• Curators in the Zebrafish Information Network (ZFIN) are annotating mutant phenotypes using the zebrafish anatomy ontology and the Phenotype And Trait Ontology (PATO). (phenoscape.org)
  • The goal of the track is to find pairwise alignments between the Environment Ontology (ENVO) and the Semantic Web for Earth and Environment Technology Ontology (SWEET), and between the Plant Trait Ontology (PTO) and the Flora Phenotype Ontology (FLOPO). (ontologymatching.org)
  • Developed as part of the Monarch Initiative in collaboration with members of the Open Biomedical Ontologies Foundry, HPO currently contains over 13,000 terms and over 156,000 annotations to hereditary diseases. (wikipedia.org)
  • The ontology contains over 50,000 annotations between phenotypes and hereditary disease. (wikipedia.org)
  • Clinical annotations within the HPO are sought from the medical and genetics community to improve the ontology. (wikipedia.org)
  • Interoperability between these ontologies would facilitate the consistent use of biomedical data in the form of annotations, allow for queries over multiple ontologies and form a rich knowledge resource for biomedicine that could be further used in solving problems and stating hypotheses. (biomedcentral.com)
  • Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. (yeastgenome.org)
  • With over 13,000 terms and over 156,000 annotations to hereditary diseases, the HPO can be leveraged as a powerful tool for phenotype-driven differential diagnostics, genomic diagnostics, precision medicine, and translational research. (phenotips.com)
  • Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. (mpg.de)
  • The Human Phenotype Ontology (HPO) is a formal ontology of human phenotypes. (wikipedia.org)
  • PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions. (github.com)
  • To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast. (ucl.ac.uk)
  • The autocomplete widget accesses ontology content from the latest version of the ontology. (bmicc.cn)
  • Specifically, the selected ontologies are the Human Phenotype (HP) Ontology, the Mammalian Phenotype (MP) Ontology, the Human Disease Ontology (DOID), and the Orphanet and Rare Diseases Ontology (ORDO). (ontologymatching.org)
  • We identified novel abnormal anatomical classes for fly phenotypes, allowing the annotation of fly genes that were not annotated before. (edu.sa)
  • Her paper "Contribution of model organism phenotypes to the computational identification of human disease genes" was selected as the Editor's Choice article in Disease Models and Mechanisms. (edu.sa)
  • This diagram displays phenotype observables (purple squares) that are shared between the given gene (yellow circle) and other genes (gray circles) based on the number of phenotype observables shared (adjustable using the slider at the bottom). (yeastgenome.org)
  • Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a more severe fitness defect or lethality under a given condition. (thebiogrid.org)
  • A genetic interaction is inferred when mutations or deletions in separate genes, each of which alone causes a minimal phenotype, result in lethality when combined in the same cell under a given condition. (thebiogrid.org)
  • Whole genome analysis of lung, sampled 24 hours after challenge, showed expression changes of not only genes belonging to several Gene Ontology groups with up-regulation of inflammatory-associated genes and those associated with lung remodeling but also genes involved in downsizing these processes. (cdc.gov)
  • Our findings reveal this correction enhances gene-disease prediction for diseases associated with cardinality phenotypes. (edu.sa)
  • The most widely used biological ontology is the Gene Ontology , which is utilized to annotate molecular function, biological processes and subcellular localization to gene products from different organisms. (phenoscape.org)
  • Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene. (jax.org)
  • The associated human phenotype of de novo heterozygous mutations in this gene is variable, but moderate to severe neurodevelopmental delay and learning disability are common to all. (bmj.com)
  • Functional significance of genic- and intergenic-CpG methylation status was tested using protein-protein or protein-DNA interactions and gene-ontology enrichment to infer networks. (cdc.gov)
  • The compound inheritance gene dosage model shows that haploinsufficiency does not cause the phenotype whereas a homozygous null allele is lethal. (cdc.gov)
  • As a result, translating a statement or transferring an annotation from one ontology to another may not always yield the correct results. (biomedcentral.com)
  • Ontologies represent the knowledge of a particular discipline and provide not only a mechanism for consistent annotation of data, but also greater interoperability among people and machines. (phenoscape.org)
  • Here, we aimed to study if improved HPO annotation for SAIDs enhanced SAID identification and to demonstrate the potential of phenotype -driven genome diagnostics using curated HPO terms for SAIDs . (bvsalud.org)
  • This talk is part of the From Genotype to Phenotype: Resources and Challenges (10th June 2009, Hinxton) series. (cam.ac.uk)
  • Psychomotor developmental outcomes appear variable between patients, and we propose a possible genotype-phenotype correlation, with disruption of Pur repeat III resulting in a more severe phenotype. (bmj.com)
  • Major breakthroughs in medical genomics have been enabled by the implementation of clinical exome sequencing (ES) for molecular diagnosis, by genomics approaches for understanding the genetic basis of complex traits and diseases, and by progress in understanding genotype–phenotype relationships. (cdc.gov)
  • This requires ontology composition, integration, and alignment, which involve creating new classes by reusing classes from different domains, aggregating types of ontologies within the same domain, and finding correspondences between ontologies within the same or similar domain. (edu.sa)
  • This track evaluates the detection of complex correspondences between ontologies of four different domains: conference, hydrography, geography and species taxonomy. (ontologymatching.org)
  • The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability. (biomedcentral.com)
  • We have developed a methodology for accurately representing canonical domain ontologies within the OBO Foundry. (biomedcentral.com)
  • A subset of these are unified under the umbrella of the Open Biomedical Ontologies (OBO) Foundry [ 7 ]. (biomedcentral.com)
  • This diagram displays up to the top 30 positive interactions (green), negative interactions (orange), and phenotypes (blue) that are shared between the given allele (black) and other alleles (purple). (yeastgenome.org)
  • We apply the formalism to ontologies of mouse anatomy and mammalian phenotypes in order to demonstrate the approach. (biomedcentral.com)
  • The first group describes a canonical or idealized view on a domain, such as an ontology of canonical anatomy. (biomedcentral.com)
  • An example of a canonical ontology is the Foundational Model of Anatomy [ 9 ] (FMA), which describes an idealized domain, i.e., it describes a prototypical, idealized human anatomy. (biomedcentral.com)
  • First, I analyzed a large aging dataset of inbred laboratory mice, using Mouse Anatomy and Mouse Pathology ontologies. (edu.sa)
  • We have initiated a multi-species ontology for ostariophysan fishes, the Teleost Anatomy Ontology (TAO) ( Dahdul et al, 2010 ), which was initialized with the terms in the zebrafish anatomical ontology. (phenoscape.org)
  • This multi-species anatomy ontology is being used in combination with the PATO ontology (see EQ format) to describe the comparative morphological characters. (phenoscape.org)
  • The data retrieved from gt;momic sequencing techniques provides the raw information required to infer the basis of mutations and their resulting phenotypes, wherein plant ontologies can be utilized in annotating said phenotypes using a common, shared vocabulary. (oregonstate.edu)
  • An ontology for Autism Spectrum Disorder (ASD) to infer ASD phenotypes from Autism Diagnostic Interview-Revised data. (bvsalud.org)
  • Inconsistencies may arise when ontologies of properties - mostly phenotype ontologies - are combined with ontologies taking a canonical view of a domain - such as many anatomical ontologies. (biomedcentral.com)
  • The taxonomic ontology will include nodes ancestral to the Ostariophysi as far back as the Vertebrata in order to associate certain anatomical terms with more inclusive clades than the Ostariophysi. (phenoscape.org)
  • The OAEI 2019 campaign will once again confront ontology matchers to ontology and data sources to be matched. (ontologymatching.org)
  • The Human Phenotype Ontology (HPO) was created to serve as a standardized vocabulary of phenotypic abnormalities that have been seen in human disease. (wikipedia.org)
  • Applications for the data in the ontology include clinical diagnostics, mapping between phenotypes of model organisms, and as a standard vocabulary for clinical databases. (wikipedia.org)
  • Sebastian Köhler, a founder of the Human Phenotype Ontology (HPO), discusses the future of this widely adopted standardized vocabulary for phenotypic abnormalities. (phenotips.com)
  • The Human Phenotype Ontology (HPO) is a standardized, structured, vocabulary that describes phenotypic abnormalities encountered in human disease. (phenotips.com)
  • The database with its web-interface, together with the extended ontologies and data curation tools, will allow researchers to ask novel questions about the genetic and developmental regulation of evolutionary morphological transitions. (phenoscape.org)
  • Curation and expansion of the Human Phenotype Ontology for systemic autoinflammatory diseases improves phenotype-driven disease-matching. (bvsalud.org)
  • Accurate and standardized phenotypic descriptions are essential in diagnosing rare diseases and discovering new diseases , and the Human Phenotype Ontology (HPO) system was developed to provide a rich collection of hierarchical phenotypic descriptions. (bvsalud.org)
  • The Rat Strain Ontology (RS) is currently being developed at the Rat Genome Database. (mcw.edu)
  • It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnostics. (elsevierpure.com)
  • Clinical Diagnostics with Semantic Similarity Searches in Ontologies. (mpg.de)
  • We are addressing this by developing a database of evolutionarily variable morphological characters for a large clade of fishes (the Ostariophysi) and connecting this database to the large collection of mutant phenotypes in the ZFIN database , the central database of the zebrafish model organism community. (phenoscape.org)
  • The evolutionary and mutant phenotypes are being described using common ontologies . (phenoscape.org)
  • PHIPO is being developed to support the comprehensive and detailed representation of phenotypes in PHI-base, the multi-species Pathogen-Host Interactions database available online at http://www.phi-base.org . (github.com)
  • Second, we integrated phenotype ontologies for human and model organism phenotypes to enable comparisons of phenotypes between and within individual species. (edu.sa)
  • Together with taxonomic experts, we have developed a taxonomic ontology (based on the Catalog of Fishes ) to relate species with particular characters and states. (phenoscape.org)
  • This thesis presents use cases where we applied ontology composition, integration, and alignment and evaluated the resulting ontologies and alignment. (edu.sa)
  • Third, we introduce a novel neural-symbolic method that combines logic fundamentals with machine learning for ontology alignment. (edu.sa)
  • Ontology alignment and link discovery systems are welcome to participate. (ontologymatching.org)
  • Cognitive phenotypes such as developmental delay/intellectual disability (DD/ID), autism, and schizophrenia are complex traits. (cdc.gov)
  • This representation resolved incorrect inferences in the utilized ontologies, enabling accurate interpretation of phenotypic descriptions. (edu.sa)
  • This ontology repository was created using the Ontology Development Kit . (github.com)
  • Ontologies may provide a basis for integrating, processing and applying biomedical data. (biomedcentral.com)
  • Ontologies are widely used in various domains, including biomedical research, to structure information, represent knowledge, and analyze data. (edu.sa)
  • Combining ontologies from different domains is crucial for systematic data analysis and comparison of similar domains. (edu.sa)
  • Sarah's research interest is in Artificial Intelligence applications in biomedical applications, specifically in leveraging biomedical ontologies to enable computational reasoning over complex biomedical data. (edu.sa)
  • Sarah has presented her work at several conferences, including the International Conference on Biomedical Ontology (ICBO), the International Society for Computational Biology (ISMB), and the Computational and Statistical Interface to Big Data. (edu.sa)
  • I think that structured data like encoded HPO or SNOMED, or whatever standard is en vogue, will play a key role [in newborn screening]. (phenotips.com)
  • Mutation Data Integration, Phenotype Ontologies, Semantic Support and Reuse. (bio.net)
  • PATO is an ontology of phenotypic qualities. (github.io)
  • PATO is a "universal" ontology of terms describing qualities (e.g. shape, color, size) that may be applied to any organism. (phenoscape.org)
  • will use NCI Thesaurus (ontology id is NCIT) and will put the class URI in the field after the user selects the class from the pull-down list. (bmicc.cn)
  • The shared interactions or phenotypes can be visualized separately using the radio button at the bottom of the graph. (yeastgenome.org)
  • Conclusions These findings provide definitive evidence for the role of PURA in causing a variable syndrome of neurodevelopmental delay, learning disability, neonatal hypotonia, feeding difficulties, abnormal movements and epilepsy in humans, and help clarify the role of PURA in the previously described 5q31.3 microdeletion phenotype. (bmj.com)
  • Additionally, We refined class definitions in phenotypic ontologies, specifically targeting cell cardinality phenotypes. (edu.sa)
  • She has also participated in several international workshops and tutorials, including The Semantic Web Applications for Health Care and Life Sciences conference (SWAT4HCLS), The International Workshop on Ontology Matching (OM), the Role of Ontologies in Biomedical AI (ROBI) tutorial and workshop, and the International Conference on Biomedical Ontology (ICBO). (edu.sa)
  • The Pistoia Alliance Ontologies Mapping project team organises and sponsors this track based on a real use case where it is required to find alignments between disease and phenotype ontologies. (ontologymatching.org)
  • Please use this repository's issue tracker to request new terms and classes, or to report errors or specific concerns related to the ontology. (github.com)
  • Ontologies are constrained, structured vocabularies with well defined relationships among terms. (phenoscape.org)
  • She has been an essential member of the Bio-Ontology Research Group (BORG) since 2015.Her research interests include the applications of artificial intelligence and statistical methods to genomics and healthcare. (edu.sa)
  • Currently, there is no support for a correct and consistent integration of such ontologies. (biomedcentral.com)
  • Summary results along with detail performance results for each ontology pair (test case) and comparison with tools' performance from last years will be provided. (ontologymatching.org)
  • This is achieved by adding an extension to the semantics for relationships in the biomedical ontologies that allows for treating canonical information as default. (biomedcentral.com)
  • The goal of the track is to find alignments within a collection of ontologies describing the domain of organising conferences. (ontologymatching.org)