3 research outputs found
Ambiguity of human gene symbols in LocusLink and MEDLINE: creating an inventory and a disambiguation test collection
Genes are discovered almost on a daily basis and new names have to be
found. Although there are guidelines for gene nomenclature, the naming
process is highly creative. Human genes are often named with a gene symbol
and a longer, more descriptive term; the short form is very often an
abbreviation of the long form. Abbreviations in biomedical language are
highly ambiguous, i.e., one gene symbol often refers to more than one
gene.Using an existing abbreviation expansion algorithm,we explore MEDLINE
for the use of human gene symbols derived from LocusLink. It turns out
that just over 40% of these symbols occur in MEDLINE, however, many of
these occurrences are not related to genes. Along the process of making an
inventory, a disambiguation test collection is constructed automatically
Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes
MOTIVATION: The advent of high-throughput experiments in molecular biology creates a need for methods to efficiently extract and use information for large numbers of genes. Recently, the associative concept space (ACS) has been developed for the representation of information extracted from biomedical literature. The ACS is a Euclidean space in which thesaurus concepts are positioned and the distances between concepts indicates their relatedness. The ACS uses co-occurrence of concepts as a source of information. In this paper we evaluate how well the system can retrieve functionally related genes and we compare its performance with a simple gene co-occurrence method. RESULTS: To assess the performance of the ACS we composed a test set of five groups of functionally related genes. With the ACS good scores were obtained for four of the five groups. When compared to the gene co-occurrence method, the ACS is capable of revealing more functional biological relations and can achieve results with less literature available per gene. Hierarchical clustering was performed on the ACS output, as a potential aid to users, and was found to provide useful clusters. Our results suggest that the algorithm can be of value for researchers studying large numbers of genes. AVAILABILITY: The ACS program is available upon request from the authors
Using contextual queries
Search engines generally treat search requests in isolation. The results
for a given query are identical, independent of the user, or the context
in which the user made the request. An approach is demonstrated that
explores implicit contexts as obtained from a document the user is
reading. The approach inserts into an original (web) document
functionality to directly activate context driven queries that yield
related articles obtained from various information sources