HistoML, a markup language for representation and exchange of histopathological features in pathology images.
PMID:35803960
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content.
PMID:35388368
The Biomedical Research Hub: a federated platform for patient research data.
PMID:35289369
Variomes: a high recall search engine to support the curation of genomic variants.
PMID:35274687
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data.
PMID:35227770
Fast and flexible analysis of linked microbiome data with mako.
PMID:34887550
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.
PMID:34788826
A Lexical-based Formal Concept Analysis Method to Identify Missing Concepts in the NCI Thesaurus.
PMID:34721941
Extracting Concepts for Precision Oncology from the Biomedical Literature.
PMID:34457142
CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects.
PMID:34345532
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses.
PMID:34156446
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model.
PMID:34015823
A resource to explore the discovery of rare diseases and their causative genes.
PMID:33947870
Catch Me if You Can: Acute Events Hidden in Structured Chronic Disease Diagnosis Descriptions Show Detectable Recording Patterns in EHR.
PMID:33936410
Improved characterisation of clinical text through ontology-based vocabulary expansion.
PMID:33845909
An empirical meta-analysis of the life sciences linked open data on the web.
PMID:33479214
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes.
PMID:33418085
Detecting missing IS-A relations in the NCI Thesaurus using an enhanced hybrid approach.
PMID:33319703
Quality assurance and enrichment of biological and biomedical ontologies and terminologies.
PMID:33319696
PK-DB: pharmacokinetics database for individualized and stratified computational modeling.
PMID:33151297
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs.
PMID:33106501
Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures.
PMID:32997669
DICOM re-encoding of volumetrically annotated Lung Imaging Database Consortium (LIDC) nodules.
PMID:32772385
An integrated chemical environment with tools for chemical safety testing.
PMID:32553663
Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review.
PMID:32508881
Building Cancer Diagnosis Text to OncoTree Mapping Pipelines for Clinical Sequencing Data Integration and Curation.
PMID:32477665
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts.
PMID:32379317
Enhancing the Quality of Hierarchic Relations in the National Cancer Institute Thesaurus to Enable Faceted Query of Cancer Registry Data.
PMID:32374632
Database of pharmacokinetic time-series data and parameters for 144 environmental chemicals.
PMID:32313097
Bootstrapping Adversarial Learning of Biomedical Ontology Alignments.
PMID:32308857
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.
PMID:32246132
Standardizing Chemotherapy Regimen Nomenclature: A Proposal and Evaluation of the HemOnc and National Cancer Institute Thesaurus Regimen Content.
PMID:31990580
A tale of three subspecialties: Diagnosis recording patterns are internally consistent but Specialty-Dependent.
PMID:31984369
Using an artificial neural network to map cancer common data elements to the biomedical research integrated domain group model in a semi-automated manner.
PMID:31865899
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
PMID:31701156
Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties.
PMID:31551780
Enabling Web-scale data integration in biomedicine through Linked Open Data.
PMID:31531395
Meta-path Based Prioritization of Functional Drug Actions with Multi-Level Biological Networks.
PMID:30940832
Overlapping Complex Concepts Have More Commission Errors, Especially in Intensive Terminology Auditing.
PMID:30815158
Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data.
PMID:30691868
Harnessing formal concepts of biological mechanism to analyze human disease.
PMID:30586388
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.
PMID:30445434
Overview of the BioCreative VI text-mining services for Kinome Curation Track.
PMID:30329035
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations.
PMID:30246165
Computerized Approach to Creating a Systematic Ontology of Hematology/Oncology Regimens.
PMID:30238070
Biopsy Records Do Not Reduce Diagnosis Variability in Cancer Patient EHRs: Are We More Uncertain After Knowing?
PMID:29888044
Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies.
PMID:29852316
The Cellosaurus, a Cell-Line Knowledge Resource.
PMID:29805321
Progress Toward Cancer Data Ecosystems.
PMID:29794537
Curated compendium of human transcriptional biomarker data.
PMID:29664470
Analyzing user interactions with biomedical ontologies: A visual perspective.
PMID:29657560
Where to search top-K biomedical ontologies?
PMID:29579141
Data collection of patient outcomes: one institution's experience.
PMID:29538757
Taxonomy-Based Approaches to Quality Assurance of Ontologies.
PMID:29158885
Evaluating Casama: Contextualized semantic maps for summarization of lung cancer studies.
PMID:29149658
PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.
PMID:29092942
Evidence-Based Precision Oncology with the Cancer Targetome.
PMID:28964549
A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies.
PMID:28819351
An ontology-driven tool for structured data acquisition using Web forms.
PMID:28764813
Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology.
PMID:28723580
Toward patient-tailored summarization of lung cancer literature.
PMID:28721401
The anatomy of phenotype ontologies: principles, properties and applications.
PMID:28387809
Consensus-Driven Development of a Terminology for Biobanking, the Duke Experience.
PMID:28338350
CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice.
PMID:28296354
Nine Principles of Semantic Harmonization.
PMID:28269840
Development of a Pediatric Adverse Events Terminology.
PMID:28028203
COSMIC: somatic cancer genetics at high-resolution.
PMID:27899578
Evolution of biomedical ontologies and mappings: Overview of recent approaches.
PMID:27642503
An information model for computable cancer phenotypes.
PMID:27629872
Using AberOWL for fast and scalable reasoning over BioPortal ontologies.
PMID:27502585
neXtA5: accelerating annotation of articles via automated approaches in neXtProt.
PMID:27374119
Facilitating a culture of responsible and effective sharing of cancer genome data.
PMID:27149219
SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care.
PMID:27018265
A Biomedical Research Permissions Ontology: Cognitive and Knowledge Representation Considerations.
PMID:26640828
Analysis and Prediction of User Editing Patterns in Ontology Development Projects.
PMID:26052350
Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.
PMID:26034559
Next generation distributed computing for cancer research.
PMID:25983539
Quality Assurance of UMLS Semantic Type Assignments Using SNOMED CT Hierarchies.
PMID:25925776
Abstraction networks for terminologies: Supporting management of "big knowledge".
PMID:25890687
Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows.
PMID:25789153
The neXtProt knowledgebase on human proteins: current status.
PMID:25593349
Ontology-based data integration between clinical and research systems.
PMID:25588043
Semantically linking in silico cancer models.
PMID:25520553
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.
PMID:25348409
A tribal abstraction network for SNOMED CT target hierarchies without attribute relationships.
PMID:25332354
A reappraisal of how to build modular, reusable models of biological systems.
PMID:25275523
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives.
PMID:25254202
Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.
PMID:24953242
Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research.
PMID:24932210
Egas: a collaborative and interactive document curation platform.
PMID:24923820
OncoSearch: cancer gene search engine with literature evidence.
PMID:24813447
Toward a common language for biobanking.
PMID:24713663
Scalability of abstraction-network-based quality assurance to large SNOMED hierarchies.
PMID:24551393
Building a common pediatric research terminology for accelerating child health research.
PMID:24534404
The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources.
PMID:24438387
How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects.
PMID:24311994
Discovering disease-disease associations by fusing systems-level molecular data.
PMID:24232732
The semantic web in translational medicine: current applications and future directions.
PMID:24197933
Effective visualization of integrated knowledge and data to enable informed decisions in drug development and translational medicine.
PMID:24098919
Automated extraction of precise protein expression patterns in lymphoma by text mining abstracts of immunohistochemical studies.
PMID:23967385
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation.
PMID:23409969
ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format.
PMID:23311978
Multiscale integration of -omic, imaging, and clinical data in biomedical informatics.
PMID:23231990
Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study.
PMID:23201637
The Disease and Gene Annotations (DGA): an annotation resource for human disease.
PMID:23197658
Accelerating cancer systems biology research through Semantic Web technology.
PMID:23188758
A UML profile for the OBO relation ontology.
PMID:23095840
Open biomedical pluralism: formalising knowledge about breast cancer phenotypes.
PMID:23046572
Leveraging EHR data for outcomes and comparative effectiveness research in oncology.
PMID:22948276
omniBiomarker: A Web-Based Application for Knowledge-Driven Biomarker Identification.
PMID:22893372
Towards linked open gene mutations data.
PMID:22536974
The mouse-human anatomy ontology mapping project.
PMID:22434834
k-Neighborhood decentralization: a comprehensive solution to index the UMLS for large scale knowledge discovery.
PMID:22154838
Disease Ontology: a backbone for disease semantic integration.
PMID:22080554
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.
PMID:21624155
OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.
PMID:21619703
Identifying Granularity Differences between Large Biomedical Ontologies through Rules.
PMID:21347114
Exposing the cancer genome atlas as a SPARQL endpoint.
PMID:20851208
Extracting cancer quality indicators from electronic medical records: evaluation of an ontology-based virtual medical record approach.
PMID:20351878
STITCH 2: an interaction network database for small molecules and proteins.
PMID:19897548
Semantic web data warehousing for caGrid.
PMID:19796399
Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.
PMID:19789731
OnEX: Exploring changes in life science ontologies.
PMID:19678926
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
A novel information retrieval model for high-throughput molecular medicine modalities.
PMID:19458790
Application and evaluation of automated semantic annotation of gene expression experiments.
PMID:19376825
Detecting role errors in the gene hierarchy of the NCI Thesaurus.
PMID:19221606
The caBIG terminology review process.
PMID:19154797
Annotating breast cancer microarray samples using ontologies.
PMID:18999108
Complexity measures to track the evolution of a SNOMED hierarchy.
PMID:18998922
Developing biomedical ontologies collaboratively.
PMID:18998901
Translational integrity and continuity: personalized biomedical data integration.
PMID:18760382
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
Automated comparative auditing of NCIT genomic roles using NCBI.
PMID:18486558
semCDI: a query formulation for semantic data integration in caBIG.
PMID:18436897
Bio*Medical Informatics and Genomic Medicine: Research and Training.
PMID:18239725
Data standards in clinical research: gaps, overlaps, challenges and future directions.
PMID:17712081
Protégé: a tool for managing and using terminology in radiology applications.
PMID:17687607
caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability.
PMID:17512259
Advancing translational research with the Semantic Web.
PMID:17493285
PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm.
PMID:17014720
The CAP cancer protocols--a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid.
PMID:16787533