yusuke1997/dblp-id-title huggingface dataset:
Identifying and relating biological concepts in the Catalogue of Life
Synthesizing evidence from clinical trials with dynamic interactive argument trees
Open semantic annotation of scientific publications using DOMEO
Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs
Digital evolution: Novo Nordisk's shift to ontology-based data management
Predicting instances of pathway ontology classes for pathway integration
Identification of sex-associated network patterns in Vaccine-Adverse Event Association Network in VAERS
Semantic validation of the use of SNOMED CT in HL7 clinical documents
Finding biomedical categories in Medline ®
Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology
Monitoring named entity recognition: the League Table
Predicting activities of daily living for cancer patients using an ontology-guided machine learning methodology
Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens
Capturing domain knowledge from multiple sources: the rare bone disorders use case
A novel method to identify pre-microRNA in various species knowledge base on various species
Reliability and type of consumer health documents on the World Wide Web: an annotation study
OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system
Ontology of physics for biology: representing physical dependencies as a basis for biological processes
A framework for ontology-based question answering with application to parasite immunology
Semantics-based composition of EMBOSS services
DCSO: towards an ontology for machine-actionable data management plans
AISO: Annotation of Image Segments with Ontologies
TrhOnt: building an ontology to assist rehabilitation processes
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update
Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery
How orthogonal are the OBO Foundry ontologies?
An annotated corpus of clinical trial publications supporting schema-based relational information extraction
Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology
Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT
Identifying disease trajectories with predicate information from a knowledge graph
Disease mentions in airport and hospital geolocations expose dominance of news events for disease concerns
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events
An ontological analysis of medical Bayesian indicators of performance
Automated Reasoning using Abduction for Interpretation of Medical Signals
Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates
A cascade of classifiers for extracting medication information from discharge summaries
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic
Protein interaction sentence detection using multiple semantic kernels
Biomedical ontology alignment: an approach based on representation learning
Introducing glycomics data into the Semantic Web
Multimodal temporal-clinical note network for mortality prediction
Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features
Neural side effect discovery from user credibility and experience-assessed online health discussions
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
DermO; an ontology for the description of dermatologic disease
The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms
Building a model for disease classification integration in oncology, an approach based on the national cancer institute thesaurus
Automatic extraction of semantic relations between medical entities: a rule based approach
InContext: curation of medical context for drug indications
Towards mature use of semantic resources for biomedical analyses
Ontology design patterns to disambiguate relations between genes and gene products in GENIA
COMODI: an ontology to characterise differences in versions of computational models in biology
Classifying literature mentions of biological pathogens as experimentally studied using natural language processing
The Drosophila anatomy ontology
An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology
Semantic Web repositories for genomics data using the eXframe platform
COEUS: "semantic web in a box" for biomedical applications
Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting
Linking gene expression to phenotypes via pathway information
Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting
Exploiting document graphs for inter sentence relation extraction
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
Generalising semantic category disambiguation with large lexical resources for fun and profit
CUILESS2016: a clinical corpus applying compositional normalization of text mentions
A fourfold pathogen reference ontology suite
An ontology-based exploration of the concepts and relationships in the activities and participation component of the international classification of functioning, disability and health
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species
Thematic series on biomedical ontologies in JBMS: challenges and new directions
Ontology-based specification, identification and analysis of perioperative risks
Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung
Matching biomedical ontologies based on formal concept analysis
Extending electronic medical records vector models with knowledge graphs to improve hospitalization prediction
Query enhancement through the practical application of ontology: the IEDB and OBI
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature
An open annotation ontology for science on web 3.0
Building Linked Open Data towards integration of biomedical scientific literature with DBpedia
SimSUM - simulated benchmark with structured and unstructured medical records
Section level search functionality in Europe PMC
BASIL DB: bioactive semantic integration and linking database
Representing annotation compositionality and provenance for the Semantic Web
An annotation and modeling schema for prescription regimens
Querying clinical data in HL7 RIM based relational model with morph-RDB
Multi-task transfer learning for the prediction of entity modifiers in clinical text: application to opioid use disorder case detection
Ontology-based literature mining of E. coli vaccine-associated gene interaction networks
Phenotype annotation with the ontology of microbial phenotypes (OMP)
Developing a semantically rich ontology for the biobank-administration domain
Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation
Rewriting and suppressing UMLS terms for improved biomedical term identification
A Maximum-Entropy approach for accurate document annotation in the biomedical domain
Representation of research hypotheses
Automated concept and relationship extraction for the semi-automated ontology management (SEAM) system
Enriching the FIDEO ontology with food-drug interactions from online knowledge sources
Why and how to engage expert stakeholders in ontology development: insights from social and behavioural sciences
Colil: a database and search service for citation contexts in the life sciences domain
Ontology based mining of pathogen-disease associations from literature
Automating generation of textual class definitions from OWL to English
Semantic enrichment of longitudinal clinical study data using the CDISC standards and the semantic statistics vocabularies
owlcpp: a C++ library for working with OWL ontologies
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes
Synthetic data for annotation and extraction of family history information from clinical text
Explanatory argumentation in natural language for correct and incorrect medical diagnoses
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology
Natural language processing for disease phenotyping in UK primary care records for research: a pilot study in myocardial infarction and death
The Proteasix Ontology
Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request
Building a biomedical ontology recommender web service
Disease Compass- a navigation system for disease knowledge based on ontology and linked data techniques
Evaluating the effect of annotation size on measures of semantic similarity
BioLemmatizer: a lemmatization tool for morphological processing of biomedical text
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms
Trivalent influenza vaccine adverse symptoms analysis based on MedDRA terminology using VAERS data in 2011
Generation of open biomedical datasets through ontology-driven transformation and integration processes
An analysis of gene/protein associations at PubMed scale
The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation
Identification of conclusive association entities in biomedical articles
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Analysis and visualization of disease courses in a semantically-enabled cancer registry
MedEval - A Swedish medical test collection with doctors and patients user groups
Making adjustments to event annotations for improved biological event extraction
A use case study on late stent thrombosis for ontology-based temporal reasoning and analysis
What's unusual in online disease outbreak news?
De-identifying free text of Japanese electronic health records
Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy
Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop
Preserving sequence annotations across reference sequences
Analysis and implementation of the DynDiff tool when comparing versions of ontology
An ontology network for Diabetes Mellitus in Mexico
Open biomedical pluralism: formalising knowledge about breast cancer phenotypes
Synonym extraction and abbreviation expansion with ensembles of semantic spaces
An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD)
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research
Temporal information extraction from mental health records to identify duration of untreated psychosis
12 years on - Is the NLM medical text indexer still useful and relevant?
OBML - Ontologies in Biomedicine and Life Sciences
Combining lexical and context features for automatic ontology extension
OAE: The Ontology of Adverse Events
Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles
An ontologically founded architecture for information systems in clinical and epidemiological research
Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards
IDOMAL: the malaria ontology revisited
SIENA: Semi-automatic semantic enhancement of datasets using concept recognition
The mouse pathology ontology, MPATH; structure and applications
Improving reusability along the data life cycle: a regulatory circuits case study
Modeling biomedical experimental processes with OBI
OBIB-a novel ontology for biobanking
The environment ontology: contextualising biological and biomedical entities
A framework for assessing the consistency of drug classes across sources
Towards refactoring the Molecular Function Ontology with a UML profile for function modeling
An ontology for major histocompatibility restriction
Defining health data elements under the HL7 development framework for metadata management
End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach
Characteristics of Finnish and Swedish intensive care nursing narratives: a comparative analysis to support the development of clinical language technologies
Functional tissue units and their primary tissue motifs in multi-scale physiology
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment
The CLEAR Principle: organizing data and metadata into semantically meaningful types of FAIR Digital Objects to increase their human explorability and cognitive interoperability
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models
Developing a web-based SKOS editor
PAV ontology: provenance, authoring and versioning
Querying archetype-based EHRs by search ontology-based XPath engineering
HyQue: evaluating hypotheses using Semantic Web technologies
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis
Project Rosetta: a childhood social, emotional, and behavioral developmental feature mapping
Ranking relations between diseases, drugs and genes for a curation task
Moonstone: a novel natural language processing system for inferring social risk from clinical narratives
Representing dispositions
Profiling structured product labeling with NDF-RT and RxNorm
An ontological modeling approach for abnormal states and its application in the medical domain
Methodologically grounded semantic analysis of large volume of chilean medical literature data applied to the analysis of medical research funding efficiency in Chile
A semantic-based method for extracting concept definitions from scientific publications: evaluation in the autism phenotype domain
Building a drug ontology based on RxNorm and other sources
NCBO Technology: Powering semantically aware applications
OWL model of clinical trial eligibility criteria compatible with partially-known information
Developing VISO: Vaccine Information Statement Ontology for patient education
Pooling annotated corpora for clinical concept extraction
Scalable representations of diseases in biomedical ontologies
Louhi 2010: Special issue on Text and Data Mining of Health Documents
Ontology-based specification and generation of search queries for post-market surveillance
Toward a comprehensive drug ontology: extraction of drug-indication relations from diverse information sources
Logic-based assessment of the compatibility of UMLS ontology sources
Automatic transparency evaluation for open knowledge extraction systems
Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse
Improving the interoperability of biomedical ontologies with compound alignments
Tackling the challenges of matching biomedical ontologies
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio
Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications
Biomedical semantics in the Semantic Web
Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference
Context-based refinement of mappings in evolving life science ontologies
Towards exergaming commons: composing the exergame ontology for publishing open game data
CAS: corpus of clinical cases in French
Organizing phenotypic data - a semantic data model for anatomy
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease
Annotation of epilepsy clinic letters for natural language processing
OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows
Toward a systematic conflict resolution framework for ontologies
The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
Dione: An OWL representation of ICD-10-CM for classifying patients' diseases
miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases
Enrichment analysis applied to disease prognosis
Neuroanatomical domain of the foundational model of anatomy ontology
Vaccine and Drug Ontology Studies (VDOS 2014)
Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts
Variation ontology: annotator guide
Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses
Consolidating drug data on a global scale using Linked Data
Ontology-based representation and analysis of host-Brucella interactions
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative
MIRO: guidelines for minimum information for the reporting of an ontology
A document-centric approach for developing the tolAPC ontology
ECLed- a tool supporting the effective use of the SNOMED CT Expression Constraint Language
Extracting a stroke phenotype risk factor from Veteran Health Administration clinical reports: an information content analysis
Standardizing adverse drug event reporting data
Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases
Erratum to: Extracting drug-enzyme relation from literature as evidence for drug drug interaction
BioUSeR: A semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements
Multi-domain knowledge graph embeddings for gene-disease association prediction
Towards an ontological representation of morbidity and mortality in Description Logics
Automatically exposing OpenLifeData via SADI semantic Web Services
Large-scale online semantic indexing of biomedical articles via an ensemble of multi-label classification models
Anatomy ontologies and potential users: bridging the gap
Enriched knowledge representation in biological fields: a case study of literature-based discovery in Alzheimer's disease
Making species checklists understandable to machines - a shift from relational databases to ontologies
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside
Improving the classification of cardinality phenotypes using collections
Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks
DMTO: a realistic ontology for standard diabetes mellitus treatment
A corpus of potentially contradictory research claims from cardiovascular research abstracts
An evolutionary approach to Function
Similarity corpus on microbial transcriptional regulation
Ontological interpretation of biomedical database content
Development of an Ontology for Periodontitis
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
The cellular microscopy phenotype ontology
Interoperability between phenotypes in research and healthcare terminologies - Investigating partial mappings between HPO and SNOMED CT
SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature
Thematic clustering of text documents using an EM-based approach
Using ontologies to study cell transitions
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
Literature mining of protein-residue associations with graph rules learned through distant supervision
Towards a more molecular taxonomy of disease
Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction
New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern
Identifying genotype-phenotype relationships in biomedical text
OHMI: the ontology of host-microbiome interactions
Implementation of linked data in the life sciences at BioHackathon 2011
Discovering opinion leaders for medical topics using news articles
Data- and expert-driven rule induction and filtering framework for functional interpretation and description of gene sets
Prefrontal fNIRS-based clinical data analysis of brain functions in individuals abusing different types of drugs
Why functions are not special dispositions: an improved classification of realizables for top-level ontologies
Disjunctive shared information between ontology concepts: application to Gene Ontology
Function of dynamic models in systems biology: linking structure to behaviour
Mapping between the OBO and OWL ontology languages
Development and validation of the early warning system scores ontology
Active learning for ontological event extraction incorporating named entity recognition and unknown word handling
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data
My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development
Linking common human diseases to their phenotypes; development of a resource for human phenomics
An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows
RecSOI: recommending research directions using statements of ignorance
Integrating terminologies into standard SQL: a new approach for research on routine data
The use of foundational ontologies in biomedical research
Integration and publication of heterogeneous text-mined relationships on the Semantic Web
Developing a kidney and urinary pathway knowledge base
Seeing the whole picture: integrated pre-surgery reports with PreOptique
Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web
Simple tricks for improving pattern-based information extraction from the biomedical literature
Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase
Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs
Mining images in biomedical publications: Detection and analysis of gel diagrams
FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example
PhenoImageShare: an image annotation and query infrastructure
OntoStudyEdit: a new approach for ontology-based representation and management of metadata in clinical and epidemiological research
An ontology-based approach for developing a harmonised data-validation tool for European cancer registration
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
GalenOWL: Ontology based drug recommendations discovery
Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data