OBO Foundry
Names
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OBO Foundry
metasource: Fairsharing.org
version: None
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:40.811789
OBO
metasource: Fairsharing.org
version: None
obo_foundry
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:40.811789
Names
More detailed information about this field from each metasource.
OBO Foundry
metasource: Fairsharing.orgversion: None
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:40.811789
OBO
metasource: Fairsharing.orgversion: None
obo_foundry
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:40.811789
Names
More detailed information about this field from each metasource.
OBO Foundry
metasource: Fairsharing.orgversion: None
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:40.811789
OBO
metasource: Fairsharing.orgversion: None
obo_foundry
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:40.811789
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
Description
More detailed information about this field from each metasource.
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
metasource: Fairsharing.orgversion: None
Community development of interoperable ontologies for the biological sciences
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:40.811789
Webpage:
http://www.obofoundry.org/Webpage
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http://www.obofoundry.org/
metasource: Fairsharing.orgversion: None
http://obofoundry.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:40.811789
Licence:
Name: CC0-1.0Licence name
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Publications:
Publications
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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
PMID: 17989687
metasource: Fairsharing.org
version: None
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
PMID: 34697637
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:40.811789
Publications
More detailed information about this field from each metasource.
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
PMID: 17989687
metasource: Fairsharing.org
version: None
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
PMID: 34697637
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:40.811789
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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
PubMed citations: 773.
773 articles citing: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
Semantics of Dairy Fermented Foods: A Microbiologist's Perspective. PMID:35804753
HistoML, a markup language for representation and exchange of histopathological features in pathology images. PMID:35803960
Whole-Genome Resequencing Deciphers New Insight Into Genetic Diversity and Signatures of Resistance in Cultivated Cotton Gossypium hirsutum. PMID:35778659
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research. PMID:35761389
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms. PMID:35758802
Dysregulation of microRNAs and tRNA-derived ncRNAs in mesothelial and mesothelioma cell lines after asbestiform fiber exposure. PMID:35654808
Assessing the Need for Semantic Data Integration for Surgical Biobanks-A Knowledge Representation Perspective. PMID:35629179
A Simple Standard for Sharing Ontological Mappings (SSSOM). PMID:35616100
eTRANSAFE: Building a sustainable framework to share reproducible drug safety knowledge with the public domain. PMID:35602243
A catalogue with semantic annotations makes multilabel datasets FAIR. PMID:35508507
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic. PMID:35468846
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation. PMID:35363306
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. PMID:35317743
Community Consensus Guidelines to Support FAIR Data Standards in Clinical Research Studies in Primary Mitochondrial Disease. PMID:35317023
Expressing and Executing Informed Consent Permissions Using SWRL: The All of Us Use Case. PMID:35309008
VectorMap-GR: A local scale operational management tool for entomological monitoring, to support vector control activities in Greece and the Mediterranean Basin. PMID:35284881
Semantic Integration of Multi-Modal Data and Derived Neuroimaging Results Using the Platform for Imaging in Precision Medicine (PRISM) in the Arkansas Imaging Enterprise System (ARIES). PMID:35224477
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. PMID:35169842
Food Recipe Ingredient Substitution Ontology Design Pattern. PMID:35161841
Authors' attitude toward adopting a new workflow to improve the computability of phenotype publications. PMID:35106535
Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation. PMID:35101121
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. PMID:35058462
Toward Data-Driven Radiation Oncology Using Standardized Terminology as a Starting Point: Cross-sectional Study. PMID:35044315
Minimal Information about MHC Multimers (MIAMM). PMID:35042788
Categorizing metadata to help mobilize computable biomedical knowledge. PMID:35036552
Systematic reporting of medical kidney biopsies. PMID:35035933
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey. PMID:34991460
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems. PMID:34956127
Concept recognition as a machine translation problem. PMID:34920707
octoFLUshow: an Interactive Tool Describing Spatial and Temporal Trends in the Genetic Diversity of Influenza A Virus in U.S. Swine. PMID:34913720
Surgical data science - from concepts toward clinical translation. PMID:34879287
An Overview of Biomedical Ontologies for Pandemics and Infectious Diseases Representation. PMID:34868401
The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts. PMID:34831777
The Data Use Ontology to streamline responsible access to human biomedical datasets. PMID:34820659
RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data. PMID:34809564
The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction. PMID:34789143
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
Cell type ontologies of the Human Cell Atlas. PMID:34750578
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. PMID:34718728
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. PMID:34697637
Context-aware multi-token concept recognition of biological entities. PMID:34674631
Genetic variations analysis for complex brain disease diagnosis using machine learning techniques: opportunities and hurdles. PMID:34616886
TCDO: A Community-Based Ontology for Integrative Representation and Analysis of Traditional Chinese Drugs and Their Properties. PMID:34603473
Modelling the bioinformatics tertiary analysis research process. PMID:34592928
The role of metadata in reproducible computational research. PMID:34553169
Leveraging the Cell Ontology to classify unseen cell types. PMID:34548483
ISA API: An open platform for interoperable life science experimental metadata. PMID:34528664
Specifying who delivers behaviour change interventions: development of an Intervention Source Ontology. PMID:34497878
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. PMID:34454610
Toward a systematic conflict resolution framework for ontologies. PMID:34372934
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
Why Is the Electronic Health Record So Challenging for Research and Clinical Care? PMID:34282602
The Infectious Disease Ontology in the age of COVID-19. PMID:34275487
Standardization of assay representation in the Ontology for Biomedical Investigations. PMID:34244718
Visual comprehension and orientation into the COVID-19 CIDO ontology. PMID:34224898
Agent-Based Semantic Role Mining for Intelligent Access Control in Multi-Domain Collaborative Applications of Smart Cities. PMID:34206164
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study. PMID:34156445
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies. PMID:33991093
The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX). PMID:33981708
Knowledge-Based Biomedical Data Science. PMID:33954284
A semantic database for integrated management of image and dosimetric data in low radiation dose research in medical imaging. PMID:33936422
Capturing Clinician Reasoning in Electronic Health Records: An Exploratory Study of Under-Treated Essential Hypertension. PMID:33936403
Semantic standards of external exposome data. PMID:33901445
Improved characterisation of clinical text through ontology-based vocabulary expansion. PMID:33845909
History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications. PMID:33841175
One Health Surveillance Codex: promoting the adoption of One Health solutions within and across European countries. PMID:33786360
An immunologically friendly classification of non-peptidic ligands. PMID:33772585
Protocol for a reproducible experimental survey on biomedical sentence similarity. PMID:33760855
isa4j: a scalable Java library for creating ISA-Tab metadata. PMID:33728038
A Second Look at FAIR in Proteomic Investigations. PMID:33719446
Decentralized but Globally Coordinated Biodiversity Data. PMID:33693407
An Early Stage Researcher's Primer on Systems Medicine Terminology. PMID:33659919
FOntCell: Fusion of Ontologies of Cells. PMID:33644039
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. PMID:33622857
Integrative Base Ontology for the Research Analysis of Alzheimer's Disease-Related Mild Cognitive Impairment. PMID:33613222
API Driven On-Demand Participant ID Pseudonymization in Heterogeneous Multi-Study Research. PMID:33611875
Public data sources to support systems toxicology applications. PMID:33604492
Gene function finding through cross-organism ensemble learning. PMID:33579334
Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. PMID:33455583
Ontologies relevant to behaviour change interventions: a method for their development. PMID:33447665
Community Approaches for Integrating Environmental Exposures into Human Models of Disease. PMID:33369481
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. PMID:33319712
Analysis of readability and structural accuracy in SNOMED CT. PMID:33319711
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes. PMID:33216896
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
Adding evidence type representation to DIDEO. PMID:33139971
Towards a foundational representation of potential drug-drug interaction knowledge. PMID:33139970
The Semantic Data Dictionary - An Approach for Describing and Annotating Data. PMID:33103120
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Semantic similarity and machine learning with ontologies. PMID:33049044
Identifiers.org: Compact Identifier services in the cloud. PMID:33031499
Ten simple rules for annotating sequencing experiments. PMID:33017400
Developing an ontology for representing the domain knowledge specific to non-pharmacological treatment for agitation in dementia. PMID:32995470
Development of an Intervention Setting Ontology for behaviour change: Specifying where interventions take place. PMID:32964137
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator. PMID:32905086
A community-based transcriptomics classification and nomenclature of neocortical cell types. PMID:32839617
Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. PMID:32819435
Identifying disease trajectories with predicate information from a knowledge graph. PMID:32819419
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. PMID:32735679
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Conditional and unconditional genome-wide association study reveal complicate genetic architecture of human body weight and impacts of smoking. PMID:32699216
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PMID:32645039
CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. PMID:32533075
DDIEM: drug database for inborn errors of metabolism. PMID:32527280
PRISM: A Platform for Imaging in Precision Medicine. PMID:32479186
Broad-coverage biomedical relation extraction with SemRep. PMID:32410573
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
Knowledge Graph-Enabled Cancer Data Analytics. PMID:32386166
Species Classification for Neuroscience Literature Based on Span of Interest Using Sequence-to-Sequence Learning Model. PMID:32372933
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
The Role and Promise of Artificial Intelligence in Medical Toxicology. PMID:32215849
Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data. PMID:32053657
ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. PMID:32047873
Organizing genome engineering for the gigabase scale. PMID:32019919
Incremental data integration for tracking genotype-disease associations. PMID:31986132
Fast Polynomial Approximation of Heat Kernel Convolution on Manifolds and Its Application to Brain Sulcal and Gyral Graph Pattern Analysis. PMID:31976883
Ontology-driven integrative analysis of omics data through Onassis. PMID:31959844
Combining lexical and context features for automatic ontology extension. PMID:31931870
OHMI: the ontology of host-microbiome interactions. PMID:31888755
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. PMID:31865910
Enhancing the drug ontology with semantically-rich representations of National Drug Codes and RxNorm unique concept identifiers. PMID:31865907
A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). PMID:31865905
Experiment design driven FAIRification of omics data matrices, an exemplar. PMID:31831744
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation. PMID:31769834
Ontology-based prediction of cancer driver genes. PMID:31757986
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. PMID:31735951
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. PMID:31725864
DisProt: intrinsic protein disorder annotation in 2020. PMID:31713636
Enabling semantic queries across federated bioinformatics databases. PMID:31697362
Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. PMID:31682632
Annot: a Django-based sample, reagent, and experiment metadata tracking system. PMID:31675914
Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective. PMID:31419826
Advances in gene ontology utilization improve statistical power of annotation enrichment. PMID:31415589
ROBOT: A Tool for Automating Ontology Workflows. PMID:31357927
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. PMID:31272389
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. PMID:31272374
An ontology for representing hematologic malignancies: the cancer cell ontology. PMID:31272372
The cell line ontology-based representation, integration and analysis of cell lines used in China. PMID:31272367
The Knowledge Object Reference Ontology (KORO): A formalism to support management and sharing of computable biomedical knowledge for learning health systems. PMID:31245583
The TRANSFoRm project: Experience and lessons learned regarding functional and interoperability requirements to support primary care. PMID:31245579
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content. PMID:31181762
Ontology-based metabolomics data integration with quality control. PMID:31179719
Multi-domain semantic similarity in biomedical research. PMID:31138117
Exploratory Gene Ontology Analysis with Interactive Visualization. PMID:31127124
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis. PMID:31032818
Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research. PMID:30987214
Using Rigorous Methods to Advance Behaviour Change Science. PMID:30931398
Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions. PMID:30918448
ODAL: A one-shot distributed algorithm to perform logistic regressions on electronic health records data from multiple clinical sites. PMID:30864308
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. PMID:30858527
How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456
The variable quality of metadata about biological samples used in biomedical experiments. PMID:30778255
Levels and building blocks-toward a domain granularity framework for the life sciences. PMID:30691505
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. PMID:30616557
The Glomerular Disease Study and Trial Consortium: A Grassroots Initiative to Foster Collaboration and Innovation. PMID:30596165
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. PMID:30576485
psims - A Declarative Writer for mzML and mzIdentML for Python. PMID:30563850
PhenoMeNal: processing and analysis of metabolomics data in the cloud. PMID:30535405
Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier. PMID:30532623
Discovery of Emerging Design Patterns in Ontologies Using Tree Mining. PMID:30505251
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals. PMID:30476141
Ontology-based semantic mapping of chemical toxicities. PMID:30468866
ECO, the Evidence & Conclusion Ontology: community standard for evidence information. PMID:30407590
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes. PMID:30400805
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. PMID:30365026
From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge. PMID:30349491
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community. PMID:30311252
Knowledge-based biomedical Data Science. PMID:30294517
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Improved ontology for eukaryotic single-exon coding sequences in biological databases. PMID:30239665
MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources. PMID:30212909
Plant data visualisation using network graphs. PMID:30186704
SNOMED CT standard ontology based on the ontology for general medical science. PMID:30170591
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. PMID:30137210
Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. PMID:30085931
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations. PMID:30057931
The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. PMID:30034908
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
Toward a standard ontology of surgical process models. PMID:30006820
Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data. PMID:29982236
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. PMID:29954318
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. PMID:29949999
Contextualising manufacturing data for lifecycle decision-making. PMID:29911681
Memory-Augmented Active Deep Learning for Identifying Relations Between Distant Medical Concepts in Electroencephalography Reports. PMID:29888063
The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps. PMID:29854221
Deep Learning Meets Biomedical Ontologies: Knowledge Embeddings for Epilepsy. PMID:29854192
The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data. PMID:29765382
Using ZFIN: Data Types, Organization, and Retrieval. PMID:29761463
Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse. PMID:29743102
Uniform resolution of compact identifiers for biomedical data. PMID:29737976
ONS: an ontology for a standardized description of interventions and observational studies in nutrition. PMID:29736190
Identification of errors in the IEDB using ontologies. PMID:29688357
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. PMID:29688354
Analyzing user interactions with biomedical ontologies: A visual perspective. PMID:29657560
Investigating Term Reuse and Overlap in Biomedical Ontologies. PMID:29636656
OC-2-KB: A software pipeline to build an evidence-based obesity and cancer knowledge base. PMID:29629236
Secondary analysis of electronic health records in critical care medicine. PMID:29610744
Disease Ontology: improving and unifying disease annotations across species. PMID:29590633
Cell type discovery using single-cell transcriptomics: implications for ontological representation. PMID:29590361
Refining the aggregate exposure pathway. PMID:29465734
AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks. PMID:29454060
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. PMID:29448949
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. PMID:29390967
InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk. PMID:29363423
MIRO: guidelines for minimum information for the reporting of an ontology. PMID:29347969
Tackling the challenges of matching biomedical ontologies. PMID:29335022
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. PMID:29329592
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. PMID:29322930
Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. PMID:29322929
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge. PMID:29322916
Cell type discovery and representation in the era of high-content single cell phenotyping. PMID:29322913
Usage of cell nomenclature in biomedical literature. PMID:29322912
Interoperability of Disease Concepts in Clinical and Research Ontologies: Contrasting Coverage and Structure in the Disease Ontology and SNOMED CT. PMID:29295235
Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. PMID:29295217
An ontology-aware integration of clinical models, terminologies and guidelines: an exploratory study of the Scale for the Assessment and Rating of Ataxia (SARA). PMID:29207981
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
Visual Analytics Tools for Sustainable Lifecycle Design: Current Status, Challenges, and Future Opportunities. PMID:29170612
Taxonomy-Based Approaches to Quality Assurance of Ontologies. PMID:29158885
Using semantics for representing experimental protocols. PMID:29132408
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. PMID:29106667
Situation Model for Situation-Aware Assistance of Dementia Patients in Outdoor Mobility. PMID:29060937
Analysis and visualization of disease courses in a semantically-enabled cancer registry. PMID:28962670
Fish Ontology framework for taxonomy-based fish recognition. PMID:28929028
Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway. PMID:28910500
A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies. PMID:28819351
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets. PMID:28792687
Towards a more molecular taxonomy of disease. PMID:28750648
Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance. PMID:28694792
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PMID:28662064
Ontological interpretation of biomedical database content. PMID:28651575
Embedding Open-domain Common-sense Knowledge from Text. PMID:28649676
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. PMID:28592275
An empirical analysis of ontology reuse in BioPortal. PMID:28583809
A Framework for Collaborative Curation of Neuroscientific Literature. PMID:28469570
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions. PMID:28469412
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
Modulated evaluation metrics for drug-based ontologies. PMID:28438189
Robotic crowd biology with Maholo LabDroids. PMID:28398329
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. PMID:28350385
An ontology-based search engine for digital reconstructions of neuronal morphology. PMID:28337675
Semantic Health Knowledge Graph: Semantic Integration of Heterogeneous Medical Knowledge and Services. PMID:28299322
Exploring biomedical ontology mappings with graph theory methods. PMID:28265499
Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request. PMID:28253937
Computer-Aided Experiment Planning toward Causal Discovery in Neuroscience. PMID:28243197
Analyzing structural changes in SNOMED CT's Bacterial infectious diseases using a visual semantic delta. PMID:28215561
Tutorial on Protein Ontology Resources. PMID:28150233
Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy. PMID:28137311
Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures. PMID:28097054
Toward a comprehensive drug ontology: extraction of drug-indication relations from diverse information sources. PMID:28069052
Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. PMID:28068484
ontologyX: a suite of R packages for working with ontological data. PMID:28062448
An ontological analysis of medical Bayesian indicators of performance. PMID:28049518
Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. PMID:28003147
The development of non-coding RNA ontology. PMID:27990175
Sharing brain mapping statistical results with the neuroimaging data model. PMID:27922621
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
Text mining resources for the life sciences. PMID:27888231
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. PMID:27867422
The BLUEPRINT Data Analysis Portal. PMID:27863955
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. PMID:27857184
Empowering pharmacoinformatics by linked life science data. PMID:27830428
Knowledge Representation and Management: a Linked Data Perspective. PMID:27830248
omicsNPC: Applying the Non-Parametric Combination Methodology to the Integrative Analysis of Heterogeneous Omics Data. PMID:27812137
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. PMID:27794045
The arc of Mass Spectrometry Exchange Formats is long, but it bends toward HDF5. PMID:27741559
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. PMID:27733503
KinView: a visual comparative sequence analysis tool for integrated kinome research. PMID:27731453
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. PMID:27664130
An information model for computable cancer phenotypes. PMID:27629872
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. PMID:27627881
OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts. PMID:27605099
Modeling biochemical pathways in the gene ontology. PMID:27589964
Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. PMID:27570653
Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development. PMID:27570648
Knowledge Discovery from Biomedical Ontologies in Cross Domains. PMID:27548262
The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. PMID:27538448
Health Concept and Knowledge Management: Twenty-five Years of Evolution. PMID:27488404
Biodiversity analysis in the digital era. PMID:27481789
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
Representing and querying disease networks using graph databases. PMID:27462371
Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research. PMID:27458549
BioWes-from design of experiment, through protocol to repository, control, standardization and back-tracking. PMID:27454467
The ontology of medically related social entities: recent developments. PMID:27406187
COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413
Anatomy Ontology Matching Using Markov Logic Networks. PMID:27382498
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies. PMID:27345947
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. PMID:27334471
The Proteasix Ontology. PMID:27259807
The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing. PMID:27246819
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. PMID:27213033
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. PMID:27189610
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. PMID:27152146
OBIB-a novel ontology for biobanking. PMID:27148435
Ontology-based annotations and semantic relations in large-scale (epi)genomics data. PMID:27142216
The Ontology for Biomedical Investigations. PMID:27128319
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. PMID:27099700
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
A Querying Method over RDF-ized Health Level Seven v2.5 Messages Using Life Science Knowledge Resources. PMID:27050304
Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates. PMID:27042287
Representing vision and blindness. PMID:27034769
Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors. PMID:27003817
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data. PMID:26918190
The Electron Microscopy eXchange (EMX) initiative. PMID:26873784
Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences. PMID:26871594
Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PMID:26870952
Ten Simple Rules for Selecting a Bio-ontology. PMID:26867217
Semantic representation of reported measurements in radiology. PMID:26801764
An ontology for major histocompatibility restriction. PMID:26759709
Emerging semantics to link phenotype and environment. PMID:26713234
Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression. PMID:26661719
Ontology-based representation and analysis of host-Brucella interactions. PMID:26445639
The digital revolution in phenotyping. PMID:26420780
The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases. PMID:26393351
Applications of comparative evolution to human disease genetics. PMID:26338499
Data integration in biological research: an overview. PMID:26336651
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
Management of Dynamic Biomedical Terminologies: Current Status and Future Challenges. PMID:26293859
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. PMID:26272982
A Framework for Global Collaborative Data Management for Malaria Research. PMID:26259944
Combining expert knowledge and knowledge automatically acquired from electronic data sources for continued ontology evaluation and improvement. PMID:26212414
Perspectives on next steps in classification of oro-facial pain - Part 3: biomarkers of chronic oro-facial pain - from research to clinic. PMID:26200973
Using natural language processing techniques to inform research on nanotechnology. PMID:26199848
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. PMID:26175801
Biomedical imaging ontologies: A survey and proposal for future work. PMID:26167381
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PMID:26154165
Development of an Ontology for Periodontitis. PMID:26140188
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. PMID:26051359
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. PMID:26048076
Visual annotation display (VLAD): a tool for finding functional themes in lists of genes. PMID:26047590
Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions. PMID:26034559
Implementation of linked data in the life sciences at BioHackathon 2011. PMID:25973165
Fostering Multilinguality in the UMLS: A Computational Approach to Terminology Expansion for Multiple Languages. PMID:25954371
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. PMID:25950236
Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference. PMID:25937879
Capturing domain knowledge from multiple sources: the rare bone disorders use case. PMID:25926964
The Da Vinci European BioBank: A Metabolomics-Driven Infrastructure. PMID:25913579
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework. PMID:25894391
Abstraction networks for terminologies: Supporting management of "big knowledge". PMID:25890687
2015, big data in healthcare: for whom the bell tolls? PMID:25886956
Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies. PMID:25880555
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278
CLO: The cell line ontology. PMID:25852852
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. PMID:25815161
Assessing the impact of case sensitivity and term information gain on biomedical concept recognition. PMID:25790125
Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. PMID:25785184
Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks. PMID:25785183
An ontology approach to comparative phenomics in plants. PMID:25774204
The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units. PMID:25759670
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Gateways to the FANTOM5 promoter level mammalian expression atlas. PMID:25723102
Describing the breakbone fever: IDODEN, an ontology for dengue fever. PMID:25646954
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. PMID:25632945
Aber-OWL: a framework for ontology-based data access in biology. PMID:25627673
AISO: Annotation of Image Segments with Ontologies. PMID:25584184
POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. PMID:25574136
Finding our way through phenotypes. PMID:25562316
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. PMID:25510499
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
linkedISA: semantic representation of ISA-Tab experimental metadata. PMID:25472428
An ontology for microbial phenotypes. PMID:25433798
The Pathogen-Host Interactions database (PHI-base): additions and future developments. PMID:25414340
An effective method of large scale ontology matching. PMID:25411633
Automatic background knowledge selection for matching biomedical ontologies. PMID:25379899
Fingerprints of a message: integrating positional information on the transcriptome. PMID:25364746
dcGOR: an R package for analysing ontologies and protein domain annotations. PMID:25356683
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. PMID:25276334
A multilayer ontology of instruments for neurological, behavioral and cognitive assessments. PMID:25240319
Text Mining Driven Drug-Drug Interaction Detection. PMID:25131635
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods. PMID:25106869
Preserving sequence annotations across reference sequences. PMID:25093075
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques. PMID:25093070
OAE: The Ontology of Adverse Events. PMID:25093068
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
OntoVIP: an ontology for the annotation of object models used for medical image simulation. PMID:25038553
OMIT: dynamic, semi-automated ontology development for the microRNA domain. PMID:25025130
Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. PMID:24999329
Computational prediction of disease microRNAs in domestic animals. PMID:24970281
The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. PMID:24963371
e!DAL--a framework to store, share and publish research data. PMID:24958009
UCbase 2.0: ultraconserved sequences database (2014 update). PMID:24951797
An ontological modeling approach for abnormal states and its application in the medical domain. PMID:24944781
Standardized metadata for human pathogen/vector genomic sequences. PMID:24936976
My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models. PMID:24936286
Egas: a collaborative and interactive document curation platform. PMID:24923820
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
Using semantic web technologies to annotate and align microarray designs. PMID:24904201
Automated semantic annotation of rare disease cases: a case study. PMID:24903515
Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri. PMID:24789338
Patterns of positive selection in seven ant genomes. PMID:24782441
WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. PMID:24771560
qcML: an exchange format for quality control metrics from mass spectrometry experiments. PMID:24760958
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. PMID:24755304
Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. PMID:24702956
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective. PMID:24667848
Ratsnake: a versatile image annotation tool with application to computer-aided diagnosis. PMID:24616617
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. PMID:24602174
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PMID:24595056
Canto: an online tool for community literature curation. PMID:24574118
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. PMID:24568621
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. PMID:24564249
Guidelines for managing data and processes in bone and cartilage tissue engineering. PMID:24564199
SNP2GO: functional analysis of genome-wide association studies. PMID:24561481
Linked data and online classifications to organise mined patterns in patient data. PMID:24551369
Design and evaluation of a bacterial clinical infectious diseases ontology. PMID:24551353
Editorial: biological ontologies and semantic biology. PMID:24550936
GOLink: Finding Cooccurring Terms across Gene Ontology Namespaces. PMID:24524070
From concept representations to ontologies: a paradigm shift in health informatics? PMID:24523987
Semantic interestingness measures for discovering association rules in the skeletal dysplasia domain. PMID:24499729
Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level. PMID:24453957
The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. PMID:24438387
Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance. PMID:24432050
Neuroanatomical domain of the foundational model of anatomy ontology. PMID:24398054
Semantic integration of gene expression analysis tools and data sources using software connectors. PMID:24341380
The environment ontology: contextualising biological and biomedical entities. PMID:24330602
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. PMID:24319146
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. PMID:24316577
The neurological disease ontology. PMID:24314207
CellFinder: a cell data repository. PMID:24304896
An ontology-based method for secondary use of electronic dental record data. PMID:24303273
The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. PMID:24279920
NeXO Web: the NeXO ontology database and visualization platform. PMID:24271398
Protein Ontology: a controlled structured network of protein entities. PMID:24270789
Representing annotation compositionality and provenance for the Semantic Web. PMID:24268021
Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD. PMID:24267899
HuPSON: the human physiology simulation ontology. PMID:24267822
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. PMID:24267744
Updates on the web-based VIOLIN vaccine database and analysis system. PMID:24259431
A neuroinformatics of brain modeling and its implementation in the Brain Operation Database BODB. PMID:24234915
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. PMID:24217912
GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. PMID:24194592
Anatomical entity mention recognition at literature scale. PMID:24162468
Variation Ontology for annotation of variation effects and mechanisms. PMID:24162187
Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. PMID:24139024
Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP. PMID:24131519
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PMID:24124474
Developing a semantically rich ontology for the biobank-administration domain. PMID:24103726
Functional tissue units and their primary tissue motifs in multi-scale physiology. PMID:24103658
Biomarkers in autism spectrum disorder: the old and the new. PMID:24096533
Toward knowledge support for analysis and interpretation of complex traits. PMID:24079802
GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework. PMID:24078711
A sea of standards for omics data: sink or swim? PMID:24076747
Using image mapping towards biomedical and biological data sharing. PMID:24059352
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
NeuroLex.org: an online framework for neuroscience knowledge. PMID:24009581
Ontology based molecular signatures for immune cell types via gene expression analysis. PMID:24004649
NCBI2RDF: enabling full RDF-based access to NCBI databases. PMID:23984425
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. PMID:23972281
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. PMID:23937709
TrOn: an anatomical ontology for the beetle Tribolium castaneum. PMID:23936240
Threats to validity in the design and conduct of preclinical efficacy studies: a systematic review of guidelines for in vivo animal experiments. PMID:23935460
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. PMID:23895341
CELDA -- an ontology for the comprehensive representation of cells in complex systems. PMID:23865855
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. PMID:23668630
Effects of guideline-based training on the quality of formal ontologies: a randomized controlled trial. PMID:23667440
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. PMID:23660285
FYPO: the fission yeast phenotype ontology. PMID:23658422
Mass spectrometry imaging with high resolution in mass and space. PMID:23652571
The comprehensive antibiotic resistance database. PMID:23650175
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. PMID:23637705
Using Semantic Web technology to support icd-11 textual definitions authoring. PMID:23601451
On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities. PMID:23587326
From ontology to semantic similarity: calculation of ontology-based semantic similarity. PMID:23533360
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. PMID:23479348
The iOSC3 system: using ontologies and SWRL rules for intelligent supervision and care of patients with acute cardiac disorders. PMID:23476717
Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. PMID:23471459
Controlled vocabularies and ontologies in proteomics: overview, principles and practice. PMID:23429179
Ontology for vector surveillance and management. PMID:23427646
Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment. PMID:23303300
Chapter 9: Analyses using disease ontologies. PMID:23300417
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. PMID:23286517
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. PMID:23256916
Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. PMID:23256563
Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. PMID:23256535
Semantically enabling a genome-wide association study database. PMID:23244533
A gene ontology inferred from molecular networks. PMID:23242164
Multiscale integration of -omic, imaging, and clinical data in biomedical informatics. PMID:23231990
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PMID:23209624
Accelerating cancer systems biology research through Semantic Web technology. PMID:23188758
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Gene Ontology annotations and resources. PMID:23161678
Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). PMID:23155465
Text-mining solutions for biomedical research: enabling integrative biology. PMID:23150036
On the ontology based representation of cell lines. PMID:23144907
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. PMID:23104991
A UML profile for the OBO relation ontology. PMID:23095840
The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications. PMID:23060901
The Units Ontology: a tool for integrating units of measurement in science. PMID:23060432
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. PMID:23046642
OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4. PMID:23046606
A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience. PMID:23043673
Predicting the extension of biomedical ontologies. PMID:23028267
Event extraction across multiple levels of biological organization. PMID:22962484
Evaluation of research in biomedical ontologies. PMID:22962340
Nanoinformatics: developing new computing applications for nanomedicine. PMID:22942787
Process attributes in bio-ontologies. PMID:22928880
Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis. PMID:22849591
Ontologies as integrative tools for plant science. PMID:22847540
BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. PMID:22847375
Computational tools for comparative phenomics: the role and promise of ontologies. PMID:22814867
Concept annotation in the CRAFT corpus. PMID:22776079
Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach. PMID:22737162
Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases. PMID:22719993
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. PMID:22693220
VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. PMID:22693211
Three ontologies to define phenotype measurement data. PMID:22654893
OLSVis: an animated, interactive visual browser for bio-ontologies. PMID:22646023
The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. PMID:22621763
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development. PMID:22565629
Linking genes to diseases with a SNPedia-Gene Wiki mashup. PMID:22541597
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. PMID:22539675
GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity Database. PMID:22536971
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Bayesian integration of networks without gold standards. PMID:22492647
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. PMID:22472218
The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain. PMID:22449239
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
Disease model curation improvements at Mouse Genome Informatics. PMID:22434831
Where to Publish and Find Ontologies? A Survey of Ontology Libraries. PMID:22408576
Improving integrative searching of systems chemical biology data using semantic annotation. PMID:22401035
Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. PMID:22383736
OMERO: flexible, model-driven data management for experimental biology. PMID:22373911
Populous: a tool for building OWL ontologies from templates. PMID:22373396
SPARQL assist language-neutral query composer. PMID:22373327
A semantic web framework to integrate cancer omics data with biological knowledge. PMID:22373303
Knowledge acquisition, semantic text mining, and security risks in health and biomedical informatics. PMID:22371823
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
vHOG, a multispecies vertebrate ontology of homologous organs groups. PMID:22285560
Toward interoperable bioscience data. PMID:22281772
The Internet and science communication: blurring the boundaries. PMID:22276045
MiDas: automatic extraction of a common domain of discourse in sleep medicine for multi-center data integration. PMID:22195180
ProKinO: an ontology for integrative analysis of protein kinases in cancer. PMID:22194913
New concepts for building vocabulary for cell image ontologies. PMID:22188658
The relationship between proteome size, structural disorder and organism complexity. PMID:22182830
HOMER: a human organ-specific molecular electronic repository. PMID:22165817
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. PMID:22140103
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. PMID:22135296
INOH: ontology-based highly structured database of signal transduction pathways. PMID:22120663
Unintended consequences of existential quantifications in biomedical ontologies. PMID:22115278
TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. PMID:22102574
The National Center for Biomedical Ontology. PMID:22081220
De novo genesis of enhancers in vertebrates. PMID:22069375
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. PMID:22041276
CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses. PMID:22039163
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Improving ontologies by automatic reasoning and evaluation of logical definitions. PMID:22032770
Controlled vocabularies and semantics in systems biology. PMID:22027554
Development and evaluation of an ontology for guiding appropriate antibiotic prescribing. PMID:22019377
Grains, components and mixtures in biomedical ontologies. PMID:21995869
The BioLexicon: a large-scale terminological resource for biomedical text mining. PMID:21992002
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PMID:21991315
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. PMID:21987712
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
The representation of protein complexes in the Protein Ontology (PRO). PMID:21929785
Data extraction, transformation, and dissemination through ZFIN. PMID:21924170
NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. PMID:21918645
The challenges of defining oral cancer: analysis of an ontological approach. PMID:21915705
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution. PMID:21914205
Disjunctive shared information between ontology concepts: application to Gene Ontology. PMID:21884591
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. PMID:21878109
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. PMID:21871085
Integrating systems biology models and biomedical ontologies. PMID:21835028
How the gene ontology evolves. PMID:21819553
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PMID:21789201
S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. PMID:21756325
OntoVisT: A general purpose Ontological Visualization Tool. PMID:21738333
PhenomeNET: a whole-phenome approach to disease gene discovery. PMID:21737429
Informatics and standards for nanomedicine technology. PMID:21721140
Computable visually observed phenotype ontological framework for plants. PMID:21702966
BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. PMID:21702939
Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases. PMID:21685092
Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets. PMID:21677865
Towards an Age-Phenome Knowledge-base. PMID:21651792
The cognitive paradigm ontology: design and application. PMID:21643732
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PMID:21637758
Ontological realism: A methodology for coordinated evolution of scientific ontologies. PMID:21637730
Representation of research hypotheses. PMID:21624164
Developing a kidney and urinary pathway knowledge base. PMID:21624162
Automating generation of textual class definitions from OWL to English. PMID:21624160
An open annotation ontology for science on web 3.0. PMID:21624159
How orthogonal are the OBO Foundry ontologies? PMID:21624157
OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript. PMID:21619703
On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data. PMID:21544172
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
Enabling collaborative research using the Biomedical Informatics Research Network (BIRN). PMID:21515543
On the formalization and reuse of scientific research. PMID:21490004
Intelligent security and privacy solutions for enabling personalized telepathology. PMID:21489199
Multi-disease data management system platform for vector-borne diseases. PMID:21468310
Module-based multiscale simulation of angiogenesis in skeletal muscle. PMID:21463529
Answering biological questions: querying a systems biology database for nutrigenomics. PMID:21437033
Customizable views on semantically integrated networks for systems biology. PMID:21414991
Standard biological parts knowledgebase. PMID:21390321
Semantics-based composition of EMBOSS services. PMID:21388574
Biomedical semantics in the Semantic Web. PMID:21388570
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
Toward an ontological treatment of disease and diagnosis. PMID:21347182
Towards interoperable reporting standards for omics data: hopes and hurdles. PMID:21347181
Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine. PMID:21347135
The Pitfalls of Thesaurus Ontologization - the Case of the NCI Thesaurus. PMID:21347074
The ontology life cycle: Integrated tools for editing, publishing, peer review, and evolution of ontologies. PMID:21347039
A common layer of interoperability for biomedical ontologies based on OWL EL. PMID:21343142
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
Saccharomyces cerevisiae as a model organism: a comparative study. PMID:21311596
Concept Systems and Ontologies: Recommendations for Basic Terminology. PMID:21308002
Meeting Report: BioSharing at ISMB 2010. PMID:21304729
SciReader enables reading of medical content with instantaneous definitions. PMID:21266060
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
Ontologies for clinical and translational research: Introduction. PMID:21241822
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. PMID:21210987
SADI, SHARE, and the in silico scientific method. PMID:21210986
A gross anatomy ontology for hymenoptera. PMID:21209921
Logical development of the cell ontology. PMID:21208450
MBAT: a scalable informatics system for unifying digital atlasing workflows. PMID:21176225
Foundations for a realist ontology of mental disease. PMID:21143905
The RIKEN integrated database of mammals. PMID:21076152
Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary. PMID:21062451
An evolutionary approach to realism-based adverse event representations. PMID:21057717
Recent progress in automatically extracting information from the pharmacogenomic literature. PMID:21047206
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
Informatics in radiology: an information model of the DICOM standard. PMID:20980665
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
Ontology and the future of dental research informatics. PMID:20884915
Cognitive neuroscience 2.0: building a cumulative science of human brain function. PMID:20884276
PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. PMID:20858292
A unified framework for biomedical terminologies and ontologies. PMID:20841844
Adding a little reality to building ontologies for biology. PMID:20838431
Exploring zebrafish genomic, functional and phenotypic data using ZFIN. PMID:20836073
Utopia documents: linking scholarly literature with research data. PMID:20823323
Relations as patterns: bridging the gap between OBO and OWL. PMID:20807438
A standard variation file format for human genome sequences. PMID:20796305
Structured digital tables on the Semantic Web: toward a structured digital literature. PMID:20739925
Curating the innate immunity interactome. PMID:20727158
Identifying informative subsets of the Gene Ontology with information bottleneck methods. PMID:20702400
Programming cells: towards an automated 'Genetic Compiler'. PMID:20702081
IDOMAL: an ontology for malaria. PMID:20698959
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. PMID:20679334
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. PMID:20677327
The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. PMID:20647237
Natural Language Processing methods and systems for biomedical ontology learning. PMID:20647054
OWL2Perl: creating Perl modules from OWL class definitions. PMID:20628074
Mouse Resource Browser--a database of mouse databases. PMID:20627861
Modeling biomedical experimental processes with OBI. PMID:20626927
Establishing a distributed system for the simple representation and integration of diverse scientific assertions. PMID:20626925
Annotation of SBML models through rule-based semantic integration. PMID:20626923
Building a biomedical ontology recommender web service. PMID:20626921
Minimum information about a protein affinity reagent (MIAPAR). PMID:20622827
Biomedical semantics: the hub for biomedical research 2.0. PMID:20618983
Multiple ontologies in action: composite annotations for biosimulation models. PMID:20601121
Pathbase and the MPATH ontology. Community resources for mouse histopathology. PMID:20587689
Statistical tests for associations between two directed acyclic graphs. PMID:20585388
OntoFox: web-based support for ontology reuse. PMID:20569493
The teleost anatomy ontology: anatomical representation for the genomics age. PMID:20547776
Semi-automated ontology generation within OBO-Edit. PMID:20529942
Using semantic web rules to reason on an ontology of pseudogenes. PMID:20529940
Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. PMID:20525291
"Just one animal among many?" Existential phenomenology, ethics, and stem cell research. PMID:20521117
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. PMID:20519284
Spatio-structural granularity of biological material entities. PMID:20509878
Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PMID:20505755
The EMBRACE web service collection. PMID:20462862
Toward an ontology-based framework for clinical research databases. PMID:20460173
Creating an ontology-based human phenotyping system: The Rockefeller University bleeding history experience. PMID:20443924
The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system. PMID:20438862
Phenotype ontologies for mouse and man: bridging the semantic gap. PMID:20427557
Combining ontologies and workflows to design formal protocols for biological laboratories. PMID:20416048
Adapting Clinical Ontologies in Real-World Environments. PMID:20390048
A set of ontologies to drive tools for the control of vector-borne diseases. PMID:20363364
Evolution of the Sequence Ontology terms and relationships. PMID:20226267
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. PMID:20214801
Semantic Web for data harmonization in Chinese medicine. PMID:20205772
Modeling sample variables with an Experimental Factor Ontology. PMID:20200009
Cross-product extensions of the Gene Ontology. PMID:20152934
Towards an ontological theory of substance intolerance and hypersensitivity. PMID:20152933
A network-theoretic approach for decompositional translation across Open Biological Ontologies. PMID:20144734
Ontology engineering. PMID:20139945
Putting biomedical ontologies to work. PMID:20135080
Hematopoietic cell types: prototype for a revised cell ontology. PMID:20123131
Head in the clouds: Re-imagining the experimental laboratory record for the web-based networked world. PMID:20098590
Integrating phenotype ontologies across multiple species. PMID:20064205
The mammalian phenotype ontology: enabling robust annotation and comparative analysis. PMID:20052305
A quick guide for developing effective bioinformatics programming skills. PMID:20041221
Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. PMID:20006477
Linking human diseases to animal models using ontology-based phenotype annotation. PMID:19956802
Calling International Rescue: knowledge lost in literature and data landslide! PMID:19929850
Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. PMID:19921742
Saccharomyces Genome Database provides mutant phenotype data. PMID:19906697
BioDEAL: community generation of biological annotations. PMID:19891799
Construction of an annotated corpus to support biomedical information extraction. PMID:19852798
GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. PMID:19850722
More than a decade of developmental gene expression atlases: where are we now? PMID:19822576
Megascience. 'Omics data sharing. PMID:19815759
Ontologies for bioinformatics. PMID:19812775
Initial implementation of a comparative data analysis ontology. PMID:19812726
Clinical diagnostics in human genetics with semantic similarity searches in ontologies. PMID:19800049
Structuring and extracting knowledge for the support of hypothesis generation in molecular biology. PMID:19796406
Bio-jETI: a framework for semantics-based service composition. PMID:19796405
BioGateway: a semantic systems biology tool for the life sciences. PMID:19796395
Between proteins and phenotypes: annotation and interpretation of mutations. PMID:19758463
An evolutionary approach to the representation of adverse events. PMID:19745369
Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research. PMID:19745321
Ontological Discovery Environment: a system for integrating gene-phenotype associations. PMID:19733230
OnEX: Exploring changes in life science ontologies. PMID:19678926
An Integrated Object Model and Method Framework for Subject-Centric e-Research Applications. PMID:19636389
Where's the mouse info? PMID:19605899
Translational bioinformatics applications in genome medicine. PMID:19566916
MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors. PMID:19547750
Generating 'omic knowledge': the role of informatics in high content screening. PMID:19531005
A systems biology network model for genetic association studies of nicotine addiction and treatment. PMID:19525886
Approaches to neuroscience data integration. PMID:19505888
myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks. PMID:19500400
BioPortal: ontologies and integrated data resources at the click of a mouse. PMID:19483092
The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. PMID:19480664
Alignment of the UMLS semantic network with BioTop: methodology and assessment. PMID:19478019
Orymold: ontology based gene expression data integration and analysis tool applied to rice. PMID:19463186
Semantic Web-based integration of cancer pathways and allele frequency data. PMID:19458791
Open Biomedical Ontology-based Medline exploration. PMID:19426463
BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. PMID:19426462
TGF-beta signaling proteins and the Protein Ontology. PMID:19426460
Issues in learning an ontology from text. PMID:19426458
Survey-based naming conventions for use in OBO Foundry ontology development. PMID:19397794
The biomedical ethics ontology proposal: excellent aims, questionable methods. PMID:19382878
Application and evaluation of automated semantic annotation of gene expression experiments. PMID:19376825
Creating a controlled vocabulary for the ethics of human research: towards a biomedical ethics ontology. PMID:19374479
Evaluation of genome-wide association study results through development of ontology fingerprints. PMID:19349285
A review of auditing methods applied to the content of controlled biomedical terminologies. PMID:19285571
An improved ontological representation of dendritic cells as a paradigm for all cell types. PMID:19243617
Detecting role errors in the gene hierarchy of the NCI Thesaurus. PMID:19221606
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. PMID:19168912
Ontologies of cellular networks. PMID:19091693
Genotype-phenotype databases: challenges and solutions for the post-genomic era. PMID:19065136
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. PMID:19038988
Using an integrated ontology and information model for querying and reasoning about phenotypes: The case of autism. PMID:18999231
The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. PMID:18975148
Modeling multi-typed structurally viewed chemicals with the UMLS Refined Semantic Network. PMID:18952946
The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. PMID:18950739
The Protein Feature Ontology: a tool for the unification of protein feature annotations. PMID:18936051
An ontology for Xenopus anatomy and development. PMID:18817563
Ethical and practical issues associated with aggregating databases. PMID:18816162
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. PMID:18766178
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. PMID:18688244
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
WikiPathways: pathway editing for the people. PMID:18651794
The ontology of biological taxa. PMID:18586729
The SWAN biomedical discourse ontology. PMID:18583197
BioLit: integrating biological literature with databases. PMID:18515836
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. PMID:18467421
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. PMID:18460187
Gene Ontology annotations: what they mean and where they come from. PMID:18460184
An anatomy ontology to represent biological knowledge in Dictyostelium discoideum. PMID:18366659
Bioinformatics and cancer research: building bridges for translational research. PMID:18258507 -
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
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ontology and terminology
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ontology and terminology
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biological databases
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