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Open Access Open Badges Methodology article

A graph-search framework for associating gene identifiers with documents

William W Cohen123* and Einat Minkov2

Author Affiliations

1 Department of Machine Learning, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA

2 Language Technology Institute, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA

3 Center for Bioimage Informatics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA

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BMC Bioinformatics 2006, 7:440  doi:10.1186/1471-2105-7-440

Published: 10 October 2006



One step in the model organism database curation process is to find, for each article, the identifier of every gene discussed in the article. We consider a relaxation of this problem suitable for semi-automated systems, in which each article is associated with a ranked list of possible gene identifiers, and experimentally compare methods for solving this geneId ranking problem. In addition to baseline approaches based on combining named entity recognition (NER) systems with a "soft dictionary" of gene synonyms, we evaluate a graph-based method which combines the outputs of multiple NER systems, as well as other sources of information, and a learning method for reranking the output of the graph-based method.


We show that named entity recognition (NER) systems with similar F-measure performance can have significantly different performance when used with a soft dictionary for geneId-ranking. The graph-based approach can outperform any of its component NER systems, even without learning, and learning can further improve the performance of the graph-based ranking approach.


The utility of a named entity recognition (NER) system for geneId-finding may not be accurately predicted by its entity-level F1 performance, the most common performance measure. GeneId-ranking systems are best implemented by combining several NER systems. With appropriate combination methods, usefully accurate geneId-ranking systems can be constructed based on easily-available resources, without resorting to problem-specific, engineered components.