NIF: Better Literature Search

Over the past couple of days we’ve looked at the data aggregating capabilities of the Neuroscience Information Framework (NIF). What about literature search? Is there any reason you should move from PubMed or Google Scholar to NIF?

NIF literature search results for 'barrel cortex'.
Figure 1. NIF literature search results for “barrel cortex.” NIF provides four tabs on the literature search results page.

NIF provides the results of a standard PubMed search under the PubMed tab. In addition, NIF provides Open Access Literature, Neuronal Morphology, and Neuroscience Literature tabs. The Open Access Literature tab provides a convenient way to go directly to relevant articles that are freely available over the Internet. The Neuronal Morphology tab provides quick access to papers associated with digitally reconstructed neurons available through The Neuroscience Literature tab lists papers returned based on a full text search using your search words. This could arguably the most valuable additional literature search service that NIF provides.

Unfortunately the majority of papers are still published in journals that are not open access. Because of legal restrictions, NIF is only able to provide full text search services on a subset of papers that include those published in open access journals and those published in the Journal of Neuroscience. NIF provides a complete list of journals searched here.

There is a large literature surrounding the amyloid beta protein. Recent evidence suggests that amyloid beta 42 is particularly important in Alzheimer’s disease. What if we only want papers that used amyloid beta 42 in their research? I decided to run a quick test of the full text search capabilities by typing the following “amyloid beta 42” into the NIF home page search box and clicking on the search icon. That didn’t even kick off a search but took me to a blank NEUROLEX page (under neurons and brain regions). The same thing happened when I typed in “amyloid-beta 42” but “abeta42” worked.

Note: All of the variants above worked when I typed them into the search box returned by the initial search from home page (like at top left in Figure 1 above). Surprisingly, searches for “amyloid beta 42” and “amyloid-beta 42” each resulted in zero hits under “Neuroscience Literature.”

A search for “abeta42” returned 161 papers under Neuroscience Literature. I checked all the articles in the first three pages and the last page and they all included abeta42 in the title or the abstract so I’m not sure if we’ve located additional articles that, for example, may have only mentioned the 42 amino acid peptide in its methods section. Also, it doesn’t look like synonyms are being used in the search.

Other related blog posts:

NIF: When You’re Looking for Neuroscience Resources Including Data

NIF: Neurons, Models, and Grants

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