images above – Courtesy  of LigerCat – All rights reserved – Copyright 2009

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As a medical librarian, I think LigerCat is a great step forward — but because the value of information lies in the eye of the beholder — I’ll wait to hear the opinions of geneticists and research scientists as they weigh in on this new search engine.

For a different example of using this resource, see this link from the blog Biology of Aging, dated Aug 21 2009.