(Q30374327)

14 August 2017

1 reference

title

Community challenges in biomedical text mining over 10 years: success, failure and the future. (English)

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14 August 2017

biomedical text mining

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1 reference

Chung-Chi Huang

1

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PMC publication ID

4719069

14 August 2017

Zhiyong Lu

series ordinal

2

1 reference

14 August 2017

1 May 2015

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Briefings in Bioinformatics

14 August 2017

1 reference

14 August 2017

17

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14 August 2017

1

1 reference

14 August 2017

132-144

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tmChem: a high performance approach for chemical named entity recognition and normalization

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

The CHEMDNER corpus of chemicals and drugs and its annotation principles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Scaling drug indication curation through crowdsourcing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

LabeledIn: cataloging labeled indications for human drugs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Overview of the gene ontology task at BioCreative IV

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

BC4GO: a full-text corpus for the BioCreative IV GO task

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

tmBioC: improving interoperability of text-mining tools with BioC.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

BioC interoperability track overview

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

BioCreative-IV virtual issue

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Accessing biomedical literature in the current information landscape

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

NCBI disease corpus: a resource for disease name recognition and concept normalization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Critical assessment of methods of protein structure prediction (CASP)--round x

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

BioC: a minimalist approach to interoperability for biomedical text processing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

DNorm: disease name normalization with pairwise learning to rank

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

PubTator: a web-based text mining tool for assisting biocuration

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Evaluating temporal relations in clinical text: 2012 i2b2 Challenge

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Collaborative biocuration--text-mining development task for document prioritization for curation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Literature mining of protein-residue associations with graph rules learned through distant supervision

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Suicide note sentiment classification: a supervised approach augmented by web data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

BioNLP Shared Task--The Bacteria Track

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

SR4GN: a species recognition software tool for gene normalization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

BioCreative III interactive task: an overview

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

The gene normalization task in BioCreative III

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

OSCAR4: a flexible architecture for chemical text-mining

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Recommending MeSH terms for annotating biomedical articles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

UniProt Knowledgebase: a hub of integrated protein data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

PubMed and beyond: a survey of web tools for searching biomedical literature

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Extracting medication information from clinical text

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Event extraction for systems biology by text mining the literature

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

CALBC silver standard corpus

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Understanding PubMed user search behavior through log analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Evaluation of Query Expansion Using MeSH in PubMed

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Recognizing obesity and comorbidities in sparse data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Overview of the protein-protein interaction annotation extraction task of BioCreative II

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Overview of BioCreative II gene normalization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

GeneRIF quality assurance as summary revision

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Identifying patient smoking status from medical discharge records

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Automating document classification for the Immune Epitope Database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Evaluating the state-of-the-art in automatic de-identification

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Finding GeneRIFs via gene ontology annotations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Automatic document classification of biological literature

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

The TREC 2004 genomics track categorization task: classifying full text biomedical documents.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Biomedical language processing: what's beyond PubMed?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Literature mining for the biologist: from information retrieval to biological discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Text mining and ontologies in biomedicine: making sense of raw text

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Informatics challenges for the impending patient information explosion

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

BioCreAtIvE task 1A: gene mention finding evaluation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Evaluation of BioCreAtIvE assessment of task 2

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Overview of BioCreAtIvE task 1B: normalized gene lists

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Overview of BioCreAtIvE: critical assessment of information extraction for biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

A survey of current work in biomedical text mining

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Entrez Gene: gene-centered information at NCBI

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Mining the biomedical literature in the genomic era: an overview

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

Medical document anonymization with a semantic lexicon.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

A large-scale experiment to assess protein structure prediction methods.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4719069

The G protein-coupled receptors in the pufferfish Takifugu rubripes.

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

MyMiner: a web application for computer-assisted biocuration and text annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Predicting gene function in a hierarchical context with an ensemble of classifiers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Evolution of orthologous tandemly arrayed gene clusters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

A ranking method for the concurrent learning of compounds with various activity profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

The FEBS Letters SDA corpus: a collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Overview of the ShARe/CLEF eHealth Evaluation Lab 2013

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Protein names and how to find them.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

A GFP-based reporter system to monitor nonsense-mediated mRNA decay

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Database resources of the National Center for Biotechnology Information

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Electronic Health Record Use and the Quality of Ambulatory Care in the United States

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV024

Evaluating relevance ranking strategies for MEDLINE retrieval

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25935162

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIB/BBV024

1 reference

14 August 2017

journals/bib/HuangL16

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

4719069

14 August 2017

PubMed publication ID

25935162

1 reference

PMC publication ID

4719069