Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges (Q36233671)

12 August 2017

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges (English)

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12 August 2017

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biomedical text mining

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Johanna McEntyre

5

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Thomas Lemberger

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4

object named as

Thomas Lemberger

1 reference

12 August 2017

Cecilia Arighi

8

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Ioannis Xenarios

series ordinal

7

object named as

Ioannis Xenarios

1 reference

12 August 2017

3

Natalie Catlett

1 reference

12 August 2017

6

Shawn Polson

1 reference

12 August 2017

9

Zhiyong Lu

1 reference

12 August 2017

2

Robert Leaman

1 reference

12 August 2017

Ayush Singhal

1

1 reference

PMC publication ID

5199160

12 August 2017

language of work or name

1 reference

26 December 2016

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12 August 2017

1 reference

12 August 2017

2016

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Overview of the interactive task in BioCreative V

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Beyond accuracy: creating interoperable and scalable text-mining web services

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Control of brain development, function, and behavior by the microbiome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Europe PMC: a full-text literature database for the life sciences and platform for innovation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

UniProt: a hub for protein information

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Overview of the gene ontology task at BioCreative IV

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

BioC interoperability track overview

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Mucosal immunity and the microbiome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

The environment ontology: contextualising biological and biomedical entities

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

The microbiome and regulation of mucosal immunity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

BioC: a minimalist approach to interoperability for biomedical text processing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Quantitative assessment of biological impact using transcriptomic data and mechanistic network models

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

VIROME: a standard operating procedure for analysis of viral metagenome sequences.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

The eFIP system for text mining of protein interaction networks of phosphorylated proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Structure, function and diversity of the healthy human microbiome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

GeneView: a comprehensive semantic search engine for PubMed

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

SR4GN: a species recognition software tool for gene normalization

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Text mining for the biocuration workflow

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

BioCreative III interactive task: an overview

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

The gene normalization task in BioCreative III

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Recommending MeSH terms for annotating biomedical articles

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

The structural and content aspects of abstracts versus bodies of full text journal articles are different

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Systematic Characterizations of Text Similarity in Full Text Biomedical Publications

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

LINNAEUS: a species name identification system for biomedical literature

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Reflect: augmented browsing for the life scientist

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Overview of BioCreative II gene normalization

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

The Protein Information Resource: an integrated public resource of functional annotation of proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Intrinsic evaluation of text mining tools may not predict performance on realistic tasks.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

Evolution of orthologous tandemly arrayed gene clusters

29 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FDATABASE%2FBAW161

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FDATABASE%2FBAW161

Database resources of the National Center for Biotechnology Information

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5199160

SourceData - a semantic platform for curating and searching figures

21 October 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FDATABASE%2FBAW161

SourceData: a semantic platform for curating and searching figures

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28025348

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/DATABASE/BAW161

1 reference

journals/biodb/SinghalLCLMPXAL16

12 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

5199160

12 August 2017

PubMed publication ID

28025348

1 reference

PMC publication ID

5199160