BioCreative III interactive task: an overview
Abstract Background The BioCreative challenge evaluation is a community-wide effort for
evaluating text mining and information extraction systems applied to the biological domain …
evaluating text mining and information extraction systems applied to the biological domain …
Concept annotation in the CRAFT corpus
M Bada, M Eckert, D Evans, K Garcia, K Shipley… - BMC …, 2012 - Springer
Background Manually annotated corpora are critical for the training and evaluation of
automated methods to identify concepts in biomedical text. Results This paper presents the …
automated methods to identify concepts in biomedical text. Results This paper presents the …
What makes a gene name? Named entity recognition in the biomedical literature
U Leser, J Hakenberg - Briefings in bioinformatics, 2005 - academic.oup.com
The recognition of biomedical concepts in natural text (named entity recognition, NER) is a
key technology for automatic or semi-automatic analysis of textual resources. Precise NER …
key technology for automatic or semi-automatic analysis of textual resources. Precise NER …
Comparative analysis of regulatory patterns in bacterial genomes
MS Gelfand, PS Novichkov, ES Novichkov… - Briefings in …, 2000 - academic.oup.com
Recognition of transcription regulatory sites in bacterial genomes is a notoriously difficult
problem. There are no algorithms capable of making reliable predictions even for well …
problem. There are no algorithms capable of making reliable predictions even for well …
High-performance gene name normalization with GeNo
Motivation: The recognition and normalization of textual mentions of gene and protein
names is both particularly important and challenging. Its importance lies in the fact that they …
names is both particularly important and challenging. Its importance lies in the fact that they …
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature
M Arguello Casteleiro, G Demetriou, W Read… - Journal of biomedical …, 2018 - Springer
Background Automatic identification of term variants or acceptable alternative free-text terms
for gene and protein names from the millions of biomedical publications is a challenging …
for gene and protein names from the millions of biomedical publications is a challenging …
[PDF][PDF] Constructing Evaluation Corpora for Automated Clinical Named Entity Recognition.
We report on the construction of a gold-standard dataset consisting of annotated clinical
notes suitable for evaluating our biomedical named entity recognition system. The dataset is …
notes suitable for evaluating our biomedical named entity recognition system. The dataset is …
Developing a standard for de-identifying electronic patient records written in Swedish: precision, recall and F-measure in a manual and computerized annotation trial
S Velupillai, H Dalianis, M Hassel… - International journal of …, 2009 - Elsevier
BACKGROUND: Electronic patient records (EPRs) contain a large amount of information
written in free text. This information is considered very valuable for research but is also very …
written in free text. This information is considered very valuable for research but is also very …
iProLINK: an integrated protein resource for literature mining
The exponential growth of large-scale molecular sequence data and of the PubMed
scientific literature has prompted active research in biological literature mining and …
scientific literature has prompted active research in biological literature mining and …
Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database
Manual curation has long been used for extracting key information found within the primary
literature for input into biological databases. The human immunodeficiency virus type 1 (HIV …
literature for input into biological databases. The human immunodeficiency virus type 1 (HIV …