UBER anatomy ONtology
Names
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UBER anatomy ONtology
metasource: Fairsharing.org
version: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
UBERON
metasource: Fairsharing.org
version: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Uber Anatomy Ontology
metasource: Biontology / Bioportal
version: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Names
More detailed information about this field from each metasource.
UBER anatomy ONtology
metasource: Fairsharing.orgversion: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
UBERON
metasource: Fairsharing.orgversion: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Uber Anatomy Ontology
metasource: Biontology / Bioportalversion: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Other names: UBERON, Uber Anatomy Ontology
Names
More detailed information about this field from each metasource.
UBER anatomy ONtology
metasource: Fairsharing.orgversion: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
UBERON
metasource: Fairsharing.orgversion: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Uber Anatomy Ontology
metasource: Biontology / Bioportalversion: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Uberon is an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies. It represents a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
Description
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Uberon is an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies. It represents a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
metasource: Fairsharing.orgversion: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
metasource: Biontology / Bioportalversion: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Webpage:
http://uberon.org/Webpage
More detailed information about this field from each metasource.
http://uberon.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
http://uberon.org
metasource: Biontology / Bioportalversion: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Licence:
Name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 3.0 Unported (CC BY 3.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/3.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Uberon, an integrative multi-species anatomy ontology
PMID: 22293552
metasource: Fairsharing.org
version: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
PMID: 25009735
metasource: Fairsharing.org
version: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
http://genomebiology.com/content/13/1/R5
metasource: Biontology / Bioportal
version: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
Publications
More detailed information about this field from each metasource.
Uberon, an integrative multi-species anatomy ontology
PMID: 22293552
metasource: Fairsharing.org
version: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
PMID: 25009735
metasource: Fairsharing.org
version: FAIRsharing.org: UBERON; UBER anatomy ONtology; DOI: https://doi.org/10.25504/FAIRsharing.4c0b6b; Last edited: June 7, 2019, 1:34 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
http://genomebiology.com/content/13/1/R5
metasource: Biontology / Bioportalversion: 2022-09-30 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/UBERON
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Uberon, an integrative multi-species anatomy ontology
PubMed citations: 257.
257 articles citing: Uberon, an integrative multi-species anatomy ontology
Semantics of Dairy Fermented Foods: A Microbiologist's Perspective. PMID:35804753
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research. PMID:35761389
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. PMID:35705903
Data standardization of plant-pollinator interactions. PMID:35639882
Past and future uses of text mining in ecology and evolution. PMID:35582795
Design and application of a knowledge network for automatic prioritization of drug mechanisms. PMID:35561182
Pleiotropic Enhancers are Ubiquitous Regulatory Elements in the Human Genome. PMID:35552697
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
Conceptual Design and Prototyping for a Primate Health History Knowledge Model. PMID:35441181
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Parallel sequence tagging for concept recognition. PMID:35331131
The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. PMID:35295213
ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research. PMID:35224820
Advances in the development of PubCaseFinder, including the new application programming interface and matching algorithm. PMID:35143083
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning. PMID:34951628
Physicochemical properties determining drug detection in skin. PMID:34793633
The IntAct database: efficient access to fine-grained molecular interaction data. PMID:34761267
Anatomical structures, cell types and biomarkers of the Human Reference Atlas. PMID:34750582
Cell type ontologies of the Human Cell Atlas. PMID:34750578
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PMID:34665801
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. PMID:34663204
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. PMID:34493866
Matching Biomedical Ontologies: Construction of Matching Clues and Systematic Evaluation of Different Combinations of Matchers. PMID:34420930
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
The Progenetix oncogenomic resource in 2021. PMID:34272855
The SPARC DRC: Building a Resource for the Autonomic Nervous System Community. PMID:34248680
Comparative Transcriptomics Reveals Distinct Patterns of Gene Expression Conservation through Vertebrate Embryogenesis. PMID:34247223
Visual comprehension and orientation into the COVID-19 CIDO ontology. PMID:34224898
Toward a Coronavirus Knowledge Graph. PMID:34209818
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Development and application of the ocular immune-mediated inflammatory diseases ontology enhanced with synonyms from online patient support forum conversation. PMID:34139439
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. PMID:34015823
The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX). PMID:33981708
CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies. PMID:33768211
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. PMID:33677548
Knowledge Representation for Multi-Scale Physiology Route Modeling. PMID:33664662
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. PMID:33622235
Integrative Base Ontology for the Research Analysis of Alzheimer's Disease-Related Mild Cognitive Impairment. PMID:33613222
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. PMID:33500403
Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. PMID:33455583
What is the abdomen? Rationalising clinical and anatomical perspectives using formal semantics. PMID:33417250
CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology. PMID:33364592
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
GTRD: an integrated view of transcription regulation. PMID:33231677
CSEA-DB: an omnibus for human complex trait and cell type associations. PMID:33211888
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. PMID:33211864
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
The ontology of the anatomy and development of the solitary ascidian Ciona: the swimming larva and its metamorphosis. PMID:33087765
Comparative Toxicogenomics Database (CTD): update 2021. PMID:33068428
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. PMID:33028186
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
COVID-19 Biomarkers in research: Extension of the OncoMX cancer biomarker data model to capture biomarker data from other diseases. PMID:32935101
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. PMID:32883995
Knowledge-Based Decision Support in Healthcare via Near Field Communication. PMID:32878204
ReDU: a framework to find and reanalyze public mass spectrometry data. PMID:32807955
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
PRISM: A Platform for Imaging in Precision Medicine. PMID:32479186
Bootstrapping Adversarial Learning of Biomedical Ontology Alignments. PMID:32308857
DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. PMID:32308806
Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body. PMID:32232057
OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. PMID:32142370
Ontology-driven integrative analysis of omics data through Onassis. PMID:31959844
Mass spectrometry searches using MASST. PMID:31894142
OHMI: the ontology of host-microbiome interactions. PMID:31888755
TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column. PMID:31832082
Ecological interactions in the Scratchpads virtual research environment. PMID:31824210
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. PMID:31725864
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
Enabling semantic queries across federated bioinformatics databases. PMID:31697362
Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung. PMID:31651362
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection. PMID:31626635
A Logical Model of Homology for Comparative Biology. PMID:31596473
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries. PMID:31419946
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. PMID:31304272
An ontology for representing hematologic malignancies: the cancer cell ontology. PMID:31272372
Literature-Based Enrichment Insights into Redox Control of Vascular Biology. PMID:31223421
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
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
ZooArchNet: Connecting zooarchaeological specimens to the biodiversity and archaeology data networks. PMID:30978247
Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions. PMID:30918448
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. PMID:30858527
Overlapping Complex Concepts Have More Commission Errors, Especially in Intensive Terminology Auditing. PMID:30815158
Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits. PMID:30668800
OGER++: hybrid multi-type entity recognition. PMID:30666476
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. PMID:30576485
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. PMID:30576482
Discovery of Emerging Design Patterns in Ontologies Using Tree Mining. PMID:30505251
The BioGRID interaction database: 2019 update. PMID:30476227
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. PMID:30467459
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
The Gene Ontology Resource: 20 years and still GOing strong. PMID:30395331
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling. PMID:30239666
Morphological description, character conceptualization and the reconstruction of ancestral states exemplified by the evolution of arthropod hearts. PMID:30235213
Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. PMID:30139913
INFERNO: inferring the molecular mechanisms of noncoding genetic variants. PMID:30113658
Glycomics@ExPASy: Bridging the Gap. PMID:30097532
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations. PMID:30057931
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
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
Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies. PMID:29852316
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. PMID:29800226
Identification of errors in the IEDB using ontologies. PMID:29688357
Disease Ontology: improving and unifying disease annotations across species. PMID:29590633
Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature. PMID:29523070
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
Tackling the challenges of matching biomedical ontologies. PMID:29335022
Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. PMID:29325126
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
Comparison, alignment, and synchronization of cell line information between CLO and EFO. PMID:29322915
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. PMID:29197409
Taxonomy-Based Approaches to Quality Assurance of Ontologies. PMID:29158885
The Human Cell Atlas: Technical approaches and challenges. PMID:29092000
A communal catalogue reveals Earth's multiscale microbial diversity. PMID:29088705
COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies. PMID:29083911
SCPortalen: human and mouse single-cell centric database. PMID:29045713
Evaluating phenotype-driven approaches for genetic diagnoses from exomes in a clinical setting. PMID:29044180
MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. PMID:29028869
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. PMID:28981708
A histological ontology of the human cardiovascular system. PMID:28969675
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Building bridges between cellular and molecular structural biology. PMID:28682240
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. PMID:28535296
From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies. PMID:28532962
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
Semantic prioritization of novel causative genomic variants. PMID:28414800
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Better living through ontologies at the Immune Epitope Database. PMID:28365732
An atlas of human long non-coding RNAs with accurate 5' ends. PMID:28241135
The importance of digitized biocollections as a source of trait data and a new VertNet resource. PMID:28025346
The ChEMBL database in 2017. PMID:27899562
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. PMID:27857184
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. PMID:27664130
Evolution of biomedical ontologies and mappings: Overview of recent approaches. PMID:27642503
Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. PMID:27570653
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
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. PMID:27334471
The FaceBase Consortium: a comprehensive resource for craniofacial researchers. PMID:27287806
PhenoImageShare: an image annotation and query infrastructure. PMID:27267125
The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing. PMID:27246819
Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PMID:27191170
The Ontology for Biomedical Investigations. PMID:27128319
DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. PMID:27084938
Extending gene ontology in the context of extracellular RNA and vesicle communication. PMID:27076901
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
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
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. PMID:26896844
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
Value, but high costs in post-deposition data curation. PMID:26861660
Using the Gene Ontology to Annotate Key Players in Parkinson's Disease. PMID:26825309
Emerging semantics to link phenotype and environment. PMID:26713234
Cross-biome comparison of microbial association networks. PMID:26579106
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development. PMID:26413258
The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases. PMID:26393351
owlcpp: a C++ library for working with OWL ontologies. PMID:26388983
Applications of comparative evolution to human disease genetics. PMID:26338499
Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types. PMID:26330083
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. PMID:26272982
Use of model organism and disease databases to support matchmaking for human disease gene discovery. PMID:26269093
Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data. PMID:26208972
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
Activity, assay and target data curation and quality in the ChEMBL database. PMID:26201396
Cross-organism analysis using InterMine. PMID:26097192
ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180
Disease insights through cross-species phenotype comparisons. PMID:26092691
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. PMID:26048076
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. PMID:26018570
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. PMID:25972520
The SwissLipids knowledgebase for lipid biology. PMID:25943471
TermGenie - a web-application for pattern-based ontology class generation. PMID:25937883
OTO: Ontology Term Organizer. PMID:25887779
What to compare and how: Comparative transcriptomics for Evo-Devo. PMID:25864439
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278
CLO: The cell line ontology. PMID:25852852
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. PMID:25815161
Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. PMID:25789153
Ontology application and use at the ENCODE DCC. PMID:25776021
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
Gateways to the FANTOM5 promoter level mammalian expression atlas. PMID:25723102
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. PMID:25656970
Finding our way through phenotypes. PMID:25562316
EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization. PMID:25550428
Gene Ontology Consortium: going forward. PMID:25428369
The BioGRID interaction database: 2015 update. PMID:25428363
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. PMID:25348409
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. PMID:25276334
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. PMID:25140222
OAE: The Ontology of Adverse Events. PMID:25093068
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
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. PMID:25009735
The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. PMID:24958384
Representing kidney development using the gene ontology. PMID:24941002
My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models. PMID:24936286
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
A wonderful network unraveled - Detailed description of capillaries in the prosomal ganglion of scorpions. PMID:24812570
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
A promoter-level mammalian expression atlas. PMID:24670764
Linking tissues to phenotypes using gene expression profiles. PMID:24634472
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
Knowledge extraction and semantic annotation of text from the encyclopedia of life. PMID:24594988
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. PMID:24568621
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
The environment ontology: contextualising biological and biomedical entities. PMID:24330602
CellFinder: a cell data repository. PMID:24304896
Updates to BioSamples database at European Bioinformatics Institute. PMID:24265224
Improved exome prioritization of disease genes through cross-species phenotype comparison. PMID:24162188
Mouse model phenotypes provide information about human drug targets. PMID:24158600
The Drosophila anatomy ontology. PMID:24139062
Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. PMID:24139024
The ontology of craniofacial development and malformation for translational craniofacial research. PMID:24124010
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. PMID:24093723
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
Ontology based molecular signatures for immune cell types via gene expression analysis. PMID:24004649
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. PMID:23972281
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
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia. PMID:23652347
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. PMID:23599415
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. PMID:23327938
Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment. PMID:23303300
A unified anatomy ontology of the vertebrate skeletal system. PMID:23251424
Semantically enabling a genome-wide association study database. PMID:23244533
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Gene Ontology annotations and resources. PMID:23161678
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 new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20). PMID:22973865
Evaluation of research in biomedical ontologies. PMID:22962340
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. PMID:22961259
Ontologies as integrative tools for plant science. PMID:22847540
PaxDb, a database of protein abundance averages across all three domains of life. PMID:22535208
The mouse-human anatomy ontology mapping project. PMID:22434834
Mouse genetic and phenotypic resources for human genetics. PMID:22422677
vHOG, a multispecies vertebrate ontology of homologous organs groups. PMID:22285560
Improving ontologies by automatic reasoning and evaluation of logical definitions. PMID:22032770
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
Integrating phenotype ontologies across multiple species. PMID:20064205 -
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
PubMed citations: 63.
63 articles citing: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY. PMID:35547570
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
GOing Forward With the Cardiac Conduction System Using Gene Ontology. PMID:35309148
Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain. PMID:35095432
Convergent evolution of venom gland transcriptomes across Metazoa. PMID:34983844
The Human Disease Ontology 2022 update. PMID:34755882
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. PMID:34634810
Sfaira accelerates data and model reuse in single cell genomics. PMID:34433466
The Infectious Disease Ontology in the age of COVID-19. PMID:34275487
The divergence of alternative splicing between ohnologs in teleost fishes. PMID:34034651
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. PMID:33677548
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Cerebrum, liver, and muscle regulatory networks uncover maternal nutrition effects in developmental programming of beef cattle during early pregnancy. PMID:33531552
Common cell type nomenclature for the mammalian brain. PMID:33372656
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
The Human Phenotype Ontology in 2021. PMID:33264411
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. PMID:33028186
Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. PMID:32500119
A Logical Model of Homology for Comparative Biology. PMID:31596473
Alliance of Genome Resources Portal: unified model organism research platform. PMID:31552413
Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries. PMID:31419946
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. PMID:30576485
MER: a shell script and annotation server for minimal named entity recognition and linking. PMID:30519990
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. PMID:30476213
ChEMBL: towards direct deposition of bioassay data. PMID:30398643
The mouse Gene Expression Database (GXD): 2019 update. PMID:30335138
Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees. PMID:30334222
Classification, Ontology, and Precision Medicine. PMID:30304648
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis. PMID:29444698
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. PMID:29325126
Improving the interoperability of biomedical ontologies with compound alignments. PMID:29316968
Drug target ontology to classify and integrate drug discovery data. PMID:29122012
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. PMID:28981708
Dead simple OWL design patterns. PMID:28583177
BRIDG: a domain information model for translational and clinical protocol-driven research. PMID:28339791
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
Computational methods for direct cell conversion. PMID:27736295
Navigating the Phenotype Frontier: The Monarch Initiative. PMID:27516611
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PMID:27191170
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. PMID:27011785
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. PMID:27009807
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
Reporting phenotypes in mouse models when considering body size as a potential confounder. PMID:26865945
Emerging semantics to link phenotype and environment. PMID:26713234
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. PMID:26500251
Use of model organism and disease databases to support matchmaking for human disease gene discovery. PMID:26269093
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. PMID:26119816
Disease insights through cross-species phenotype comparisons. PMID:26092691
The mouse gene expression database: New features and how to use them effectively. PMID:26045019
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. PMID:26018570
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. PMID:25972520
Linking gene expression to phenotypes via pathway information. PMID:25901272
What to compare and how: Comparative transcriptomics for Evo-Devo. PMID:25864439
Finding our way through phenotypes. PMID:25562316
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. PMID:25140222
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. PMID:24568621 - http://genomebiology.com/content/13/1/R5
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