OntoLearn-clj
Clojure XML
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src/indications
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README.md
parse.clj
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redis.conf

README.md

This is work in process and getting up to speed with Clojure. Definitely not something you'd want to use in production.

Clojure PubMed to LibSVM utility

Collection of utilities for retrieving and processing PubMed files into to LibSVM data format.

Used for matching ontologies to MeSH annotated articles and inferring labels for those not annotated using Support Vector Machines with linear kernel.

Specifically used with Human Disease Ontology and the disease tree of MeSH 2013 (transform available as xslt in resources). The mesh-owl xslt has some kinks, specifically it doesn't traverse the tree all that well, so use common sense. Parsed a large-isch (5 GB) collection Randomized Clinical Trials.

Usage

  • import/retrieve contains a wrapper for downloading XML Records based on a query to disk.
  • import/process contains utilities for writing fields in PubMed XML files to a Redis back-end by using Xpath.
  • pre-process includes stop-word filtering and stemming using Lucene on article abstracts
  • core includes code to write to .libsvm files

License

Copyright (c) 2012, Joel Kuiper All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the organization nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL JOEL KUIPER BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.