10 Result(s)
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Article
Open AccessMeSH Now: automatic MeSH indexing at PubMed scale via learning to rank
MeSH indexing is the task of assigning relevant MeSH terms based on a manual reading of scholarly publications by human indexers. The task is highly important for improving literature retrieval and many other ...
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Article
Open AccessIdentifying named entities from PubMed® for enriching semantic categories
Controlled vocabularies such as the Unified Medical Language System (UMLS®) and Medical Subject Headings (MeSH®) are widely used for biomedical natural language processing (NLP) tasks. However, the standard te...
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Article
Open AccessPathway-based drug repositioning using causal inference
Recent in vivo studies showed new hopes of drug repositioning through causality inference from drugs to disease. Inspired by their success, here we present an in silico method for building a causal network (Cause...
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Article
Open AccessThe gene normalization task in BioCreative III
We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 full...
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Article
Open AccessBioCreative III interactive task: an overview
The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of bi...
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Open AccessOverview of the BioCreative III Workshop
The overall goal of the BioCreative Workshops is to promote the development of text mining and text processing tools which are useful to the communities of researchers and database curators in the biological s...
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Open AccessThe Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional ...
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Open AccessA context-blocks model for identifying clinical relationships in patient records
Patient records contain valuable information regarding explanation of diagnosis, progression of disease, prescription and/or effectiveness of treatment, and more. Automatic recognition of clinically important ...
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Article
Open AccessSemantic role labeling for protein transport predicates
Automatic semantic role labeling (SRL) is a natural language processing (NLP) technique that maps sentences to semantic representations. This technique has been widely studied in the recent years, but mostly w...
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Article
Open AccessOpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a ...
