Currently biomedical literature is largely disconnected from its metadata. While there are freely accessible centralised metadata repositories the publications themselves are split among a large number of repositories. We address this problem by harvesting freely accessible biomedical publications from the Web and integrating them with the corresponding metadata. The system involves title recognition applied on the harvested publications using knowledge-based algorithm and a fuzzy match between the extracted title and the metadata records using edit distance metric. So far we were able to locate +300.000 publications on the Web and achieve +96% precision and nearly 85% recall on a random sample of 250 documents harvested from the Web.

We present a system for extracting citation data from Pubmed-indexed papers available online based on a knowledge-based algorithm. We achieve nearly 92% accuracy on a sample of 156 papers from 78 different journals. We describe the issues faced, our approach, the results achieved and the future directions of our work.

UNLABELLED: To allow efficient and systematic retrieval of statements from Medline we have developed EBIMed, a service that combines document retrieval with co-occurrence-based analysis of Medline abstracts. Upon keyword query, EBIMed retrieves the abstracts from EMBL-EBI's installation of Medline and filters for sentences that contain biomedical terminology maintained in public bioinformatics resources. The extracted sentences and terminology are used to generate an overview table on proteins, Gene Ontology (GO) annotations, drugs and species used in the same biological context. All terms in retrieved abstracts and extracted sentences are linked to their entries in biomedical databases. We assessed the quality of the identification of terms and relations in the retrieved sentences. More than 90% of the protein names found indeed represented a protein. According to the analysis of four protein-protein pairs from the Wnt pathway we estimated that 37% of the statements containing such a pair mentioned a meaningful interaction and clarified the interaction of Dkk with LRP. We conclude that EBIMed improves access to information where proteins and drugs are involved in the same biological process, e.g. statements with GO annotations of proteins, protein-protein interactions and effects of drugs on proteins. AVAILABILITY: Available at http://www.ebi.ac.uk/Rebholz-srv/ebimed

SUMMARY: The EMBL Nucleotide Sequence Database, maintained at the European Bioinformatics institute, is Europe's primary nucleotide sequences database. Its entries are subject to changes, but only the most recent versions are preserved in the database. The EMBL Sequence Version Archive is a new publicly available database retaining also the earlier versions of these entries. AVAILABILITY: http://www.ebi.ac.uk/embl/sva/

This paper describes a system of generally applicable index files provided on the EMBL sequence databases CD-ROM to facilitate the development of front-end software to the sequence databases available on this CD-ROM. The index files are used by a new versatile and user-friendly database retrieval program for the Apple Macintosh, EMBL-Search, which allows the easy construction of complex database queries. EMBL-Search utilizes cross-reference information contained in the databases to support navigation between different information resources. The ability to run EMBL-Search on a local computer network accessing a shared database CD-ROM makes its use particularly cost effective.

An algorithm that allows rapid searching of nucleic acid sequences based on pregenerated index files is described. The programs and index files for searching the entire EMBL nucleotide sequence collection are being distributed on the EMBL Data Library's CD-ROM.