BioText – a search engine for open access figures

At the ISMB conference we met Anna Divoli, a postdoc at the University of
California, Berkeley, who showed us the BioText Search Engine, which she was presenting as a poster, and has recently published.

BioText Search Engine logo

came across it briefly earlier this month thanks to the blog of medical
librarian David Rothman, who described it as "A supercool way to search PubMed
Central", which is a
pretty good description!

It is part of the text mining BioText project, and goes beyond the abstract searching in MEDLINE
seen previously to extend searching
to the figure legends of Open Access journals in PubMed Central.

As the homepage of PubMed Central
notes, "All the articles in PMC are free (sometimes on a delayed basis). Some
journals go beyond free, to Open Access". Because Open Access explicitly
allows the reuse of the content of the articles in these journals (which include
all 170+ BioMed Central journals) this has allowed the BioText people to
create a search engine that allows keyword searching of abstracts, figure
legends, titles and authors, returning results sorted by date and relevance, and
in two formats: abstracts with figure thumbnails and
or figure
legends with thumbnails.


example, by running a ‘Captions’ search for "Drosophila eye", I quickly found
these three images from
BMC Developmental
, Journal of Biology and
BMC Cell

Verdier et al., BMC Developmental Biology 2006    Junger et al., Journal of Biology 2003    Minakhina et al., BMC Cell Biology 2005

Anna hinted at upcoming functions such as returning snippets
that match the search terms from the full text of the article (much as Google
does). We look forward to these further
developments, and we’d like to thank Anna, Marti Hearst and the others on the
BioText team for developing such a useful and user friendly tool.
is a great example of how Open Access allows others to make further use of
published work, in ways that the authors or publishers had not

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