An overview of biomedical entity linking throughout the years

A simple neural vector space model for medical concept normalization using concept embeddings

(2022) Dongfang Xu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

BertMCN: Mapping colloquial phrases to standard medical concepts using BERT and highway network

(2021) Katikapalli Subramanyam Kalyan et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Medical concept normalization in French using multilingual terminologies and contextual embeddings

(2021) Perceval Wajsbürt et al.   JOURNAL OF BIOMEDICAL INFORMATICS

NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature

(2021) Rezarta Islamaj et al.   Scientific Data

Medical concept normalization in clinical trials with drug and disease representation learning

(2021) Zulfat Miftahutdinov et al.   BIOINFORMATICS

Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort Collaborative

(2021) Tellen D. Bennett et al.   JAMA Network Open

A study of entity-linking methods for normalizing Chinese diagnosis and procedure terms to ICD codes

(2020) Qiong Wang et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization

(2020) Dongfang Xu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Distant supervision for medical concept normalization

(2020) Nikhil Pattisapu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Clinical concept normalization with a hybrid natural language processing system combining multilevel matching and machine learning ranking

(2020) Long Chen et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature

(2020) Pedro Ruas et al.   Journal of Cheminformatics

Ambiguity in medical concept normalization: An analysis of types and coverage in electronic health record datasets

(2020) Denis Newman-Griffis et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0)

(2019) Abhyuday Jagannatha et al.   DRUG SAFETY

MCN: A comprehensive corpus for medical concept normalization

(2019) Yen-Fu Luo et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries

(2019) Yipei Wang et al.   BMC BIOINFORMATICS

Medical concept normalization in social media posts with recurrent neural networks

(2018) Elena Tutubalina et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Multi-task Character-Level Attentional Networks for Medical Concept Normalization

(2018) Jinghao Niu et al.   NEURAL PROCESSING LETTERS

CUILESS2016: a clinical corpus applying compositional normalization of text mentions

(2018) John D. Osborne et al.   Journal of Biomedical Semantics

OUP accepted manuscript

(2018)   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

RysannMD: A biomedical semantic annotator balancing speed and accuracy

(2017) John Cuzzola et al.   JOURNAL OF BIOMEDICAL INFORMATICS

CLAMP – a toolkit for efficiently building customized clinical natural language processing pipelines

(2017) Ergin Soysal et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

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

(2016) Robert Leaman et al.   BIOINFORMATICS

NOBLE – Flexible concept recognition for large-scale biomedical natural language processing

(2016) Eugene Tseytlin et al.   BMC BIOINFORMATICS

Bridging semantics and syntax with graph algorithms—state-of-the-art of extracting biomedical relations

(2016) Yuan Luo et al.   BRIEFINGS IN BIOINFORMATICS

Use of “off-the-shelf” information extraction algorithms in clinical informatics: A feasibility study of MetaMap annotation of Italian medical notes

(2016) Emma Chiaramello et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Cadec: A corpus of adverse drug event annotations

(2015) Sarvnaz Karimi et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features

(2015) A. Nikfarjam et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC

(2015) Jan A Kors et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text

(2015) Chih-Hsuan Wei et al.   IEEE Journal of Biomedical and Health Informatics

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

(2014) Rezarta Islamaj Doğan et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Quantifying the Impact and Extent of Undocumented Biomedical Synonymy

(2014) David R. Blair et al.   PLoS Computational Biology

DNorm: disease name normalization with pairwise learning to rank

(2013) R. Leaman et al.   BIOINFORMATICS

OSCAR4: a flexible architecture for chemical text-mining

(2011) David M Jessop et al.   Journal of Cheminformatics

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications

(2010) Guergana K Savova et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Abbreviation definition identification based on automatic precision estimates

(2008) Sunghwan Sohn et al.   BMC BIOINFORMATICS