Biomedical subjects

Barend Mons

Publications and source records attributed to Barend Mons.

5 recordsLinked to original sources

PubMed2004

Contextual annotation of web pages for interactive browsing.

With the information on the World Wide Web and in specialized databases exploding, researchers and physicians are in dire need to browse efficiently though the large corpus of information resources in their field of interest. The focus is not any longer to find everything related to your interest, but it shifts to zooming in, based on context and expanding again in neighboring knowledge domains. This paper describes an attempt to develop a completely new, interactive way of browsing distributed corpora of information without the need for multiple different queries in different information resources. Classical search engines generally treat search requests in isolation. The results for a given query are identical, and do not automatically take on board the context in which the user made the request. The system described here explores implicit contexts as obtained from the document that the user is reading. The new approach merges the searching and browsing into one combined "read-and-search" mode and alleviates the shift users are normally forced to between searching and reading.

Hypermedia↗

PubMed2003

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.

Algorithms↗

PubMed2003

Mining microarray datasets aided by knowledge stored in literature.

DNA microarray technology produces large amounts of data. For data mining of these datasets, background information on genes can be helpful. Unfortunately most information is stored in free text. Here, we present an approach to use this information for DNA microarray data mining.

Databases, Genetic↗

PubMed2003

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.

Databases as Topic↗

PubMed2002

Research for research: tools for knowledge discovery and visualization.

This paper describes a method to construct from a set of documents a spatial representation that can be used for information retrieval and knowledge discovery. The proposed method has been implemented in a prototype system and allows the researcher to browse interactively and in real-time a network of relationships obtained from a set of full text articles. These relationships are combined with the potential relationships between concepts as defined in the UMLS semantic network. The browser allows the user to select a seed term and find all related concepts, to find a path between concepts (hypothesis testing), and to retrieve the references to documents or database entries that support the relationship between concepts.

Biomedical Research↗