Web applications
Description
PubTator is a text-mining tool for annotating the entire PubMed articles with key biological entities (e.g. genes & diseases) and is available through both Web and API access.
PubTator is a text-mining tool for annotating the entire PubMed articles with key biological entities (e.g. genes & diseases) and is available through both Web and API access.
Description
LitVar is a semantic search engine for linking genomic variant data in PubMed and PMC
LitVar is a semantic search engine for linking genomic variant data in PubMed and PMC
Description
LitCovid is a literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus, first created in February 2020.
LitCovid is a literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus, first created in February 2020.
Description
LitSuggest is a web-based system for literature triage and document classification using AI and machine learning.
LitSuggest is a web-based system for literature triage and document classification using AI and machine learning.
Description
LitSense helps make sense of the biomedical literature at the sentence level by finding the best-matching sentences given a query via a cutting-edge neural embedding approach.
LitSense helps make sense of the biomedical literature at the sentence level by finding the best-matching sentences given a query via a cutting-edge neural embedding approach.
Description
TeamTat is a web-based text annotation tool for biomedical text and beyond.
TeamTat is a web-based text annotation tool for biomedical text and beyond.
Software
Description
TaggerOne is a general toolkit for biomedical named entity recognition and normalization. As a machine learning system it is not entity-specific but does require training data.
TaggerOne is a general toolkit for biomedical named entity recognition and normalization. As a machine learning system it is not entity-specific but does require training data.
Description
tmChem is an open-source software tool for identifying chemical names. tmChem achieved the highest performance in BioCreative CHEMDNER task (over 87% F-measure)
tmChem is an open-source software tool for identifying chemical names. tmChem achieved the highest performance in BioCreative CHEMDNER task (over 87% F-measure)
Description
DNorm is the first technique to use machine learning to recognize and normalize disease names in biomedical text.
DNorm is the first technique to use machine learning to recognize and normalize disease names in biomedical text.
Description
GNormPlus is an end-to-end system that handles both gene/protein name and identifier detection in biomedical literature, including gene/protein mentions, family names and domain names.
GNormPlus is an end-to-end system that handles both gene/protein name and identifier detection in biomedical literature, including gene/protein mentions, family names and domain names.
Description
SR4GN is an open source tool for species recognition/disambiguation and is optimized for the Gene Normalization task.
SR4GN is an open source tool for species recognition/disambiguation and is optimized for the Gene Normalization task.
Description
tmVar extracts a wide range of sequence variants in both protein and gene levels (e.g. substitution, deletion, etc) in HGVS formats.
tmVar extracts a wide range of sequence variants in both protein and gene levels (e.g. substitution, deletion, etc) in HGVS formats.
Description
SimConcept uses patterns to identify individual mentions from a composite named entity (e.g. SMAD 1, 5, and 8).
SimConcept uses patterns to identify individual mentions from a composite named entity (e.g. SMAD 1, 5, and 8).
Description
NegBio is a high-performance tool for negation and uncertainty detection in clinical text (e.g. radiology reports).
NegBio is a high-performance tool for negation and uncertainty detection in clinical text (e.g. radiology reports).