-
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 ...
-
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...
-
Article
Open AccessOverview of BioCreative II gene normalization
The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a cha...
-
Article
Open AccessConcept recognition for extracting protein interaction relations from biomedical text
Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasin...
-
Article
Nuclear entry of active caspase-3 is facilitated by its p3-recognition-based specific cleavage activity
As a critical apoptosis executioner, caspase-3 becomes activated and then enters into the nucleus to exert its function. However, the molecular mechanism of this nuclear entry of active caspase-3 is still unkn...
-
Article
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 ...
-
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...
-
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...
-
Article
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...
-
Article
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 ...
-
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...
-
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...
-
Article
Open AccessDIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks
An orphan disease is any disease that affects a small percentage of the population. Orphan diseases are a great burden to patients and society, and most of them are genetic in origin. Unfortunately, our curren...
-
Article
How user intelligence is improving PubMed
Machine learning and natural language processing methods are applied to learn from PubMed searches and improve user experience.
-
Article
Open AccessDetecting visually significant cataract using retinal photograph-based deep learning
Age-related cataracts are the leading cause of visual impairment among older adults. Many significant cases remain undiagnosed or neglected in communities, due to limited availability or accessibility to catar...
-
Article
Open AccessAuthor Correction: Detecting visually significant cataract using retinal photograph-based deep learning