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