Textpresso for Neuroscience: Searching the Full Text of Thousands of Neuroscience Research Papers

Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. Here we describe Textpresso for Neuroscience, part of the core Neuroscience Information Framework (NIF). The Textpresso site currently consists of 67,500 full text papers and 131,300 abstracts. We show that using categories in literature can make a pure keyword query more refined and meaningful. We also show how semantic queries can be formulated with categories only. We explain the build and content of the database and describe the main features of the web pages and the advanced search options. We also give detailed illustrations of the web service developed to provide programmatic access to Textpresso. This web service is used by the NIF interface to access Textpresso. The standalone website of Textpresso for Neuroscience can be accessed at http://www.textpresso.org/neuroscience

Distributed Information Retrieval using Keyword Auctions

This report motivates the need for large-scale distributed approaches to information retrieval, and proposes solutions based on keyword auctions

GPERF : a perfect hash function generator

gperf is a widely available perfect hash function generator written in C++. It automates a common system software operation: keyword recognition. gperf translates an n element user-specified keyword list keyfile into source code containing a k element lookup table and a pair of functions, phash and in_word_set. phash uniquely maps keywords in keyfile onto the range 0 .. k - 1, where k >/= n. If k = n, then phash is considered a minimal perfect hash function. in_word_set uses phash to determine whether a particular string of characters str occurs in the keyfile, using at most one string comparison.This paper describes the user-interface, options, features, algorithm design and implementation strategies incorporated in gperf. It also presents the results from an empirical comparison between gperf-generated recognizers and other popular techniques for reserved word lookup

Learning to Extract Keyphrases from Text

Many academic journals ask their authors to provide a list of about five to fifteen key words, to appear on the first page of each article. Since these key words are often phrases of two or more words, we prefer to call them keyphrases. There is a surprisingly wide variety of tasks for which keyphrases are useful, as we discuss in this paper. Recent commercial software, such as Microsoft?s Word 97 and Verity?s Search 97, includes algorithms that automatically extract keyphrases from documents. In this paper, we approach the problem of automatically extracting keyphrases from text as a supervised learning task. We treat a document as a set of phrases, which the learning algorithm must learn to classify as positive or negative examples of keyphrases. Our first set of experiments applies the C4.5 decision tree induction algorithm to this learning task. The second set of experiments applies the GenEx algorithm to the task. We developed the GenEx algorithm specifically for this task. The third set of experiments examines the performance of GenEx on the task of metadata generation, relative to the performance of Microsoft?s Word 97. The fourth and final set of experiments investigates the performance of GenEx on the task of highlighting, relative to Verity?s Search 97. The experimental results support the claim that a specialized learning algorithm (GenEx) can generate better keyphrases than a general-purpose learning algorithm (C4.5) and the non-learning algorithms that are used in commercial software (Word 97 and Search 97)