UMLS

Unified Medical Language System integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records.

Webpage:

https://www.nlm.nih.gov/research/umls/

Licence:

Name: UMLS - specific
URL: https://www.nlm.nih.gov/research/umls/faq_main.html

Publications:

Publications
More detailed information about this field from each metasource.

The Unified Medical Language System (UMLS): integrating biomedical terminology
PMID: 14681409
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

The Unified Medical Language System (UMLS): integrating biomedical terminology PubMed citations: 984.

984 articles citing: The Unified Medical Language System (UMLS): integrating biomedical terminology

Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python. PMID:35308962
Discovering Associations between Social Determinants and Health Outcomes: Merging Knowledge Graphs from Literature and Electronic Health Data. PMID:35308956
Controversial Trials First: Identifying Disagreement Between Clinical Guidelines and New Evidence. PMID:35308948
Reducing Physicians' Cognitive Load During Chart Review: A Problem-Oriented Summary of the Patient Electronic Record. PMID:35308927
The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. PMID:35295213
Assessment of Machine Learning-Based Medical Directives to Expedite Care in Pediatric Emergency Medicine. PMID:35294539
Leveraging non-lattice subgraphs for suggestion of new concepts for SNOMED CT. PMID:35291311
Challenges and Barriers in Applying Natural Language Processing to Medical Examiner Notes from Fatal Opioid Poisoning Cases. PMID:35282306
A Data-Driven Medical Decision Framework for Associating Adverse Drug Events with Drug-Drug Interaction Mechanisms. PMID:35281526
Automatic Classification of Cancer Pathology Reports: A Systematic Review. PMID:35242443
DOTA: Deep Learning Optimal Transport Approach to Advance Drug Repositioning for Alzheimer's Disease. PMID:35204697
Uncovering interpretable potential confounders in electronic medical records. PMID:35197467
Sleep apnea phenotyping and relationship to disease in a large clinical biobank. PMID:35156000
Monitoring COVID-19 on Social Media: Development of an End-to-End Natural Language Processing Pipeline Using a Novel Triage and Diagnosis Approach. PMID:35142636
DDIT: An Online Predictor for Multiple Clinical Phenotypic Drug-Disease Associations. PMID:35126114
MCRWR: a new method to measure the similarity of documents based on semantic network. PMID:35105306
Text mining-based measurement of precision of polysomnographic reports as basis for intervention. PMID:35101128
Predictive structured-unstructured interactions in EHR models: A case study of suicide prediction. PMID:35087182
Analysis of E-mental health research: mapping the relationship between information technology and mental healthcare. PMID:35078432
The Cosmos Collaborative: A Vendor-Facilitated Electronic Health Record Data Aggregation Platform. PMID:35071993
An ensemble approach for healthcare application and diagnosis using natural language processing. PMID:35069926
An Unsupervised Approach to Structuring and Analyzing Repetitive Semantic Structures in Free Text of Electronic Medical Records. PMID:35055340
Patient Representation Learning From Heterogeneous Data Sources and Knowledge Graphs Using Deep Collective Matrix Factorization: Evaluation Study. PMID:35049514
Toward Data-Driven Radiation Oncology Using Standardized Terminology as a Starting Point: Cross-sectional Study. PMID:35044315
Predicting the impact of online news articles - is information necessary?: Application to COVID-19 articles. PMID:35035262
Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination. PMID:35021991
HLA-SPREAD: a natural language processing based resource for curating HLA association from PubMed abstracts. PMID:34991484
HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey. PMID:34991460
Development of a Lexicon for Pain. PMID:34966903
Composition-driven symptom phrase recognition for Chinese medical consultation corpora. PMID:34961490
Analyzing transfer learning impact in biomedical cross-lingual named entity recognition and normalization. PMID:34920703
Gender-sensitive word embeddings for healthcare. PMID:34918101
Using the Symptom Patient Similarity Network to Explore the Difference between the Chinese and Western Medicine Pathways of Ischemic Stroke and its Comorbidities. PMID:34899950
The Utility of Different Data Standards to Document Adverse Drug Event Symptoms and Diagnoses: Mixed Methods Study. PMID:34890351
A Comparison of Natural Language Processing Methods for the Classification of Lumbar Spine Imaging Findings Related to Lower Back Pain. PMID:34862122
Diversity and molecular network patterns of symptom phenotypes. PMID:34848731
A Pipeline to Understand Emerging Illness Via Social Media Data Analysis: Case Study on Breast Implant Illness. PMID:34847064
Incorporating Domain Knowledge Into Language Models by Using Graph Convolutional Networks for Assessing Semantic Textual Similarity: Model Development and Performance Comparison. PMID:34842531
Retaining Privileged Information for Multi-Task Learning. PMID:34796042
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure. PMID:34791105
Zero-Shot Clinical Acronym Expansion via Latent Meaning Cells. PMID:34790898
Enhancing unsupervised medical entity linking with multi-instance learning. PMID:34789262
The Human Disease Ontology 2022 update. PMID:34755882
Identification of missing concepts in biomedical terminologies using sequence-based formal concept analysis. PMID:34753458
Temporally informed random forests for suicide risk prediction. PMID:34725687
A Lexical-based Formal Concept Analysis Method to Identify Missing Concepts in the NCI Thesaurus. PMID:34721941
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion. PMID:34717542
Cognitive Impairments in Schizophrenia: A Study in a Large Clinical Sample Using Natural Language Processing. PMID:34713182
Adverse Drug Event Prediction Using Noisy Literature-Derived Knowledge Graphs: Algorithm Development and Validation. PMID:34694230
Clinical Concept Extraction with Lexical Semantics to Support Automatic Annotation. PMID:34682315
Quantifying the Severity of Adverse Drug Reactions Using Social Media: Network Analysis. PMID:34673524
An atomic approach to the design and implementation of a research data warehouse. PMID:34613409
On the robustness of generalization of drug-drug interaction models. PMID:34607569
SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations. PMID:34607568
A natural language processing pipeline to synthesize patient-generated notes toward improving remote care and chronic disease management: a cystic fibrosis case study. PMID:34604710
Assigning ICD-O-3 Codes to Pathology Reports using Neural Multi-Task Training with Hierarchical Regularization. PMID:34541582
Distantly supervised biomedical relation extraction using piecewise attentive convolutional neural network and reinforcement learning. PMID:34524450
Biomedical Vocabulary Alignment at Scale in the UMLS Metathesaurus. PMID:34514472
ParaMed: a parallel corpus for English-Chinese translation in the biomedical domain. PMID:34488734
A Review of Recent Work in Transfer Learning and Domain Adaptation for Natural Language Processing of Electronic Health Records. PMID:34479396
Systematic Review of Approaches to Preserve Machine Learning Performance in the Presence of Temporal Dataset Shift in Clinical Medicine. PMID:34470057
Using the Unified Medical Language System to Expand the Operative Stress Score - First Use Case. PMID:34464893
A Policy-Driven Approach to Secure Extraction of COVID-19 Data From Research Papers. PMID:34458724
An automated method to enrich consumer health vocabularies using GloVe word embeddings and an auxiliary lexical resource. PMID:34458573
An Examination of the Statistical Laws of Semantic Change in Clinical Notes. PMID:34457167
Empirical Findings on the Role of Structured Data, Unstructured Data, and their Combination for Automatic Clinical Phenotyping. PMID:34457160
A Comparison between Human and NLP-based Annotation of Clinical Trial Eligibility Criteria Text Using The OMOP Common Data Model. PMID:34457154
Analysis of Health Trajectories Leading to Adverse Opioid-Related Events. PMID:34457139
Clinical Phenotypic Spectrum of 4095 Individuals with Down Syndrome from Text Mining of Electronic Health Records. PMID:34440331
An Alignment-Based Implementation of a Holistic Ontology Integration Method. PMID:34434866
Natural language processing for automated annotation of medication mentions in primary care visit conversations. PMID:34423262
Matching Biomedical Ontologies: Construction of Matching Clues and Systematic Evaluation of Different Combinations of Matchers. PMID:34420930
Improving broad-coverage medical entity linking with semantic type prediction and large-scale datasets. PMID:34390853
A proteomic platform to identify off-target proteins associated with therapeutic modalities that induce protein degradation or gene silencing. PMID:34349202
COVID term: a bilingual terminology for COVID-19. PMID:34344385
Text mining of gene-phenotype associations reveals new phenotypic profiles of autism-associated genes. PMID:34315992
Improving the Efficiency of Clinical Trial Recruitment Using an Ensemble Machine Learning to Assist With Eligibility Screening. PMID:34296815
Disease ontologies for knowledge graphs. PMID:34289807
ITEXT-BIO: Intelligent Term EXTraction for BIOmedical analysis. PMID:34276970
DeepADEMiner: a deep learning pharmacovigilance pipeline for extraction and normalization of adverse drug event mentions on Twitter. PMID:34270701
Improving early diagnosis of rare diseases using Natural Language Processing in unstructured medical records: an illustration from Dravet syndrome. PMID:34256808
Relation Classification for Bleeding Events From Electronic Health Records Using Deep Learning Systems: An Empirical Study. PMID:34255697
The Unified Medical Language System at 30 Years and How It Is Used and Published: Systematic Review and Content Analysis. PMID:34236337
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank. PMID:34225788
Metabolomics and Network Pharmacology-Based Investigation into the Mechanisms Underlying the Therapeutic Effect of a New Chinese Traditional Medicine (Cui Nai Ling) on Bromocriptine-Induced Hypogalactia. PMID:34221092
A novel computational drug repurposing approach for Systemic Lupus Erythematosus (SLE) treatment using Semantic Web technologies. PMID:34220244
Toward a Coronavirus Knowledge Graph. PMID:34209818
A Literature-Derived Knowledge Graph Augments the Interpretation of Single Cell RNA-seq Datasets. PMID:34200671
Leveraging network analysis to evaluate biomedical named entity recognition tools. PMID:34188248
Predicting circRNA-Disease Associations Based on Deep Matrix Factorization with Multi-source Fusion. PMID:34185304
A National, Semantic-Driven, Three-Pillar Strategy to Enable Health Data Secondary Usage Interoperability for Research Within the Swiss Personalized Health Network: Methodological Study. PMID:34185008
What's in a Summary? Laying the Groundwork for Advances in Hospital-Course Summarization. PMID:34179900
Translational NLP: A New Paradigm and General Principles for Natural Language Processing Research. PMID:34179899
Biomedical and clinical English model packages for the Stanza Python NLP library. PMID:34157094
Node Similarity Based Graph Convolution for Link Prediction in Biological Networks. PMID:34152393
TextEssence: A Tool for Interactive Analysis of Semantic Shifts Between Corpora. PMID:34151319
Development and application of the ocular immune-mediated inflammatory diseases ontology enhanced with synonyms from online patient support forum conversation. PMID:34139439
Constructing High-Fidelity Phenotype Knowledge Graphs for Infectious Diseases With a Fine-Grained Semantic Information Model: Development and Usability Study. PMID:34128811
Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272
Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network. PMID:34113801
Stroke Risk Among Non-Elderly Users of Haloperidol or First-Generation Antipsychotics vs Second-Generation Antipsychotics: A Cohort Study from a US Health Insurance Claims Database. PMID:34109564
Integration of Immunome With Disease-Gene Network Reveals Common Cellular Mechanisms Between IMIDs and Drug Repurposing Strategies. PMID:34108969
A deep database of medical abbreviations and acronyms for natural language processing. PMID:34078918
Biomedical Text Link Prediction for Drug Discovery: A Case Study with COVID-19. PMID:34073456
Neural Machine Translation-Based Automated Current Procedural Terminology Classification System Using Procedure Text: Development and Validation Study. PMID:34037526
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
Extracting Adverse Drug Event Information with Minimal Engineering. PMID:34027520
Mining news media for understanding public health concerns. PMID:33948233
Collecting specialty-related medical terms: Development and evaluation of a resource for Spanish. PMID:33947365
AI Accelerated Human-in-the-loop Structuring of Radiology Reports. PMID:33936507
Timely and Efficient AI Insights on EHR: System Design. PMID:33936494
Retrieving Lab Test Related Questions from Social Q&A Sites by Combining Shallow Features and Deep Representations. PMID:33936453
Comparative Study of Various Approaches for Ensemble-based De-identification of Electronic Health Record Narratives. PMID:33936439
Retrofitting Vector Representations of Adverse Event Reporting Data to Structured Knowledge to Improve Pharmacovigilance Signal Detection. PMID:33936411
RadLex Normalization in Radiology Reports. PMID:33936406
Machine Learning and Syncope Management in the ED: The Future Is Coming. PMID:33917508
SeBioGraph: Semi-supervised Deep Learning for the Graph via Sustainable Knowledge Transfer. PMID:33867966
A System for Phenotype Harmonization in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Program. PMID:33861317
Semantic categorization of Chinese eligibility criteria in clinical trials using machine learning methods. PMID:33858409
When text simplification is not enough: could a graph-based visualization facilitate consumers' comprehension of dietary supplement information? PMID:33855274
Ontology-driven weak supervision for clinical entity classification in electronic health records. PMID:33795682
Development of a COVID-19 Application Ontology for the ACT Network. PMID:33791734
NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature. PMID:33767203
Protocol for a reproducible experimental survey on biomedical sentence similarity. PMID:33760855
Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings. PMID:33746351
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Building a semantically annotated corpus for chronic disease complications using two document types. PMID:33735207
A Pattern-Based Method for Medical Entity Recognition From Chinese Diagnostic Imaging Text. PMID:33733090
Using computable knowledge mined from the literature to elucidate confounders for EHR-based pharmacovigilance. PMID:33716168
Discovering microbe-disease associations from the literature using a hierarchical long short-term memory network and an ensemble parser model. PMID:33627732
The tumor therapy landscape of synthetic lethality. PMID:33627666
OncoTree: A Cancer Classification System for Precision Oncology. PMID:33625877
A clinical trials corpus annotated with UMLS entities to enhance the access to evidence-based medicine. PMID:33618727
SEED: Symptom Extraction from English Social Media Posts using Deep Learning and Transfer Learning. PMID:33594374
Gene function finding through cross-organism ensemble learning. PMID:33579334
Drug repurposing for COVID-19 via knowledge graph completion. PMID:33571675
COVID-19 and dementia: Analyses of risk, disparity, and outcomes from electronic health records in the US. PMID:33559975
Advancement in predicting interactions between drugs used to treat psoriasis and its comorbidities by integrating molecular and clinical resources. PMID:33544847
Electronic Medical Record-Based Case Phenotyping for the Charlson Conditions: Scoping Review. PMID:33522976
Artificial Intelligence Pipeline to Bridge the Gap between Bench Researchers and Clinical Researchers in Precision Medicine. PMID:33511289
Generating Accurate Electronic Health Assessment from Medical Graph. PMID:33491009
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
Early Detection of Septic Shock Onset Using Interpretable Machine Learners. PMID:33467539
Automated Identification of Common Disease-Specific Outcomes for Comparative Effectiveness Research Using ClinicalTrials.gov: Algorithm Development and Validation Study. PMID:33460388
Clinical Term Normalization Using Learned Edit Patterns and Subconcept Matching: System Development and Evaluation. PMID:33443483
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
Drug repurposing for opioid use disorders: integration of computational prediction, clinical corroboration, and mechanism of action analyses. PMID:33432189
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
A computational approach to predict multi-pathway drug-drug interactions: A case study of irinotecan, a colon cancer medication. PMID:33424244
Generating real-world evidence from unstructured clinical notes to examine clinical utility of genetic tests: use case in BRCAness. PMID:33407429
Automatic Identification of Information Quality Metrics in Health News Stories. PMID:33392124
Nursing documentation of symptoms is associated with higher risk of emergency department visits and hospitalizations in homecare patients. PMID:33386145
Predicting mortality in critically ill patients with diabetes using machine learning and clinical notes. PMID:33380338
Annotation and extraction of age and temporally-related events from clinical histories. PMID:33380319
Using indication embeddings to represent patient health for drug safety studies. PMID:33376961
Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach. PMID:33372893
BioRel: towards large-scale biomedical relation extraction. PMID:33323106
Ambiguity in medical concept normalization: An analysis of types and coverage in electronic health record datasets. PMID:33319905
Analysis of readability and structural accuracy in SNOMED CT. PMID:33319711
Extending import detection algorithms for concept import from two to three biomedical terminologies. PMID:33319702
KGen: a knowledge graph generator from biomedical scientific literature. PMID:33317512
Analyses of Risk, Racial Disparity, and Outcomes Among US Patients With Cancer and COVID-19 Infection. PMID:33300956
Language models are an effective representation learning technique for electronic health record data. PMID:33290879
Multiscale classification of heart failure phenotypes by unsupervised clustering of unstructured electronic medical record data. PMID:33288774
Text mining approaches for dealing with the rapidly expanding literature on COVID-19. PMID:33279995
The Impact of Pretrained Language Models on Negation and Speculation Detection in Cross-Lingual Medical Text: Comparative Study. PMID:33270027
Predicting the relationships between gut microbiota and mental disorders with knowledge graphs. PMID:33262885
Prediction of breast cancer distant recurrence using natural language processing and knowledge-guided convolutional neural network. PMID:33250149
When hematologic malignancies meet COVID-19 in the United States: Infections, death and disparities. PMID:33187811
A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. PMID:33181823
Patient Triage by Topic Modeling of Referral Letters: Feasibility Study. PMID:33155985
Amplifying Domain Expertise in Clinical Data Pipelines. PMID:33151150
Prediction of severe chest injury using natural language processing from the electronic health record. PMID:33131794
COVID-19 detection in radiological text reports integrating entity recognition. PMID:33130435
Automatic Structuring of Ontology Terms Based on Lexical Granularity and Machine Learning: Algorithm Development and Validation. PMID:33127601
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501
Importance of scientific collaboration in contemporary drug discovery and development: a detailed network analysis. PMID:33050894
The impact of learning Unified Medical Language System knowledge embeddings in relation extraction from biomedical texts. PMID:33029619
Use of word and graph embedding to measure semantic relatedness between Unified Medical Language System concepts. PMID:33029614
Increased risk of COVID-19 infection and mortality in people with mental disorders: analysis from electronic health records in the United States. PMID:33026219
Phenotypically Similar Rare Disease Identification from an Integrative Knowledge Graph for Data Harmonization: Preliminary Study. PMID:33006565
Sociodemographic data and APOE-ε4 augmentation for MRI-based detection of amnestic mild cognitive impairment using deep learning systems. PMID:32976486
PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records. PMID:32974638
The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task on clinical concept normalization for clinical records. PMID:32968800
Employing computational linguistics techniques to identify limited patient health literacy: Findings from the ECLIPPSE study. PMID:32966630
A Personalized Voice-Based Diet Assistant for Caregivers of Alzheimer Disease and Related Dementias: System Development and Validation. PMID:32955452
An interactive retrieval system for clinical trial studies with context-dependent protocol elements. PMID:32946464
Assessing the enrichment of dietary supplement coverage in the Unified Medical Language System. PMID:32940692
Unlocking the Potential of Electronic Health Records for Health Research. PMID:32935049
Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. PMID:32930711
COVID-19 risk and outcomes in patients with substance use disorders: analyses from electronic health records in the United States. PMID:32929211
A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System. PMID:32918476
Cross-lingual Unified Medical Language System entity linking in online health communities. PMID:32910823
Adverse drug event detection using reason assignments in FDA drug labels. PMID:32890727
International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium. PMID:32864472
Evaluation of standard and semantically-augmented distance metrics for neurology patients. PMID:32843023
A topic modeling framework for spatio-temporal information management. PMID:32836694
Biomedical Holistic Ontology for People with Rare Diseases. PMID:32825147
A corpus-driven standardization framework for encoding clinical problems with HL7 FHIR. PMID:32814201
Increased Morbidity and Mortality in Hypertensive Patients With Substance Use Disorders: Electronic Health Record Findings. PMID:32800083
Clinical concept extraction: A methodology review. PMID:32768446
A review of auditing techniques for the Unified Medical Language System. PMID:32766692
Semantic Deep Learning: Prior Knowledge and a Type of Four-Term Embedding Analogy to Acquire Treatments for Well-Known Diseases. PMID:32759099
Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)-based ranking for concept normalization. PMID:32719838
Prediction of Medical Concepts in Electronic Health Records: Similar Patient Analysis. PMID:32706678
Identification of early stage recurrence endometrial cancer biomarkers using bioinformatics tools. PMID:32705231
Conditional and unconditional genome-wide association study reveal complicate genetic architecture of human body weight and impacts of smoking. PMID:32699216
UMLS users and uses: a current overview. PMID:32683453
Combining phenome-driven drug-target interaction prediction with patients' electronic health records-based clinical corroboration toward drug discovery. PMID:32657406
Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing. PMID:32657387
KGHC: a knowledge graph for hepatocellular carcinoma. PMID:32646496
Hybrid phenotype mining method for investigating off-target protein and underlying side effects of anti-tumor immunotherapy. PMID:32646421
Neural side effect discovery from user credibility and experience-assessed online health discussions. PMID:32641159
open-japanese-mesh: assigning MeSH UIDs to Japanese medical terms via open Japanese-English glossaries. PMID:32634876
Can Unified Medical Language System-based semantic representation improve automated identification of patient safety incident reports by type and severity? PMID:32574362
Ontology-driven aspect-based sentiment analysis classification: An infodemiological case study regarding infectious diseases in Latin America. PMID:32572291
Automatic extraction, prioritization and analysis of gut microbial metabolites from biomedical literature. PMID:32561832
An integrated chemical environment with tools for chemical safety testing. PMID:32553663
pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms. PMID:32552728
Assessing the accuracy of automatic speech recognition for psychotherapy. PMID:32550644
Semantic text mining in early drug discovery for type 2 diabetes. PMID:32542027
Deep learning in mental health outcome research: a scoping review. PMID:32532967
GOcats: A tool for categorizing Gene Ontology into subgraphs of user-defined concepts. PMID:32525872
CORD-19: The Covid-19 Open Research Dataset. PMID:32510522
Molecular basis of mood and cognitive adverse events elucidated via a combination of pharmacovigilance data mining and functional enrichment analysis. PMID:32504122
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships. PMID:32504002
A bibliometric analysis and visualization of medical data mining research. PMID:32481411
Data-driven Sublanguage Analysis for Cancer Genomics Knowledge Modeling: Applications in Mining Oncological Genetics Information from Patients' Genetic Reports. PMID:32477695
A deep-learning based system for accurate extraction of blood pressure data in clinical narratives. PMID:32477693
Developing a Search Engine for Precision Medicine. PMID:32477680
Normalizing Adverse Events using Recurrent Neural Networks with Attention. PMID:32477654
BERT-based Ranking for Biomedical Entity Normalization. PMID:32477646
sig2db: a Workflow for Processing Natural Language from Prescription Instructions for Clinical Data Warehouses. PMID:32477641
Natural Language Processing for Surveillance of Cervical and Anal Cancer and Precancer: Algorithm Development and Split-Validation Study. PMID:32469840
Extraction of Information Related to Drug Safety Surveillance From Electronic Health Record Notes: Joint Modeling of Entities and Relations Using Knowledge-Aware Neural Attentive Models. PMID:32459650
An Informatics Framework to Assess Consumer Health Language Complexity Differences: Proof-of-Concept Study. PMID:32436849
Broad-coverage biomedical relation extraction with SemRep. PMID:32410573
Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach. PMID:32399556
Knowledge Graph-Enabled Cancer Data Analytics. PMID:32386166
Combining Social Media and FDA Adverse Event Reporting System to Detect Adverse Drug Reactions. PMID:32385840
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PMID:32324731
Prevalence and Risk Factors for Opioid-Induced Constipation in an Older National Veteran Cohort. PMID:32318129
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Bootstrapping Adversarial Learning of Biomedical Ontology Alignments. PMID:32308857
Integrated querying and version control of context-specific biological networks. PMID:32294194
Constructing fine-grained entity recognition corpora based on clinical records of traditional Chinese medicine. PMID:32252745
Classifying and Summarizing Information from Microblogs During Epidemics. PMID:32214879
Health Professionals' Perception about Big Data Technology in Greece. PMID:32210515
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Automatic approach for constructing a knowledge graph of knee osteoarthritis in Chinese. PMID:32175080
A Neuro-ontology for the neurological examination. PMID:32131804
DISNET: a framework for extracting phenotypic disease information from public sources. PMID:32110491
iDISK: the integrated DIetary Supplements Knowledge base. PMID:32068839
Using natural language processing to construct a metastatic breast cancer cohort from linked cancer registry and electronic medical records data. PMID:32025650
Using routine referral data for patients with knee and hip pain to improve access to specialist care. PMID:32013997
Sentiment Analysis in Health and Well-Being: Systematic Review. PMID:32012057
Annotating and detecting phenotypic information for chronic obstructive pulmonary disease. PMID:31984360
STAT: A Web-based Semantic Text Annotation Tool to Assist Building Mental Health Knowledge Base. PMID:31903451
Health Effects Associated With Electronic Cigarette Use: Automated Mining of Online Forums. PMID:31899452
Genome analysis and knowledge-driven variant interpretation with TGex. PMID:31888639
Family member information extraction via neural sequence labeling models with different tag schemes. PMID:31881965
Ontologies for Liver Diseases Representation: A Systematic Literature Review. PMID:31848894
Efficient Reuse of Natural Language Processing Models for Phenotype-Mention Identification in Free-text Electronic Medical Records: A Phenotype Embedding Approach. PMID:31845899
Advancing the state of the art in automatic extraction of adverse drug events from narratives. PMID:31841150
StudyPortal - Geovisualization of Study Research Networks. PMID:31823031
Improving reference prioritisation with PICO recognition. PMID:31805934
Combining entity co-occurrence with specialized word embeddings to measure entity relation in Alzheimer's disease. PMID:31801521
A Literature-Based Knowledge Graph Embedding Method for Identifying Drug Repurposing Opportunities in Rare Diseases. PMID:31797619
Clinical Concept Embeddings Learned from Massive Sources of Multimodal Medical Data. PMID:31797605
Text-mining clinically relevant cancer biomarkers for curation into the CIViC database. PMID:31796060
A hybrid deep learning framework for bacterial named entity recognition with domain features. PMID:31787075
Adverse drug event rates in pediatric pulmonary hypertension: a comparison of real-world data sources. PMID:31769835
A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications. PMID:31754458
Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes. PMID:31728432
Mapping the perturbome network of cellular perturbations. PMID:31723137
KLOSURE: Closing in on open-ended patient questionnaires with text mining. PMID:31711536
FoodBase corpus: a new resource of annotated food entities. PMID:31682732
The DisGeNET knowledge platform for disease genomics: 2019 update. PMID:31680165
Computational Methods for Identifying Similar Diseases. PMID:31678735
Visualizing a field of research: A methodology of systematic scientometric reviews. PMID:31671124
Data-driven method to enhance craniofacial and oral phenotype vocabularies. PMID:31668172
ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data. PMID:31633087
Broadening horizons: the case for capturing function and the role of health informatics in its use. PMID:31615472
GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. PMID:31612961
Leaf: an open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research. PMID:31592524
Graph embedding on biomedical networks: methods, applications and evaluations. PMID:31584634
Predicting emergency department orders with multilabel machine learning techniques and simulating effects on length of stay. PMID:31578568
Ontology-Based Healthcare Named Entity Recognition from Twitter Messages Using a Recurrent Neural Network Approach. PMID:31569654
Cohort selection for clinical trials: n2c2 2018 shared task track 1. PMID:31562516
Quantitative prediction of repeat dose toxicity values using GenRA. PMID:31550520
Ontology based mining of pathogen-disease associations from literature. PMID:31533864
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Fine-Tuning Bidirectional Encoder Representations From Transformers (BERT)-Based Models on Large-Scale Electronic Health Record Notes: An Empirical Study. PMID:31516126
A Lightweight API-Based Approach for Building Flexible Clinical NLP Systems. PMID:31511785
Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting. PMID:31504605
Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts. PMID:31504205
Challenges in the construction of knowledge bases for human microbiome-disease associations. PMID:31488215
Automatic extraction and assessment of lifestyle exposures for Alzheimer's disease using natural language processing. PMID:31476655
Towards a characterization of apparent contradictions in the biomedical literature using context analysis. PMID:31473364
Active deep learning for the identification of concepts and relations in electroencephalography reports. PMID:31470094
Automatic Identification of Individual Drugs in Death Certificates. PMID:31437910
Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries. PMID:31419946
ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database. PMID:31412866
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
DQueST: dynamic questionnaire for search of clinical trials. PMID:31390010
Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol). PMID:31378813
A Real-Time Automated Patient Screening System for Clinical Trials Eligibility in an Emergency Department: Design and Evaluation. PMID:31342909
ToxRefDB version 2.0: Improved utility for predictive and retrospective toxicology analyses. PMID:31340180
Convolutional Neural Network and Bidirectional Long Short-Term Memory-Based Method for Predicting Drug-Disease Associations. PMID:31336774
SemNet: Using Local Features to Navigate the Biomedical Concept Graph. PMID:31334227
UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER. PMID:31329239
Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases. PMID:31323264
Current approaches to identify sections within clinical narratives from electronic health records: a systematic review. PMID:31319802
Fully connecting the Observational Health Data Science and Informatics (OHDSI) initiative with the world of linked open data. PMID:31307128
Detecting false-positive disease references in veterinary clinical notes without manual annotations. PMID:31304379
Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings. PMID:31292438
G-Computation and Hierarchical Models for Estimating Multiple Causal Effects From Observational Disease Registries With Irregular Visits. PMID:31259036
A Hybrid Normalization Method for Medical Concepts in Clinical Narrative using Semantic Matching. PMID:31259030
Evaluating the Impact of Dictionary Updates on Automatic Annotations Based on Clinical NLP Systems. PMID:31259028
Adversarial Learning of Knowledge Embeddings for the Unified Medical Language System. PMID:31259009
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. PMID:31236786
The Generalized Data Model for clinical research. PMID:31234921
Analysis of disease organ as a novel phenotype towards disease genetics understanding. PMID:31207382
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
ICARUS: Minimizing Human Effort in Iterative Data Completion. PMID:31179156
ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer. PMID:31169290
CODA-ML: context-specific biological knowledge representation for systemic physiology analysis. PMID:31138123
Drug repositioning of herbal compounds via a machine-learning approach. PMID:31138103
In silico Identification and Mechanism Exploration of Hepatotoxic Ingredients in Traditional Chinese Medicine. PMID:31130860
The use of natural language processing to identify Tdap-related local reactions at five health care systems in the Vaccine Safety Datalink. PMID:31128829
Leveraging genetic interactions for adverse drug-drug interaction prediction. PMID:31125330
deepDR: a network-based deep learning approach to in silico drug repositioning. PMID:31116390
Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning. PMID:31094361
Specific phenotype semantics facilitate gene prioritization in clinical exome sequencing. PMID:31053788
Alternative classification of identical concepts in different terminologies: Different ways to view the world. PMID:31048072
Minimalistic Approach to Coreference Resolution in Lithuanian Medical Records. PMID:31015858
PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. PMID:30999867
Interactive biomedical ontology matching. PMID:30995257
On building a diabetes centric knowledge base via mining the web. PMID:30961582
Natural language processing and recurrent network models for identifying genomic mutation-associated cancer treatment change from patient progress notes. PMID:30944913
Clinical text classification with rule-based features and knowledge-guided convolutional neural networks. PMID:30943960
Discovering associations between problem list and practice setting. PMID:30943957
Meta-path Based Prioritization of Functional Drug Actions with Multi-Level Biological Networks. PMID:30940832
Prediction of drug-disease associations based on ensemble meta paths and singular value decomposition. PMID:30925858
Network-based prediction of drug combinations. PMID:30867426
Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning. PMID:30864315
Extended Analysis of Topological-Pattern-Based Ontology Enrichment. PMID:30854243
Leveraging Big Data to Transform Drug Discovery. PMID:30848458
Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases. PMID:30815196
The Sublanguage of Clinical Problem Lists: A Corpus Analysis. PMID:30815190
Disease comorbidity-guided drug repositioning: a case study in schizophrenia. PMID:30815174
A Preliminary Study of Clinical Concept Detection Using Syntactic Relations. PMID:30815146
Using Convolutional Neural Networks to Support Insertion of New Concepts into SNOMED CT. PMID:30815117
Leveraging Horizontal Density Differences between Ontologies to Identify Missing Child Concepts: A Proof of Concept. PMID:30815106
Identifying Windows of Susceptibility by Temporal Gene Analysis. PMID:30809014
Using natural language processing and machine learning to classify health literacy from secure messages: The ECLIPPSE study. PMID:30794616
Few-Shot and Zero-Shot Multi-Label Learning for Structured Label Spaces. PMID:30775726
Rare disease knowledge enrichment through a data-driven approach. PMID:30764825
Criteria2Query: a natural language interface to clinical databases for cohort definition. PMID:30753493
Detection of Bleeding Events in Electronic Health Record Notes Using Convolutional Neural Network Models Enhanced With Recurrent Neural Network Autoencoders: Deep Learning Approach. PMID:30735140
Mining social media data to assess the risk of skin and soft tissue infections from allergen immunotherapy. PMID:30721764
Big Data Readiness in Radiation Oncology: An Efficient Approach for Relabeling Radiation Therapy Structures With Their TG-263 Standard Name in Real-World Data Sets. PMID:30706028
CMEP: a database for circulating microRNA expression profiling. PMID:30668638
Improving Electronic Health Record Note Comprehension With NoteAid: Randomized Trial of Electronic Health Record Note Comprehension Interventions With Crowdsourced Workers. PMID:30664453
Adverse Drug Events Detection in Clinical Notes by Jointly Modeling Entities and Relations Using Neural Networks. PMID:30649738
Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0). PMID:30649735
Beyond opinion classification: Extracting facts, opinions and experiences from health forums. PMID:30625206
Constructing tissue-specific transcriptional regulatory networks via a Markov random field. PMID:30598101
Novel disease syndromes unveiled by integrative multiscale network analysis of diseases sharing molecular effectors and comorbidities. PMID:30598089
Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing. PMID:30587224
SIA: a scalable interoperable annotation server for biomedical named entities. PMID:30552534
Integrating molecular networks with genetic variant interpretation for precision medicine. PMID:30548534
Use of natural language processing in electronic medical records to identify pregnant women with suicidal behavior: towards a solution to the complex classification problem. PMID:30535584
SBLC: a hybrid model for disease named entity recognition based on semantic bidirectional LSTMs and conditional random fields. PMID:30526592
Variant information systems for precision oncology. PMID:30463544
A reference set of curated biomedical data and metadata from clinical case reports. PMID:30457569
A method for harmonization of clinical abbreviation and acronym sense inventories. PMID:30414475
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. PMID:30407536
Using Compact Coevolutionary Algorithm for Matching Biomedical Ontologies. PMID:30405706
Microfluidic-Based Multi-Organ Platforms for Drug Discovery. PMID:30404334
SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes. PMID:30400805
Effect of vocabulary mapping for conditions on phenotype cohorts. PMID:30395248
Disease networks identify specific conditions and pleiotropy influencing multimorbidity in the general population. PMID:30374096
Drug Repurposing Prediction for Immune-Mediated Cutaneous Diseases using a Word-Embedding-Based Machine Learning Approach. PMID:30342048
Machine learning to support social media empowered patients in cancer care and cancer treatment decisions. PMID:30335805
Web-Based Information Infrastructure Increases the Interrater Reliability of Medical Coders: Quasi-Experimental Study. PMID:30322834
Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response. PMID:30319692
Classification, Ontology, and Precision Medicine. PMID:30304648
LION LBD: a literature-based discovery system for cancer biology. PMID:30304355
Pathway networks generated from human disease phenome. PMID:30255817
Modeling Terminologies for Reusability in Faceted Systems. PMID:30221256
Advancing the State of the Art in Clinical Natural Language Processing through Shared Tasks. PMID:30157522
Recent Developments in Clinical Terminologies - SNOMED CT, LOINC, and RxNorm. PMID:30157516
Creation of Individual Scientific Concept-Centered Semantic Maps Based on Automated Text-Mining Analysis of PubMed. PMID:30147721
Biomedical ontology alignment: an approach based on representation learning. PMID:30111369
Annotation and detection of drug effects in text for pharmacovigilance. PMID:30105604
Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence. PMID:30096807
Automatic Normalization of Anatomical Phrases in Radiology Reports Using Unsupervised Learning. PMID:30076490
Phenotype-oriented network analysis for discovering pharmacological effects of natural compounds. PMID:30076354
Improving Consumer Understanding of Medical Text: Development and Validation of a New SubSimplify Algorithm to Automatically Generate Term Explanations in English and Spanish. PMID:30072361
Ontology-Based Approach for Liver Cancer Diagnosis and Treatment. PMID:30066122
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
Natural Language Processing for EHR-Based Computational Phenotyping. PMID:29994486
Screening Colonoscopy Withdrawal Time Threshold for Adequate Proximal Serrated Polyp Detection Rate. PMID:29974376
CogStack - experiences of deploying integrated information retrieval and extraction services in a large National Health Service Foundation Trust hospital. PMID:29941004
Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed. PMID:29912209
Validation of a Natural Language Processing Algorithm for Detecting Infectious Disease Symptoms in Primary Care Electronic Medical Records in Singapore. PMID:29907560
Relation extraction for biological pathway construction using node2vec. PMID:29897325
The Data Gap in the EHR for Clinical Research Eligibility Screening. PMID:29888090
Memory-Augmented Active Deep Learning for Identifying Relations Between Distant Medical Concepts in Electroencephalography Reports. PMID:29888063
GNOMICS: A one-stop shop for biomedical and genomic data. PMID:29888054
Automatically Linking Registered Clinical Trials to their Published Results with Deep Highway Networks. PMID:29888040
Repurposing sertraline sensitizes non-small cell lung cancer cells to erlotinib by inducing autophagy. PMID:29875309
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. PMID:29854225
Mining Hierarchies and Similarity Clusters from Value Set Repositories. PMID:29854206
Deep Learning Meets Biomedical Ontologies: Knowledge Embeddings for Epilepsy. PMID:29854192
Detection of Adverse Drug Reactions using Medical Named Entities on Twitter. PMID:29854190
Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud. PMID:29854169
Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator. PMID:29846492
Screening pregnant women for suicidal behavior in electronic medical records: diagnostic codes vs. clinical notes processed by natural language processing. PMID:29843698
Automated extraction of Biomarker information from pathology reports. PMID:29783980
Public Opinions Toward Diseases: Infodemiological Study on News Media Data. PMID:29739741
In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers. PMID:29712429
Quantifying predictive capability of electronic health records for the most harmful breast cancer. PMID:29706685
ComprehENotes, an Instrument to Assess Patient Reading Comprehension of Electronic Health Record Notes: Development and Validation. PMID:29695372
Analyzing user interactions with biomedical ontologies: A visual perspective. PMID:29657560
LipidPedia: a comprehensive lipid knowledgebase. PMID:29648583
A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration. PMID:29642848
Investigating Term Reuse and Overlap in Biomedical Ontologies. PMID:29636656
Validating UMLS Semantic Type Assignments Using SNOMED CT Semantic Tags. PMID:29621830
Clinical Natural Language Processing in languages other than English: opportunities and challenges. PMID:29602312
IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics. PMID:29531263
Jointly learning word embeddings using a corpus and a knowledge base. PMID:29529052
PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data. PMID:29479581
Assessing the practice of biomedical ontology evaluation: Gaps and opportunities. PMID:29462669
Comparing deep learning and concept extraction based methods for patient phenotyping from clinical narratives. PMID:29447188
Supporting shared hypothesis testing in the biomedical domain. PMID:29422110
Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts. PMID:29375930
In silico profiling of systemic effects of drugs to predict unexpected interactions. PMID:29371651
SemEHR: A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research. PMID:29361077
DataMed - an open source discovery index for finding biomedical datasets. PMID:29346583
Tackling the challenges of matching biomedical ontologies. PMID:29335022
An automatic approach for constructing a knowledge base of symptoms in Chinese. PMID:29297414
Interoperability of Disease Concepts in Clinical and Research Ontologies: Contrasting Coverage and Structure in the Disease Ontology and SNOMED CT. PMID:29295235
Perceiving the Usefulness of the National Cancer Institute Metathesaurus for Enriching NCIt with Topological Patterns. PMID:29295222
Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis. PMID:29295220
Retrofitting Concept Vector Representations of Medical Concepts to Improve Estimates of Semantic Similarity and Relatedness. PMID:29295178
Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology. PMID:29295162
Monitoring prescribing patterns using regression and electronic health records. PMID:29258594
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Automated Screening of Emergency Department Notes for Drug-Associated Bleeding Adverse Events Occurring in Older Adults. PMID:29241242
Supervised Learning and Knowledge-Based Approaches Applied to Biomedical Word Sense Disambiguation. PMID:29236676
A semantic-based workflow for biomedical literature annotation. PMID:29220478
Multi-field query expansion is effective for biomedical dataset retrieval. PMID:29220457
Text mining and expert curation to develop a database on psychiatric diseases and their genes. PMID:29220439
Identifying natural health product and dietary supplement information within adverse event reporting systems. PMID:29218888
Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer. PMID:29214177
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. PMID:29197409
Medical subdomain classification of clinical notes using a machine learning-based natural language processing approach. PMID:29191207
Evaluating Casama: Contextualized semantic maps for summarization of lung cancer studies. PMID:29149658
Indicators for the use of robotic labs in basic biomedical research: a literature analysis. PMID:29134146
Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization. PMID:29132636
Need of informatics in designing interoperable clinical registries. PMID:29132635
Temporal Annotation in the Clinical Domain. PMID:29082229
An Interpretable Classification Framework for Information Extraction from Online Healthcare Forums. PMID:29065580
Capturing the Patient's Perspective: a Review of Advances in Natural Language Processing of Health-Related Text. PMID:29063568
Recommending Education Materials for Diabetic Questions Using Information Retrieval Approaches. PMID:29038097
DISNOR: a disease network open resource. PMID:29036667
LiverWiki: a wiki-based database for human liver. PMID:29029599
CNN-based ranking for biomedical entity normalization. PMID:28984180
A histological ontology of the human cardiovascular system. PMID:28969675
Mimvec: a deep learning approach for analyzing the human phenome. PMID:28950906
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Design of an extensive information representation scheme for clinical narratives. PMID:28893314
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain. PMID:28881973
Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports. PMID:28862395
Informatics Support for Basic Research in Biomedicine. PMID:28838071
Word2Vec inversion and traditional text classifiers for phenotyping lupus. PMID:28830409
A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies. PMID:28819351
Populating Physician Biographical Pages Based on EMR Data. PMID:28815152
Identifying Metastases-related Information from Pathology Reports of Lung Cancer Patients. PMID:28815141
Active Deep Learning-Based Annotation of Electroencephalography Reports for Cohort Identification. PMID:28815135
Discovering adverse drug events combining spontaneous reports with electronic medical records: a case study of conventional DMARDs and biologics for rheumatoid arthritis. PMID:28815115
CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects. PMID:28790372
An Interoperable Similarity-based Cohort Identification Method Using the OMOP Common Data Model version 5.0. PMID:28776047
TEPAPA: a novel in silico feature learning pipeline for mining prognostic and associative factors from text-based electronic medical records. PMID:28761061
Medical Question Answering for Clinical Decision Support. PMID:28758046
A cascaded approach for Chinese clinical text de-identification with less annotation effort. PMID:28756160
Towards a more molecular taxonomy of disease. PMID:28750648
Cataloguing Treatments Discussed and Used in Online Autism Communities. PMID:28736777
Using Closure Tables to Enable Cross-Querying of Ontologies in Database-Driven Applications. PMID:28725879
Toward patient-tailored summarization of lung cancer literature. PMID:28721401
Sharing Annotated Audio Recordings of Clinic Visits With Patients-Development of the Open Recording Automated Logging System (ORALS): Study Protocol. PMID:28684387
Prescription extraction using CRFs and word embeddings. PMID:28684255
Assigning factuality values to semantic relations extracted from biomedical research literature. PMID:28678823
An Ontology-Enabled Natural Language Processing Pipeline for Provenance Metadata Extraction from Biomedical Text (Short Paper). PMID:28664200
Embedding Open-domain Common-sense Knowledge from Text. PMID:28649676
Leveraging Food and Drug Administration Adverse Event Reports for the Automated Monitoring of Electronic Health Records in a Pediatric Hospital. PMID:28634427
A Computable Phenotype Improves Cohort Ascertainment in a Pediatric Pulmonary Hypertension Registry. PMID:28625502
Machine learning workflow to enhance predictions of Adverse Drug Reactions (ADRs) through drug-gene interactions: application to drugs for cutaneous diseases. PMID:28623363
Quantifying and filtering knowledge generated by literature based discovery. PMID:28617217
Counting trees in Random Forests: Predicting symptom severity in psychiatric intake reports. PMID:28602906
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. PMID:28592275
Text Mining of the Electronic Health Record: An Information Extraction Approach for Automated Identification and Subphenotyping of HFpEF Patients for Clinical Trials. PMID:28585184
An empirical analysis of ontology reuse in BioPortal. PMID:28583809
Automatic recognition of symptom severity from psychiatric evaluation records. PMID:28576748
The effects of natural language processing on cross-institutional portability of influenza case detection for disease surveillance. PMID:28561130
Modulated evaluation metrics for drug-based ontologies. PMID:28438189
Constructing a biodiversity terminological inventory. PMID:28414821
Modeling Integration and Reuse of Heterogeneous Terminologies in Faceted Browsing Systems. PMID:28413840
EHR-based phenotyping: Bulk learning and evaluation. PMID:28410982
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Development of an automated assessment tool for MedWatch reports in the FDA adverse event reporting system. PMID:28371826
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. PMID:28365720
A neural joint model for entity and relation extraction from biomedical text. PMID:28359255
The druggable genome and support for target identification and validation in drug development. PMID:28356508
Semantic Health Knowledge Graph: Semantic Integration of Heterogeneous Medical Knowledge and Services. PMID:28299322
CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice. PMID:28296354
A standard database for drug repositioning. PMID:28291243
Evaluating Terminologies to Enable Imaging-Related Decision Rule Sharing. PMID:28269968
Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. PMID:28269947
GT2RDF: Semantic Representation of Genetic Testing Data. PMID:28269903
Using Natural Language Processing and Network Analysis to Develop a Conceptual Framework for Medication Therapy Management Research. PMID:28269895
Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions. PMID:28269888
Feasibility of Extracting Key Elements from ClinicalTrials.gov to Support Clinicians' Patient Care Decisions. PMID:28269867
Assessing the population representativeness of colorectal cancer treatment clinical trials. PMID:28268936
Computer-Aided Experiment Planning toward Causal Discovery in Neuroscience. PMID:28243197
Predicting disease-related genes using integrated biomedical networks. PMID:28198675
Opportunities and challenges of whole-genome and -exome sequencing. PMID:28193154
Building a model for disease classification integration in oncology, an approach based on the national cancer institute thesaurus. PMID:28173841
Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy. PMID:28137311
Automatic health record review to help prioritize gravely ill Social Security disability applicants. PMID:28108546
Context-sensitive network-based disease genetics prediction and its implications in drug discovery. PMID:28062449
Drug-drug interaction discovery and demystification using Semantic Web technologies. PMID:28031284
Large-scale identification of patients with cerebral aneurysms using natural language processing. PMID:27927935
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. PMID:27924018
mutLBSgeneDB: mutated ligand binding site gene DataBase. PMID:27907895
The Human Phenotype Ontology in 2017. PMID:27899602
Consumers' Use of UMLS Concepts on Social Media: Diabetes-Related Textual Data Analysis in Blog and Social Q&A Sites. PMID:27884812
Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. PMID:27860440
Efficient Results in Semantic Interoperability for Health Care. Findings from the Section on Knowledge Representation and Management. PMID:27830249
Discovering Outliers of Potential Drug Toxicities Using a Large-scale Data-driven Approach. PMID:27812279
DrugCentral: online drug compendium. PMID:27789690
FEDRR: fast, exhaustive detection of redundant hierarchical relations for quality improvement of large biomedical ontologies. PMID:27777627
Leveraging graph topology and semantic context for pharmacovigilance through twitter-streams. PMID:27766937
Introducing the Big Knowledge to Use (BK2U) challenge. PMID:27750400
ODMSummary: A Tool for Automatic Structured Comparison of Multiple Medical Forms Based on Semantic Annotation with the Unified Medical Language System. PMID:27736972
Tumor reference resolution and characteristic extraction in radiology reports for liver cancer stage prediction. PMID:27729234
TrhOnt: building an ontology to assist rehabilitation processes. PMID:27716359
Expansion of medical vocabularies using distributional semantics on Japanese patient blogs. PMID:27671202
Automatic classification of registered clinical trials towards the Global Burden of Diseases taxonomy of diseases and injuries. PMID:27659604
Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain-Specific Terminological Resource. PMID:27643689
Evolution of biomedical ontologies and mappings: Overview of recent approaches. PMID:27642503
Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PMID:27632082
An Infinite Mixture Model for Coreference Resolution in Clinical Notes. PMID:27595047
Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. PMID:27585838
Finding Related Publications: Extending the Set of Terms Used to Assess Article Similarity. PMID:27570676
Towards Evidence-based Precision Medicine: Extracting Population Information from Biomedical Text using Binary Classifiers and Syntactic Patterns. PMID:27570671
A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). PMID:27539197
DTMiner: identification of potential disease targets through biomedical literature mining. PMID:27506226
SentiHealth: creating health-related sentiment lexicon using hybrid approach. PMID:27504237
Using AberOWL for fast and scalable reasoning over BioPortal ontologies. PMID:27502585
Prediction of scaffold proteins based on protein interaction and domain architectures. PMID:27490120
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
Common disease signatures from gene expression analysis in Huntington's disease human blood and brain. PMID:27476530
Drug drug interaction extraction from biomedical literature using syntax convolutional neural network. PMID:27466626
The effect of word sense disambiguation accuracy on literature based discovery. PMID:27455071
Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction. PMID:27338146
Using Social Media Data to Identify Potential Candidates for Drug Repurposing: A Feasibility Study. PMID:27311964
DermO; an ontology for the description of dermatologic disease. PMID:27296450
Demographic-Based Content Analysis of Web-Based Health-Related Social Media. PMID:27296242
DrugQuest - a text mining workflow for drug association discovery. PMID:27295093
HITSZ_CDR: an end-to-end chemical and disease relation extraction system for BioCreative V. PMID:27270713
Temporal bone radiology report classification using open source machine learning and natural langue processing libraries. PMID:27267768
DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research. PMID:27257542
Statin Intensity or Achieved LDL? Practice-based Evidence for the Evaluation of New Cholesterol Treatment Guidelines. PMID:27227451
Argo: enabling the development of bespoke workflows and services for disease annotation. PMID:27189607
Learning disease relationships from clinical drug trials. PMID:27189012
Extracting a stroke phenotype risk factor from Veteran Health Administration clinical reports: an information content analysis. PMID:27175226
BELTracker: evidence sentence retrieval for BEL statements. PMID:27173525
Ontology-based annotations and semantic relations in large-scale (epi)genomics data. PMID:27142216
A Natural Language Processing Tool for Large-Scale Data Extraction from Echocardiography Reports. PMID:27124000
An Interoperability Platform Enabling Reuse of Electronic Health Records for Signal Verification Studies. PMID:27123451
Automated identification of molecular effects of drugs (AIMED). PMID:27107438
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. PMID:27087307
Utilizing uncoded consultation notes from electronic medical records for predictive modeling of colorectal cancer. PMID:27085847
Extraction of chemical-induced diseases using prior knowledge and textual information. PMID:27081155
Sortal anaphora resolution to enhance relation extraction from biomedical literature. PMID:27080229
In silico methods for drug repurposing and pharmacology. PMID:27080087
Efficient identification of nationally mandated reportable cancer cases using natural language processing and machine learning. PMID:27026618
A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes. PMID:27026610
CD-REST: a system for extracting chemical-induced disease relation in literature. PMID:27016700
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. PMID:27011785
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. PMID:27009807
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
Analyzing Self-Help Forums with Ontology-Based Text Mining: An Exploration in Kidney Space. PMID:26958281
DenguePredict: An Integrated Drug Repositioning Approach towards Drug Discovery for Dengue. PMID:26958268
Knowledge Extraction from MEDLINE by Combining Clustering with Natural Language Processing. PMID:26958228
JuFiT: A Configurable Rule Engine for Filtering and Generating New Multilingual Umls Terms. PMID:26958195
COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance. PMID:26958178
Mining and Visualizing Family History Associations in the Electronic Health Record: A Case Study for Pediatric Asthma. PMID:26958171
Extracting drug-enzyme relation from literature as evidence for drug drug interaction. PMID:26955465
The Implicitome: A Resource for Rationalizing Gene-Disease Associations. PMID:26919047
Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data. PMID:26918190
Modeling-Enabled Systems Nutritional Immunology. PMID:26909350
Interoperability between phenotypes in research and healthcare terminologies--Investigating partial mappings between HPO and SNOMED CT. PMID:26865946
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. PMID:26851224
Multivariate analysis of the population representativeness of related clinical studies. PMID:26820188
Weakly supervised learning of biomedical information extraction from curated data. PMID:26817711
Automated Outcome Classification of Computed Tomography Imaging Reports for Pediatric Traumatic Brain Injury. PMID:26766600
Text Mining the History of Medicine. PMID:26734936
Clinicians' Reports in Electronic Health Records Versus Patients' Concerns in Social Media: A Pilot Study of Adverse Drug Reactions of Aspirin and Atorvastatin. PMID:26715498
Ontology Alignment Repair through Modularization and Confidence-Based Heuristics. PMID:26710335
A numerical similarity approach for using retired Current Procedural Terminology (CPT) codes for electronic phenotyping in the Scalable Collaborative Infrastructure for a Learning Health System (SCILHS). PMID:26655696
The Assessment of the Readiness of Molecular Biomarker-Based Mobile Health Technologies for Healthcare Applications. PMID:26644316
Comparing high-dimensional confounder control methods for rapid cohort studies from electronic health records. PMID:26634383
An Overview of Biomolecular Event Extraction from Scientific Documents. PMID:26587051
Building integrated ontological knowledge structures with efficient approximation algorithms. PMID:26550571
Modular organization of the human disease genes: a text-based network inference. PMID:26527852
Global Data Sharing in Alzheimer Disease Research. PMID:26523713
ccmGDB: a database for cancer cell metabolism genes. PMID:26519468
Biomedical literature classification using encyclopedic knowledge: a Wikipedia-based bag-of-concepts approach. PMID:26468436
Learning probabilistic phenotypes from heterogeneous EHR data. PMID:26464024
Semantic biomedical resource discovery: a Natural Language Processing framework. PMID:26423616
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. PMID:26420781
The digital revolution in phenotyping. PMID:26420780
Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. PMID:26387907
Comparison of machine learning classifiers for influenza detection from emergency department free-text reports. PMID:26385375
Beegle: from literature mining to disease-gene discovery. PMID:26384564
Comparison of UMLS terminologies to identify risk of heart disease using clinical notes. PMID:26375493
An automatic system to identify heart disease risk factors in clinical texts over time. PMID:26362344
KneeTex: an ontology-driven system for information extraction from MRI reports. PMID:26347806
Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types. PMID:26330083
Adapting existing natural language processing resources for cardiovascular risk factors identification in clinical notes. PMID:26318122
Learning Semantic Tags from Big Data for Clinical Text Representation. PMID:26306286
Incorporating Statistical Topic Models in the Retrieval of Healthcare Documents. PMID:26306280
NEO: Systematic Non-Lattice Embedding of Ontologies for Comparing the Subsumption Relationship in SNOMED CT and in FMA Using MapReduce. PMID:26306275
Methods for Linking EHR Notes to Education Materials. PMID:26306273
Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction. PMID:26306271
Extending the coverage of phenotypes in SNOMED CT through post-coordination. PMID:26262161
Evaluation of Herbal and Dietary Supplement Resource Term Coverage. PMID:26262159
Fingerprinting Biomedical Terminologies--Automatic Classification and Visualization of Biomedical Vocabularies through UMLS Semantic Group Profiles. PMID:26262156
Identification of Patients with Family History of Pancreatic Cancer--Investigation of an NLP System Portability. PMID:26262122
A systematic comparison of feature space effects on disease classifier performance for phenotype identification of five diseases. PMID:26241355
Combining expert knowledge and knowledge automatically acquired from electronic data sources for continued ontology evaluation and improvement. PMID:26212414
Challenges in clinical natural language processing for automated disorder normalization. PMID:26187250
Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers. PMID:26156524
PhenoPredict: A disease phenome-wide drug repositioning approach towards schizophrenia drug discovery. PMID:26151312
A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat. PMID:26100814
SNOMED CT in a language isolate: an algorithm for a semiautomatic translation. PMID:26100112
Using text mining techniques to extract phenotypic information from the PhenoCHF corpus. PMID:26099853
A survey on the computational approaches to identify drug targets in the postgenomic era. PMID:26060814
kpath: integration of metabolic pathway linked data. PMID:26055101
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. PMID:26047637
Discovering transnosological molecular basis of human brain diseases using biclustering analysis of integrated gene expression data. PMID:26043779
Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury. PMID:25992264
Automating the generation of lexical patterns for processing free text in clinical documents. PMID:25977405
Exploring relation types for literature-based discovery. PMID:25971437
Extracting patient demographics and personal medical information from online health forums. PMID:25954455
A method for analyzing commonalities in clinical trial target populations. PMID:25954450
Automatically Detecting Acute Myocardial Infarction Events from EHR Text: A Preliminary Study. PMID:25954440
Desiderata for an authoritative Representation of MeSH in RDF. PMID:25954433
An empirically derived taxonomy of errors in SNOMED CT. PMID:25954397
Fostering Multilinguality in the UMLS: A Computational Approach to Terminology Expansion for Multiple Languages. PMID:25954371
A Semantic-based Approach for Exploring Consumer Health Questions Using UMLS. PMID:25954347
A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC. PMID:25948699
Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. PMID:25929596
Capturing domain knowledge from multiple sources: the rare bone disorders use case. PMID:25926964
A comparative analysis of the density of the SNOMED CT conceptual content for semantic harmonization. PMID:25890688
Abstraction networks for terminologies: Supporting management of "big knowledge". PMID:25890687
Feature engineering for MEDLINE citation categorization with MeSH. PMID:25887792
OTO: Ontology Term Organizer. PMID:25887779
Wide-coverage relation extraction from MEDLINE using deep syntax. PMID:25887686
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis. PMID:25841438
Large-scale automatic extraction of side effects associated with targeted anticancer drugs from full-text oncological articles. PMID:25817969
Recognition of chemical entities: combining dictionary-based and grammar-based approaches. PMID:25810767
Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing. PMID:25729430
Longitudinal analysis of new information types in clinical notes. PMID:25717418
Automated Tools for Clinical Research Data Quality Control using NCI Common Data Elements. PMID:25717402
Categorizing the Relationships between Structurally Congruent Concepts from Pairs of Terminologies for Semantic Harmonization. PMID:25717400
Application of clinical text data for phenome-wide association studies (PheWASs). PMID:25657332
FXR antagonism of NSAIDs contributes to drug-induced liver injury identified by systems pharmacology approach. PMID:25631039
Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. PMID:25621321
Visual aggregate analysis of eligibility features of clinical trials. PMID:25615940
Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes. PMID:25607983
Next generation phenotyping using the unified medical language system. PMID:25601137
Enabling online studies of conceptual relationships between medical terms: developing an efficient web platform. PMID:25600290
Targeted exploration and analysis of large cross-platform human transcriptomic compendia. PMID:25581801
Semi-supervised learning of causal relations in biomedical scientific discourse. PMID:25559746
DCDB 2.0: a major update of the drug combination database. PMID:25539768
Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles. PMID:25445920
ContextD: an algorithm to identify contextual properties of medical terms in a Dutch clinical corpus. PMID:25432799
OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. PMID:25428349
Sculpting the UMLS Refined Semantic Network. PMID:25422719
An effective method of large scale ontology matching. PMID:25411633
Exploiting Literature-derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs. PMID:25392688
Automatic background knowledge selection for matching biomedical ontologies. PMID:25379899
Engagement with health agencies on twitter. PMID:25379727
ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms. PMID:25361966
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. PMID:25348409
Functional evaluation of out-of-the-box text-mining tools for data-mining tasks. PMID:25336595
A tribal abstraction network for SNOMED CT target hierarchies without attribute relationships. PMID:25332354
Predicting high-throughput screening results with scalable literature-based discovery methods. PMID:25295575
Comparative analysis of a novel disease phenotype network based on clinical manifestations. PMID:25277758
Quantifying the impact and extent of undocumented biomedical synonymy. PMID:25255227
Network medicine analysis of COPD multimorbidities. PMID:25248857
Predicting disease associations via biological network analysis. PMID:25228247
EHR Big Data Deep Phenotyping. Contribution of the IMIA Genomic Medicine Working Group. PMID:25123744
De-identification of clinical narratives through writing complexity measures. PMID:25106934
Generalising semantic category disambiguation with large lexical resources for fun and profit. PMID:25093067
Multi-topic assignment for exploratory navigation of consumer health information in NetWellness using formal concept analysis. PMID:25086916
Effectively processing medical term queries on the UMLS Metathesaurus by layered dynamic programming. PMID:25079259
On combining image-based and ontological semantic dissimilarities for medical image retrieval applications. PMID:25036769
Processing biological literature with customizable Web services supporting interoperable formats. PMID:25006225
Network based integrated analysis of phenotype-genotype data for prioritization of candidate symptom genes. PMID:24991551
Clinic-genomic association mining for colorectal cancer using publicly available datasets. PMID:24987669
Augmenting microarray data with literature-based knowledge to enhance gene regulatory network inference. PMID:24921649
DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. PMID:24895436
Unraveling human protein interaction networks underlying co-occurrences of diseases and pathological conditions. PMID:24731539
Evaluating word representation features in biomedical named entity recognition tasks. PMID:24729964
Using large clinical corpora for query expansion in text-based cohort identification. PMID:24680983
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
Knowledge extraction and semantic annotation of text from the encyclopedia of life. PMID:24594988
Knowledge-based extraction of adverse drug events from biomedical text. PMID:24593054
Automated detection of off-label drug use. PMID:24586689
Integrating systems biology sources illuminates drug action. PMID:24577151
HMPAS: Human Membrane Protein Analysis System. PMID:24564858
Exploring the relationship between drug side-effects and therapeutic indications. PMID:24551427
Automatically extracting clinically useful sentences from UpToDate to support clinicians' information needs. PMID:24551389
Lessons learned in replicating data-driven experiments in multiple medical systems and patient populations. PMID:24551375
Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox. PMID:24551329
Building a common pediatric research terminology for accelerating child health research. PMID:24534404
From concept representations to ontologies: a paradigm shift in health informatics? PMID:24523987
Evaluation of a novel Conjunctive Exploratory Navigation Interface for consumer health information: a crowdsourced comparative study. PMID:24513593
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. PMID:24484917
Auditing the multiply-related concepts within the UMLS. PMID:24464853
Walking on a tissue-specific disease-protein-complex heterogeneous network for the discovery of disease-related protein complexes. PMID:24455720
Exploring the FDA adverse event reporting system to generate hypotheses for monitoring of disease characteristics. PMID:24448476
Using semantic predications to uncover drug-drug interactions in clinical data. PMID:24448204
Word sense disambiguation in the clinical domain: a comparison of knowledge-rich and knowledge-poor unsupervised methods. PMID:24441986
NCBI disease corpus: a resource for disease name recognition and concept normalization. PMID:24393765
A multi-part matching strategy for mapping LOINC with laboratory terminologies. PMID:24363318
Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning. PMID:24334612
Network based elucidation of drug response: from modulators to targets. PMID:24330611
The mouse age phenome knowledgebase and disease-specific inter-species age mapping. PMID:24312529
Automated Detection of Systematic Off-label Drug Use in Free Text of Electronic Medical Records. PMID:24303308
Biomedical Terminology Mapper for UML projects. PMID:24303278
DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data. PMID:24302579
Chronology of your health events: approaches to extracting temporal relations from medical narratives. PMID:24286753
Generic information can retrieve known biological associations: implications for biomedical knowledge discovery. PMID:24260124
A neuroinformatics of brain modeling and its implementation in the Brain Operation Database BODB. PMID:24234915
CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations. PMID:24225062
The semantic web in translational medicine: current applications and future directions. PMID:24197933
Automatic signal extraction, prioritizing and filtering approaches in detecting post-marketing cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS). PMID:24177320
Anatomical entity mention recognition at literature scale. PMID:24162468
Mouse model phenotypes provide information about human drug targets. PMID:24158600
SIDD: a semantically integrated database towards a global view of human disease. PMID:24146757
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PMID:24124474
Cross-domain targeted ontology subsets for annotation: the case of SNOMED CORE and RxNorm. PMID:24095962
Improved de-identification of physician notes through integrative modeling of both public and private medical text. PMID:24083569
Toward knowledge support for analysis and interpretation of complex traits. PMID:24079802
A modular framework for biomedical concept recognition. PMID:24063607
Combining an expert-based medical entity recognizer to a machine-learning system: methods and a case study. PMID:24052691
Automated outcome classification of emergency department computed tomography imaging reports. PMID:24033628
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. PMID:23989082
The age-phenome database. PMID:23984222
Unsupervised biomedical named entity recognition: experiments with clinical and biological texts. PMID:23954592
Standardized drug and pharmacological class network construction. PMID:23920899
Enabling complex queries to drug information sources through functional composition. PMID:23920645
A method for controlling complex confounding effects in the detection of adverse drug reactions using electronic health records. PMID:23907285
Content-based medical image retrieval: a survey of applications to multidimensional and multimodality data. PMID:23846532
Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature. PMID:23828786
Clustering cliques for graph-based summarization of the biomedical research literature. PMID:23742159
Toward creation of a cancer drug toxicity knowledge base: automatically extracting cancer drug-side effect relationships from the literature. PMID:23686935
Feasibility of feature-based indexing, clustering, and search of clinical trials. A case study of breast cancer trials from ClinicalTrials.gov. PMID:23666475
Leveraging concept-based approaches to identify potential phyto-therapies. PMID:23665360
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. PMID:23660285
Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text. PMID:23631733
Using chief complaints for syndromic surveillance: a review of chief complaint based classifiers in North America. PMID:23602781
Eventual situations for timeline extraction from clinical reports. PMID:23571851
A unified structural/terminological interoperability framework based on LexEVS: application to TRANSFoRm. PMID:23571850
Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. PMID:23564629
Analysis of free online physician advice services. PMID:23555848
Leveraging biodiversity knowledge for potential phyto-therapeutic applications. PMID:23518859
crcTRP: a translational research platform for colorectal cancer. PMID:23431356
Incorporating expert terminology and disease risk factors into consumer health vocabularies. PMID:23424146
Redundancy in electronic health record corpora: analysis, impact on text mining performance and mitigation strategies. PMID:23323800
A reference standard for evaluation of methods for drug safety signal detection using electronic healthcare record databases. PMID:23315292
Inter-annotator reliability of medical events, coreferences and temporal relations in clinical narratives by annotators with varying levels of clinical expertise. PMID:23304416
Deterministic binary vectors for efficient automated indexing of MEDLINE/PubMed abstracts. PMID:23304369
OPIC: Ontology-driven Patient Information Capturing system for epilepsy. PMID:23304354
Towards a semantic lexicon for clinical natural language processing. PMID:23304329
Pooling annotated corpora for clinical concept extraction. PMID:23294871
Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project. PMID:23195749
InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. PMID:23158523
Automatically extracting sentences from Medline citations to support clinicians' information needs. PMID:23100128
A UML profile for the OBO relation ontology. PMID:23095840
Unsupervised grammar induction of clinical report sublanguage. PMID:23046834
SemMedDB: a PubMed-scale repository of biomedical semantic predications. PMID:23044550
Using rule-based natural language processing to improve disease normalization in biomedical text. PMID:23043124
Rule-based support system for multiple UMLS semantic type assignments. PMID:23041716
Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles. PMID:23021552
Event extraction across multiple levels of biological organization. PMID:22962484
Evaluation of research in biomedical ontologies. PMID:22962340
Improving image retrieval effectiveness via query expansion using MeSH hierarchical structure. PMID:22952301
A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. PMID:22909066
Discovering discovery patterns with Predication-based Semantic Indexing. PMID:22841748
Network medicine: linking disorders. PMID:22825316
Towards an Oncology Database (ONCOD) Using a Warehousing Approach. PMID:22779060
An automated bayesian framework for integrative gene expression analysis and predictive medicine. PMID:22779059
A bayesian translational framework for knowledge propagation, discovery, and integration under specific contexts. PMID:22779044
Quantifying multi-ethnic representation in genetic studies of high mortality diseases. PMID:22779041
Discriminative application of string similarity methods to chemical and non-chemical names for biomedical abbreviation clustering. PMID:22759617
Biological event composition. PMID:22759461
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. PMID:22759456
A Taxonomy of Representation Strategies in Iconic Communication. PMID:22754274
Automatic discourse connective detection in biomedical text. PMID:22744958
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. PMID:22718037
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. PMID:22711793
Extending ontologies by finding siblings using set expansion techniques. PMID:22689774
Integrative approach to pain genetics identifies pain sensitivity loci across diseases. PMID:22685391
A mutation-centric approach to identifying pharmacogenomic relations in text. PMID:22683993
Extracting semantically enriched events from biomedical literature. PMID:22621266
A chemical specialty semantic network for the Unified Medical Language System. PMID:22577759
Identification of pneumonia and influenza deaths using the Death Certificate Pipeline. PMID:22569097
Mining electronic health records: towards better research applications and clinical care. PMID:22549152
Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes. PMID:22541596
Boosting automatic event extraction from the literature using domain adaptation and coreference resolution. PMID:22539668
Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases. PMID:22511877
Automatic filtering and substantiation of drug safety signals. PMID:22496632
Making sense out of massive data by going beyond differential expression. PMID:22447773
MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database. PMID:22434833
Exploring and linking biomedical resources through multidimensional semantic spaces. PMID:22373409
Clustering of PubMed abstracts using nearer terms of the domain. PMID:22359430
Large-scale elucidation of drug response pathways in humans. PMID:22300318
A closed literature-based discovery technique finds a mechanistic link between hypogonadism and diminished sleep quality in aging men. PMID:22294819
Towards Structuring Unstructured GenBank Metadata for Enhancing Comparative Biological Studies. PMID:22211174
Constructing a semantic predication gold standard from the biomedical literature. PMID:22185221
Ranking gene-drug relationships in biomedical literature using Latent Dirichlet Allocation. PMID:22174297
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. PMID:22166494
k-Neighborhood decentralization: a comprehensive solution to index the UMLS for large scale knowledge discovery. PMID:22154838
A unified framework for managing provenance information in translational research. PMID:22126369
The National Center for Biomedical Ontology. PMID:22081220
Identifying and relating biological concepts in the Catalogue of Life. PMID:22004596
The BioLexicon: a large-scale terminological resource for biomedical text mining. PMID:21992002
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. PMID:21987712
Modeling paradigms for medical diagnostic decision support: a survey and future directions. PMID:21964969
Overcoming an obstacle in expanding a UMLS semantic type extent. PMID:21925287
NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. PMID:21918645
Enhancing biomedical text summarization using semantic relation extraction. PMID:21887336
Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts. PMID:21871110
PhenomeNET: a whole-phenome approach to disease gene discovery. PMID:21737429
Using machine learning for concept extraction on clinical documents from multiple data sources. PMID:21709161
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. PMID:21696594
Exploiting drug-disease relationships for computational drug repositioning. PMID:21690101
Collocation analysis for UMLS knowledge-based word sense disambiguation. PMID:21658291
PREDICT: a method for inferring novel drug indications with application to personalized medicine. PMID:21654673
Resolution of redundant semantic type assignments for organic chemicals in the UMLS. PMID:21646001
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. PMID:21635749
How orthogonal are the OBO Foundry ontologies? PMID:21624157
Predicting adverse drug reactions using publicly available PubChem BioAssay data. PMID:21613989
Protein localization as a principal feature of the etiology and comorbidity of genetic diseases. PMID:21613983
Degree centrality for semantic abstraction summarization of therapeutic studies. PMID:21575741
Linked open drug data for pharmaceutical research and development. PMID:21575203
Logic-based assessment of the compatibility of UMLS ontology sources. PMID:21388571
LabKey Server: an open source platform for scientific data integration, analysis and collaboration. PMID:21385461
CSI-OMIM--Clinical Synopsis Search in OMIM. PMID:21362185
Mining human phenome to investigate modularity of complex disorders. PMID:21347123
Using the UMLS and Simple Statistical Methods to Semantically Categorize Causes of Death on Death Certificates. PMID:21347064
A Knowledge Intensive Approach to Mapping Clinical Narrative to LOINC. PMID:21346974
Using Co-Authoring and Cross-Referencing Information for MEDLINE Indexing. PMID:21346958
GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products. PMID:21342572
Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes. PMID:21251264
Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. PMID:21138947
The reference human genome demonstrates high risk of type 1 diabetes and other disorders. PMID:21121051
Knowledge-based biomedical word sense disambiguation: comparison of approaches. PMID:21092226
Effectiveness of lexico-syntactic pattern matching for ontology enrichment with clinical documents. PMID:21057720
VnD: a structure-centric database of disease-related SNPs and drugs. PMID:21051351
Recent progress in automatically extracting information from the pharmacogenomic literature. PMID:21047206
Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PMID:21042586
Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. PMID:20962136
Impact of sex, age, race, ethnicity and aspirin use on bleeding symptoms in healthy adults. PMID:20942847
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PMID:20885780
Combining relevance assignment with quality of the evidence to support guideline development. PMID:20841778
Associating clinical archetypes through UMLS Metathesaurus term clusters. PMID:20827566
Quantitative analysis of ontology research articles in the radiologic domain. PMID:20821092
Medication information extraction with linguistic pattern matching and semantic rules. PMID:20819858
Commentary: mouse genetic nomenclature. Standardization of strain, gene, and protein symbols. PMID:20685919
Supporting retrieval of diverse biomedical data using evidence-aware queries. PMID:20643225
Building a biomedical ontology recommender web service. PMID:20626921
Rewriting and suppressing UMLS terms for improved biomedical term identification. PMID:20618981
PhenoHM: human-mouse comparative phenome-genome server. PMID:20507906
Document classification for mining host pathogen protein-protein interactions. PMID:20472411
Creating an ontology-based human phenotyping system: The Rockefeller University bleeding history experience. PMID:20443924
Phenotype ontologies for mouse and man: bridging the semantic gap. PMID:20427557
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. PMID:20360561
Predication-based semantic indexing: permutations as a means to encode predications in semantic space. PMID:20351833
Two approaches to integrating phenotype and clinical information. PMID:20351826
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining. PMID:20331846
mspecLINE: bridging knowledge of human disease with the proteome. PMID:20219133
A reference guide for tree analysis and visualization. PMID:20175922
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PMID:20140234
An integrative modular approach to systematically predict gene-phenotype associations. PMID:20122238
A quick guide for developing effective bioinformatics programming skills. PMID:20041221
Advances in translational bioinformatics: computational approaches for the hunting of disease genes. PMID:20007728
Novel protein-protein interactions inferred from literature context. PMID:19924298
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics. PMID:19781082
Disease signatures are robust across tissues and experiments. PMID:19756046
An integrative network approach to map the transcriptome to the phenome. PMID:19630539
Translational disease interpretation with molecular networks. PMID:19591646
Automated multidimensional phenotypic profiling using large public microarray repositories. PMID:19590007
Systematic evaluation of drug-disease relationships to identify leads for novel drug uses. PMID:19571805
Expanding the extent of a UMLS semantic type via group neighborhood auditing. PMID:19567802
Integration of prostate cancer clinical data using an ontology. PMID:19497389
Alignment of the UMLS semantic network with BioTop: methodology and assessment. PMID:19478019
The Neighborhood Auditing Tool: a hybrid interface for auditing the UMLS. PMID:19475725
Auditing associative relations across two knowledge sources. PMID:19475724
Semantic Web-based integration of cancer pathways and allele frequency data. PMID:19458791
Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. PMID:19426461
Application and evaluation of automated semantic annotation of gene expression experiments. PMID:19376825
Fast max-margin clustering for unsupervised word sense disambiguation in biomedical texts. PMID:19344480
Analyzing polysemous concepts from a clinical perspective: application to auditing concept categorization in the UMLS. PMID:19303057
Automated semantic indexing of figure captions to improve radiology image retrieval. PMID:19261938
Identification of discriminating biomarkers for human disease using integrative network biology. PMID:19209693
Ontology-driven indexing of public datasets for translational bioinformatics. PMID:19208184
Integrative disease classification based on cross-platform microarray data. PMID:19208125
Data-driven methods to discover molecular determinants of serious adverse drug events. PMID:19177064
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. PMID:19159460
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases. PMID:19091018
BioTagger-GM: a gene/protein name recognition system. PMID:19074302
Multi-label literature classification based on the Gene Ontology graph. PMID:19063730
A computational linguistics motivated mapping of ICPC-2 PLUS to SNOMED CT. PMID:19007442
Gene-L'EXPO: a tool to extract knowledge From transcriptomes and find 'Literature-Sparse' relationships between genes and tissues. PMID:18999036
Experience in Aligning Anatomical Ontologies. PMID:18974854
miR2Disease: a manually curated database for microRNA deregulation in human disease. PMID:18927107
Overview of BioCreative II gene mention recognition. PMID:18834493
A proposed taxonomy for characterization and assessment of avian influenza outbreaks. PMID:18805050
Translational integrity and continuity: personalized biomedical data integration. PMID:18760382
An automated standardized system for managing adverse events in clinical research networks. PMID:18759506
A study of abbreviations in clinical notes. PMID:18693951
Enhancing acronym/abbreviation knowledge bases with semantic information. PMID:18693933
The @neurIST ontology of intracranial aneurysms: providing terminological services for an integrated IT infrastructure. PMID:18693797
Accessing and integrating data and knowledge for biomedical research. PMID:18660883
Biomedical ontologies in action: role in knowledge management, data integration and decision support. PMID:18660879
Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease. PMID:18577208
Anni 2.0: a multipurpose text-mining tool for the life sciences. PMID:18549479
Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation. PMID:18541046
Calling on a million minds for community annotation in WikiProteins. PMID:18507872
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. PMID:18460187
Mapping proteins to disease terminologies: from UniProt to MeSH. PMID:18460185
Terminologies for text-mining; an experiment in the lipoprotein metabolism domain. PMID:18460175
Extraction of semantic biomedical relations from text using conditional random fields. PMID:18433469
Heterogeneous but "standard" coding systems for adverse events: Issues in achieving interoperability between apples and oranges. PMID:18406213
Bioinformatics and cancer research: building bridges for translational research. PMID:18258507
Corpus annotation for mining biomedical events from literature. PMID:18182099
A comparison study on algorithms of detecting long forms for short forms in biomedical text. PMID:18047706
Framework for a protein ontology. PMID:18047702
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. PMID:17989687
Automated acquisition of disease drug knowledge from biomedical and clinical documents: an initial study. PMID:17947625
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
Topological analysis of large-scale biomedical terminology structures. PMID:17712094
Using contextual and lexical features to restructure and validate the classification of biomedical concepts. PMID:17650333
Towards Semantic e-Science for Traditional Chinese Medicine. PMID:17493289
Ontology-based annotation and query of tissue microarray data. PMID:17238433
Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. PMID:17238312
Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation. PMID:17233900
Analysis of a study of the users, uses, and future agenda of the UMLS. PMID:17213497
Automated recognition of malignancy mentions in biomedical literature. PMID:17090325
Auditing as part of the terminology design life cycle. PMID:16929044
Bio-ontologies: current trends and future directions. PMID:16899495
Gene and protein nomenclature in public databases. PMID:16899134
Bio-Ontology and text: bridging the modeling gap. PMID:16870928
Quantitative assessment of dictionary-based protein named entity tagging. PMID:16799122
A system for automated lexical mapping. PMID:16501186
Creation and implications of a phenome-genome network. PMID:16404398
Trial Registration at ClinicalTrials.gov between May and October 2005. PMID:16382064
The Gene Ontology (GO) project in 2006. PMID:16381878
Integration of text- and data-mining using ontologies successfully selects disease gene candidates. PMID:15767279
Genestrace: phenomic knowledge discovery via structured terminology. PMID:15759618
Non-lexical approaches to identifying associative relations in the gene ontology. PMID:15759617
Design of Genetics Home Reference: a new NLM consumer health resource. PMID:15298997

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The Unified Medical Language System (UMLS): integrating biomedical terminology
PMID: 14681409
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Better Rx BRIT2 Patient GP Dataset

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Publications: Publications More detailed information about this field from each metasource. × The Unified Medical Language System (UMLS): integrating biomedical terminology PMID: 14681409 metasource: BiŌkeanós-Medsourcing version: 0.0.1:2022-11-04T13:34:25.975929 Close

More to explore:

1/20

UMLS Semantic Network

Metathesaurus CPT Hierarchical Terms

Veterans Health Administration National Drug File

WHO Adverse Reaction Terminology

Coding Symbols for a Thesaurus of Adverse Reaction Terms

PubMed

Visible Human Project

eRAM

Medical Subject Headings

RxNORM

NCBI Taxonomy

Better Rx BRIT2 Patient GP Dataset

PubMed Central

NCBI Bookshelf

Gene Expression Omnibus

BioSystems

NIH Genetic Testing Registry

Medical Data Models

Traditional Medicine Signs and Symptoms Value Set

Molecular Modeling Database

Publications:

Publications
More detailed information about this field from each metasource.

The Unified Medical Language System (UMLS): integrating biomedical terminology
PMID: 14681409
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929