BlogForever: D3.1 Preservation Strategy Report

This report describes preservation planning approaches and strategies recommended by the BlogForever project as a core component of a weblog repository design. More specifically, we start by discussing why we would want to preserve weblogs in the first place and what it is exactly that we are trying to preserve. We further present a review of past and present work and highlight why current practices in web archiving do not address the needs of weblog preservation adequately. We make three distinctive contributions in this volume: a) we propose transferable practical workflows for applying a combination of established metadata and repository standards in developing a weblog repository, b) we provide an automated approach to identifying significant properties of weblog content that uses the notion of communities and how this affects previous strategies, c) we propose a sustainability plan that draws upon community knowledge through innovative repository design

Large-scale event extraction from literature with multi-level gene normalization

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license

Mapping Subsets of Scholarly Information

We illustrate the use of machine learning techniques to analyze, structure, maintain, and evolve a large online corpus of academic literature. An emerging field of research can be identified as part of an existing corpus, permitting the implementation of a more coherent community structure for its practitioners.Comment: 10 pages, 4 figures, presented at Arthur M. Sackler Colloquium on "Mapping Knowledge Domains", 9--11 May 2003, Beckman Center, Irvine, CA, proceedings to appear in PNA

A cascaded approach to normalising gene mentions in biomedical literature

Linking gene and protein names mentioned in the literature to unique identifiers in referent genomic databases is an essential step in accessing and integrating knowledge in the biomedical domain. However, it remains a challenging task due to lexical and terminological variation, and ambiguity of gene name mentions in documents. We present a generic and effective rule-based approach to link gene mentions in the literature to referent genomic databases, where pre-processing of both gene synonyms in the databases and gene mentions in text are first applied. The mapping method employs a cascaded approach, which combines exact, exact-like and token-based approximate matching by using flexible representations of a gene synonym dictionary and gene mentions generated during the pre-processing phase. We also consider multi-gene name mentions and permutation of components in gene names. A systematic evaluation of the suggested methods has identified steps that are beneficial for improving either precision or recall in gene name identification. The results of the experiments on the BioCreAtIvE2 data sets (identification of human gene names) demonstrated that our methods achieved highly encouraging results with F-measure of up to 81.20%