Ontology for Biomedical Investigations
Names
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Ontology for Biomedical Investigations
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
OBI
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
Names
More detailed information about this field from each metasource.
Ontology for Biomedical Investigations
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
OBI
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
Names
More detailed information about this field from each metasource.
Ontology for Biomedical Investigations
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
OBI
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI fosters clear communication about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more.
Description
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The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI fosters clear communication about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more.
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
OBI is an ontology of investigations, the protocols and instrumentation used, the material used, the data generated and the types of analysis performed on it. <br><br> To import,<br> Latest version: <a href="http://purl.obolibrary.org/obo/obi.owl">http://purl.obolibrary.org/obo/obi.owl</a><br> <br> Latest release notes at <a href="http://purl.obolibrary.org/obo/obi/release-notes.html">http://purl.obolibrary.org/obo/obi/release-notes.html</a><br> <br> Note: BFO 2.0 pre-Graz release (not official release version) was used in this release.
metasource: Biontology / Bioportalversion: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
Webpage:
http://obi-ontology.org/Webpage
More detailed information about this field from each metasource.
http://obi-ontology.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
http://purl.obolibrary.org/obo/obi
metasource: Biontology / Bioportalversion: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
Licence:
Name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)Licence name
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Creative Commons Attribution 3.0 Unported (CC BY 3.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Licence URL
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https://creativecommons.org/licenses/by/3.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
(6)
Publications
More detailed information about this field from each metasource.
Modeling biomedical experimental processes with OBI
PMID: 20626927
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The Ontology for Biomedical Investigations
PMID: 27128319
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Query enhancement through the practical application of ontology: the IEDB and OBI
PMID: 23734660
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach
PMID: 25632945
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Minimum Information about a Genotyping Experiment (MIGEN)
PMID: 22180825
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
http://purl.obolibrary.org/obo/obi/Technical_Reports
metasource: Biontology / Bioportal
version: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
Publications
More detailed information about this field from each metasource.
Modeling biomedical experimental processes with OBI
PMID: 20626927
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The Ontology for Biomedical Investigations
PMID: 27128319
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Query enhancement through the practical application of ontology: the IEDB and OBI
PMID: 23734660
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach
PMID: 25632945
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Minimum Information about a Genotyping Experiment (MIGEN)
PMID: 22180825
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
http://purl.obolibrary.org/obo/obi/Technical_Reports
metasource: Biontology / Bioportalversion: 2022-07-11 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/OBI
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Modeling biomedical experimental processes with OBI
PubMed citations: 144.
144 articles citing: Modeling biomedical experimental processes with OBI
End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach. PMID:34991705
ECO: the Evidence and Conclusion Ontology, an update for 2022. PMID:34986598
Standardization of assay representation in the Ontology for Biomedical Investigations. PMID:34244718
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Understanding experiments and research practices for reproducibility: an exploratory study. PMID:33976964
Towards a foundational representation of potential drug-drug interaction knowledge. PMID:33139970
Standards-based Semantic Integration of Manufacturing Information: Past, Present, and Future. PMID:32116404
The cell line ontology-based representation, integration and analysis of cell lines used in China. PMID:31272367
Organizing phenotypic data-a semantic data model for anatomy. PMID:31221226
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
How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456
Discovery of Emerging Design Patterns in Ontologies Using Tree Mining. PMID:30505251
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations. PMID:30057931
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. PMID:29322930
Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. PMID:29295217
Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China. PMID:29061976
Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance. PMID:28694792
Dead simple OWL design patterns. PMID:28583177
Scientific Reproducibility in Biomedical Research: Provenance Metadata Ontology for Semantic Annotation of Study Description. PMID:28269904
Nine Principles of Semantic Harmonization. PMID:28269840
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 Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. PMID:27627881
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. PMID:27570653
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
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base. PMID:27433158
First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine. PMID:27405781
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing. PMID:27246819
OBIB-a novel ontology for biobanking. PMID:27148435
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. PMID:27099700
An accurate and precise representation of drug ingredients. PMID:27096073
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
Vaxar: A Web-Based Database of Laboratory Animal Responses to Vaccinations and Its Application in the Meta-Analysis of Different Animal Responses to Tuberculosis Vaccinations. PMID:27053566
Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors. PMID:27003817
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
Ten Simple Rules for Selecting a Bio-ontology. PMID:26867217
Value, but high costs in post-deposition data curation. PMID:26861660
Semantic representation of reported measurements in radiology. PMID:26801764
An ontology for major histocompatibility restriction. PMID:26759709
Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PMID:26716837
Emerging semantics to link phenotype and environment. PMID:26713234
Literature Mining and Ontology based Analysis of Host-Brucella Gene-Gene Interaction Network. PMID:26696993
Terminology development towards harmonizing multiple clinical neuroimaging research repositories. PMID:26688838
GeneWeaver: data driven alignment of cross-species genomics in biology and disease. PMID:26656951
Ontology-based representation and analysis of host-Brucella interactions. PMID:26445639
Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. PMID:26387907
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
A Framework for Global Collaborative Data Management for Malaria Research. PMID:26259944
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
Reporting biological assay screening results for maximum impact. PMID:26194585
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
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. PMID:25957950
CLO: The cell line ontology. PMID:25852852
An integrated, ontology-driven approach to constructing observational databases for research. PMID:25817919
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. PMID:25815161
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. PMID:25785185
Ontology application and use at the ENCODE DCC. PMID:25776021
Semantic framework for mapping object-oriented model to semantic web languages. PMID:25762923
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. PMID:25632945
TypOn: the microbial typing ontology. PMID:25584183
Finding our way through phenotypes. PMID:25562316
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
EXACT2: the semantics of biomedical protocols. PMID:25472549
linkedISA: semantic representation of ISA-Tab experimental metadata. PMID:25472428
The immune epitope database (IEDB) 3.0. PMID:25300482
Structuring research methods and data with the research object model: genomics workflows as a case study. PMID:25276335
A multilayer ontology of instruments for neurological, behavioral and cognitive assessments. PMID:25240319
Evolving BioAssay Ontology (BAO): modularization, integration and applications. PMID:25093074
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
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. PMID:25068035
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. PMID:24963371
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
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
Software and hardware infrastructure for research in electrophysiology. PMID:24639646
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
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
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. PMID:24564732
From concept representations to ontologies: a paradigm shift in health informatics? PMID:24523987
Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). PMID:24518066
Ontodog: a web-based ontology community view generation tool. PMID:24413522
The neurological disease ontology. PMID:24314207
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
Updates to BioSamples database at European Bioinformatics Institute. PMID:24265224
A neuroinformatics of brain modeling and its implementation in the Brain Operation Database BODB. PMID:24234915
Pheno-Pub: a total support system for the publication of mouse phenotypic data on the web. PMID:24220852
Developing a semantically rich ontology for the biobank-administration domain. PMID:24103726
A formal representation for numerical data presented in published clinical trial reports. PMID:23920679
CLASSIFYING PROCESSES: AN ESSAY IN APPLIED ONTOLOGY. PMID:23888086
Ontology-Based Querying with Bio2RDF's Linked Open Data. PMID:23735196
Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. PMID:23735014
Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV). PMID:23684873
A unified structural/terminological interoperability framework based on LexEVS: application to TRANSFoRm. PMID:23571850
Neurocarta: aggregating and sharing disease-gene relations for the neurosciences. PMID:23442263
Controlled vocabularies and ontologies in proteomics: overview, principles and practice. PMID:23429179
Improving the accuracy of therapy descriptions in clinical trials using a bottom-up approach. PMID:23304419
OntoMaton: a bioportal powered ontology widget for Google Spreadsheets. PMID:23267176
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. PMID:23256916
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
Systematic annotation and analysis of "virmugens"-virulence factors whose mutants can be used as live attenuated vaccines. PMID:23219434
Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). PMID:23155465
On the ontology based representation of cell lines. PMID:23144907
The Units Ontology: a tool for integrating units of measurement in science. PMID:23060432
Event extraction across multiple levels of biological organization. PMID:22962484
Ontologies as integrative tools for plant science. PMID:22847540
A human-computer collaborative approach to identifying common data elements in clinical trial eligibility criteria. PMID:22846169
Bioinformatics advances in saliva diagnostics. PMID:22699264
The immune epitope database: a historical retrospective of the first decade. PMID:22681406
The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. PMID:22621763
Structure-based classification and ontology in chemistry. PMID:22480202
Improving integrative searching of systems chemical biology data using semantic annotation. PMID:22401035
Populous: a tool for building OWL ontologies from templates. PMID:22373396
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
A semantic problem solving environment for integrative parasite research: identification of intervention targets for Trypanosoma cruzi. PMID:22272365
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. PMID:22190598
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. PMID:22041276
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PMID:21991315
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case. PMID:21859449
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. PMID:21856757
Emerging vaccine informatics. PMID:21772787
BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. PMID:21702939
The cognitive paradigm ontology: design and application. PMID:21643732
Representation of research hypotheses. PMID:21624164
Developing a kidney and urinary pathway knowledge base. PMID:21624162
How orthogonal are the OBO Foundry ontologies? PMID:21624157
Sharing and archiving nucleic acid structure mapping data. PMID:21610212
On the formalization and reuse of scientific research. PMID:21490004
Genetic Analysis in Translational Medicine: The 2010 GOLDEN HELIX Symposium. PMID:21438074
Logical development of the cell ontology. PMID:21208450
Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. PMID:20875156
Application of neuroanatomical ontologies for neuroimaging data annotation. PMID:20725521
Selected papers from the 12th annual Bio-Ontologies meeting. PMID:20626920 -
The Ontology for Biomedical Investigations
PubMed citations: 79.
79 articles citing: The Ontology for Biomedical Investigations
Establishing a Common Nutritional Vocabulary - From Food Production to Diet. PMID:35811979
Semantics of Dairy Fermented Foods: A Microbiologist's Perspective. PMID:35804753
Assessing the Need for Semantic Data Integration for Surgical Biobanks-A Knowledge Representation Perspective. PMID:35629179
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
Ontologies and Knowledge Graphs in Oncology Research. PMID:35454813
Food Recipe Ingredient Substitution Ontology Design Pattern. PMID:35161841
Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation. PMID:35101121
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems. PMID:34956127
An Overview of Biomedical Ontologies for Pandemics and Infectious Diseases Representation. PMID:34868401
ENIGMA + COINSTAC: Improving Findability, Accessibility, Interoperability, and Re-usability. PMID:34846691
The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts. PMID:34831777
Using Artificial Intelligence With Natural Language Processing to Combine Electronic Health Record's Structured and Free Text Data to Identify Nonvalvular Atrial Fibrillation to Decrease Strokes and Death: Evaluation and Case-Control Study. PMID:34751659
Identifying and classifying goals for scientific knowledge. PMID:34661112
Modelling the bioinformatics tertiary analysis research process. PMID:34592928
The Infectious Disease Ontology in the age of COVID-19. PMID:34275487
Standardization of assay representation in the Ontology for Biomedical Investigations. PMID:34244718
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. PMID:34156446
A Minimal Information Model for Potential Drug-Drug Interactions. PMID:33762928
Toward assessing clinical trial publications for reporting transparency. PMID:33647518
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Ontologies relevant to behaviour change interventions: a method for their development. PMID:33447665
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. PMID:33319712
Pancreatlas: Applying an Adaptable Framework to Map the Human Pancreas in Health and Disease. PMID:33294866
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. PMID:32819435
Enabling ad-hoc reuse of private data repositories through schema extraction. PMID:32641124
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. PMID:32533075
PRISM: A Platform for Imaging in Precision Medicine. PMID:32479186
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
A structured model for immune exposures. PMID:32283555
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
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection. PMID:31626635
EIP on AHA Ontology for adherence: Knowledge representation advanced tools. PMID:31360667
Reporting and connecting cell type names and gating definitions through ontologies. PMID:31272390
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
Centralized scientific communities are less likely to generate replicable results. PMID:31264964
Organizing phenotypic data-a semantic data model for anatomy. PMID:31221226
Ontology-based metabolomics data integration with quality control. PMID:31179719
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
How Sustainable are Biomedical Ontologies? PMID:30815087
PhenoMeNal: processing and analysis of metabolomics data in the cloud. PMID:30535405
ECO, the Evidence & Conclusion Ontology: community standard for evidence information. PMID:30407590
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
The Immune Epitope Database (IEDB): 2018 update. PMID:30357391
Classification, Ontology, and Precision Medicine. PMID:30304648
Knowledge-based biomedical Data Science. PMID:30294517
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. PMID:30152011
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. PMID:30137210
The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. PMID:30034908
A guideline for reporting experimental protocols in life sciences. PMID:29868256
Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. PMID:29854250
The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps. PMID:29854221
Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse. PMID:29743102
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
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. PMID:29329592
Cell type discovery and representation in the era of high-content single cell phenotyping. PMID:29322913
Data discovery with DATS: exemplar adoptions and lessons learned. PMID:29228196
Using semantics for representing experimental protocols. PMID:29132408
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. PMID:29106667
Dietary and health biomarkers-time for an update. PMID:28974991
Analysis and visualization of disease courses in a semantically-enabled cancer registry. PMID:28962670
The Immune Epitope Database: How Data Are Entered and Retrieved. PMID:28634590
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. PMID:28592275
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Better living through ontologies at the Immune Epitope Database. PMID:28365732
Computer-Aided Experiment Planning toward Causal Discovery in Neuroscience. PMID:28243197
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. PMID:27733503
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. PMID:27627881 -
Query enhancement through the practical application of ontology: the IEDB and OBI
PubMed citations: 11.
11 articles citing: Query enhancement through the practical application of ontology: the IEDB and OBI
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection. PMID:31626635
The Immune Epitope Database (IEDB): 2018 update. PMID:30357391
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
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
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. PMID:29329592
Robotic crowd biology with Maholo LabDroids. PMID:28398329
Better living through ontologies at the Immune Epitope Database. PMID:28365732
Perspectives on next steps in classification of oro-facial pain - Part 3: biomarkers of chronic oro-facial pain - from research to clinic. PMID:26200973
Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting. PMID:23735191 -
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach
PubMed citations: 4.
4 articles citing: Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach
The Ontology for Biomedical Investigations. PMID:27128319
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
Biomedical imaging ontologies: A survey and proposal for future work. PMID:26167381
linkedISA: semantic representation of ISA-Tab experimental metadata. PMID:25472428 -
Minimum Information about a Genotyping Experiment (MIGEN)
PubMed citations: 1.
1 articles citing: Minimum Information about a Genotyping Experiment (MIGEN)
Propelling the paradigm shift from reductionism to systems nutrition. PMID:28138347
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assay
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
data transformation
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
device
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
protocol
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
reagent
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
report
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
study design
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
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More detailed information about this field from each metasource.
assay
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
data transformation
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
device
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
protocol
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
reagent
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
report
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
study design
metasource: Fairsharing.orgversion: FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
assay data transformation device protocol reagent report study design
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