• The Foundational Model of Anatomy is a medical ontology developed by the University of Washington. (ontologymatching.org)
  • The FMA stands for Foundational Model of Anatomy ontology. (washington.edu)
  • The Foundational Model of Anatomy ontology is one of the information resources integrated in the distributed framework of the Anatomy Information System developed and maintained by the Structural Informatics Group at the University of Washington . (washington.edu)
  • Golbreich C, Zhang S, Bodenreider O. (2006) The foundational model of anatomy in OWL: Experience and perspectives. (washington.edu)
  • 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)
  • The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. (bioregistry.io)
  • Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. (beds.ac.uk)
  • International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). (oregonstate.edu)
  • 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)
  • 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 FMA is a reference ontology for the domain of anatomy. (washington.edu)
  • In order to meet our objectives, we need to create a common anatomy reference ontology (CARO) designed to ensure interoperability of the anatomy ontologies developed for specific organisms. (bioontology.org)
  • The Common Anatomy Reference Ontology (CARO) provides an upper-level structure that should be used as superclasses in OBO anatomy ontologies. (obofoundry.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)
  • https://web.cci.emory.edu/confluence/download/attachments/4033450/CCI-TR-2012-1.pdf]\] # Zheng S, Wang F, Lu J, Saltz J. *Enabling Ontology Based Semantic Queries in Biomedical Database Systems. (nih.gov)
  • Anatomy provides the foundation for the other biomedical sciences or information domains. (washington.edu)
  • Therefore, anatomy is fundamental to all biomedical sciences, and the classes represented in the FMA generalize to essentially all biomedical domains. (washington.edu)
  • This means that anatomy is foundational to non-anatomical biomedical disciplines because they reuse anatomical classes. (washington.edu)
  • Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. (biomedcentral.com)
  • The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability. (biomedcentral.com)
  • 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)
  • Biomedical ontologies require a new class of relations that can be used in conjunction with default knowledge, thereby extending those currently in use. (biomedcentral.com)
  • Ontologies may provide a basis for integrating, processing and applying biomedical data. (biomedcentral.com)
  • 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)
  • A subset of these are unified under the umbrella of the Open Biomedical Ontologies (OBO) Foundry [ 7 ]. (biomedcentral.com)
  • One particular difficulty in making these ontologies interoperable results from the existence of two particular types of biomedical ontologies. (biomedcentral.com)
  • The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Anatomy. (bioontology.org)
  • Ontologies are widely used in various domains, including biomedical research, to structure information, represent knowledge, and analyze data. (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)
  • She has served as a reviewer for ICBO, the ISMB Bio-Ontologies track, BMC Medical Informatics and Decision Making, and the Journal of Biomedical Semantics (JBMS). (edu.sa)
  • As both anatomical ontologies are being used to annotate different types of research data for mouse and human, respectively, this cross-mapping between the two ontologies facilitates the integration of mouse and human data, and the translation of basic research discoveries into clinical settings. (nih.gov)
  • 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 main focus of this workshop is to pave the way for interoperability between the anatomical ontologies developed for various organisms (including human) by agreeing on shared methodologies for building our respective ontologies. (bioontology.org)
  • The JAX Synteny Browser for mouse-human comparative genomics. (symapdb.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)
  • We have developed a methodology for accurately representing canonical domain ontologies within the OBO Foundry. (biomedcentral.com)
  • Welcome to the OBO Foundry Anatomy Portal! (obofoundry.org)
  • The Human Phenotype Ontology (HPO) is a formal ontology of human phenotypes. (wikipedia.org)
  • The ontology contains over 50,000 annotations between phenotypes and hereditary 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)
  • Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. (biomedcentral.com)
  • We apply the formalism to ontologies of mouse anatomy and mammalian phenotypes in order to demonstrate the approach. (biomedcentral.com)
  • Second, we integrated phenotype ontologies for human and model organism phenotypes to enable comparisons of phenotypes between and within individual species. (edu.sa)
  • Additionally, We refined class definitions in phenotypic ontologies, specifically targeting cell cardinality phenotypes. (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)
  • Gene Prospector provides an online gateway for searching for evidence about human genes in relation to diseases, other phenotypes, and risk factors, and provides links to published literature and other online data sources. (cdc.gov)
  • First, I analyzed a large aging dataset of inbred laboratory mice, using Mouse Anatomy and Mouse Pathology ontologies. (edu.sa)
  • Structuring phenotype data using ontologies assists in its algorithmic use to shed new light on how biological systems function across time and scale. (cohenveteransbioscience.org)
  • Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. (biomedcentral.com)
  • We show how this extension can be used to achieve interoperability between ontologies, and further allows for the inclusion of more knowledge within them. (biomedcentral.com)
  • The inclusion of default knowledge is necessary in order to ensure interoperability between ontologies. (biomedcentral.com)
  • The absence of clear principles for achieving interoperability between different ontologies hinders the development of advanced applications and analysis tools based on these ontologies. (biomedcentral.com)
  • Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. (biomedcentral.com)
  • We have developed a novel algorithm (PVP) which augments existing strategies by using the similarity of the patients phenotype to known phenotype-genotype data in human and model organism databases to further rank potential candidate genes. (plos.org)
  • The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. (biomedcentral.com)
  • Uberon is a multi-species anatom ontology covering metazoa (animals). (obofoundry.org)
  • It combines parts of several biological ontologies, covering domains such as anatomy, disease and chemical compounds. (nih.gov)
  • The FMA contains anatomical classes and relationships necessary to model the structure of the entire human body. (washington.edu)
  • It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. (bioregistry.io)
  • The analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions. (biomedcentral.com)
  • These books will aid you in your studies and enhance your understanding of Anatomy & Physiology, Structural Kinesiology (the study of muscles, their attachments, and Movements), and Therapeutic Relationships. (rolf.org)
  • CARO will be embedded in a set of principles for constructing anatomy ontologies for different organisms at different developmental stages. (bioontology.org)
  • Gene expression profiles of several thousand genes are formalized in both wild-type and experimental conditions-manipulated, using anatomy formal ontology. (symapdb.org)
  • A group of faculty and students in the biological and computer sciences departments at the University of Missouri-Rolla are working with experts from around the world to develop a formal vocabulary, called an ontology, to describe the anatomy of more than 6,200 species of amphibians. (mst.edu)
  • Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). (obofoundry.org)
  • We demonstrate the distinct contributions of each species' phenotypic data to detecting human diseases using Pheno--e, and show mouse phenotypic data contributes the most to the discovery of gene-disease associations. (edu.sa)
  • At the Workshop for the Ontology of Anatomy we want to gather researchers who are actively involved in the development and improvement of particular anatomy for a variety of organisms. (bioontology.org)
  • Unfortunately this did not resolve all these issues, as CARO was not designed to provide a large set of terms for specific structures shared across species, but rather to provide an organizational framework for constructing anatomy ontologies. (biomedcentral.com)
  • It can be used to bridge other species-specific animal anatomy ontologies, see the documentation for details. (obofoundry.org)
  • EVS staff participated in developing the classifications of mouse diagnoses used for annotating the mouse models, and provided support for additional terminology such as strains and anatomy. (nih.gov)
  • caMOD annotates information with NCIt terminology, and uses the LexEVS API directly to generate anatomy and diagnosis tree hierarchies. (nih.gov)
  • It is a symbolic representation of the phenotypic structure of the human body. (washington.edu)
  • 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)
  • This representation resolved incorrect inferences in the utilized ontologies, enabling accurate interpretation of phenotypic descriptions. (edu.sa)
  • EVS Related References+ # Malone J, Rayner TF, Bradley XZ, Parkinson H. *Developing an application focused experimental factor ontology: embracing the OBO Community. (nih.gov)
  • In this new reiteration of GUDMAP, human data will be generated and incorporated into the GUDMAP database. (nih.gov)
  • Gene expression data from 24 experiments for 8 different cell types of the human myelopoietic lineage were used to generate an integrated myelopoiesis dataset of 9,425 genes, each reliably associated to a unique genomic position and chromosomal coordinate. (biomedcentral.com)
  • The human anatomy atlas CAVEman is linked to the BRENDA Tissue Ontology terms providing a connection between anatomical and functional enzyme data. (elsevierpure.com)
  • The focus of the meeting is to explore new and existing uses of common ontologies to support sharing and discovery of data and resources, researcher networking, and particularly to support the evaluation of research. (bioontology.org)
  • Combining ontologies from different domains is crucial for systematic data analysis and comparison of similar domains. (edu.sa)
  • For a portion of the data, the pre-populated data types were converted to the requested ontology terms and corresponding IDs in the Google spreadsheet using OntoMaton. (pentaconhq.org)
  • Information concerning OntoMaton is available here: http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-search-tagging-for-google-spreadsheets/ For recently added data, parsed data was imported directly into the gene curation tool, Curatus, where requested ontology terms could be added or converted. (pentaconhq.org)
  • Fascinatingly, the team used DNA methylation mapping to infer gene expression patterns, which they first utilized to reconstruct the skeletal morphology of chimps and Neanderthals to compare against known anatomy. (epigenie.com)
  • The evidence code P is used for publications that (1) predict presence based on evidence in mice/rabbits (2) use bioinformatics tools to identify human genes and (3) contain non-traceable author statements. (pentaconhq.org)
  • Bioinformatics approaches would include using conserved sequence motifs to identify candidate genes, using a known human gene to identify sequences with significant identity (and finding cDNA in EST database). (pentaconhq.org)
  • Regardless of organism differences, if we use common methodologies and principles to build our ontologies then, ultimately, this will enable us to tackle the big issue: to recognize homologous anatomical structures of different species. (bioontology.org)
  • Currently, there is no support for a correct and consistent integration of such ontologies. (biomedcentral.com)
  • www.ctsacentral.org/committee/ikfc-clinical-and-translational-science-affinity-group-ctso-ag IKFC Clinical and Translational Science Ontology Affinity Group] which has been established to leverage the use of common ontologies to support different aspects of information-driven clinical and translational research. (bioontology.org)
  • The goal is to have the groundwork laid so that, with support, the project can continue until a comprehensive ontology is built. (mst.edu)
  • The use of cross-species anatomy and phenotype ontologies can be combined with genomic analysis to support disease diagnosis, prognosis, and treatment selection. (cohenveteransbioscience.org)
  • This paper describes the modelling of the LUCADA lung cancer ontology in OWL 2 and how this ontology is utilised by the online clinical decision support application Lung Cancer Assistant (LCA) for categorising patients and producing guideline-based treatment recommendations with the help of ontological inference. (ox.ac.uk)
  • In recent years, the availability of the human genome sequence disclosed novel opportunities to study biological processes from a higher level perspective. (biomedcentral.com)
  • WormBase is supported by grant #U24 HG002223 from the National Human Genome Research Institute at the US National Institutes of Health , the UK Medical Research Council and the UK Biotechnology and Biological Sciences Research Council . (wormbase.org)
  • Although the implementation is currently limited to the browser on the reference genome for the laboratory mouse and human, this software platform agnostic deliberately genome. (symapdb.org)
  • Millions of single nucleotide polymorphisms have been identified as a result of the human genome project and the rapid advance of high throughput genotyping technology. (cdc.gov)
  • Variation in the human genome contributes to differences in response to environmental risk factors and disease susceptibility [ 1 ]. (cdc.gov)
  • As a result of the Human Genome Project [ 2 ] and advances in new genotyping technology [ 3 ], genetic association studies have been flourishing. (cdc.gov)
  • Gene Prospector ranks the genes according to the amount of published literature in human genome epidemiology, as well as relevant, published research in two animal (rat and mouse) models. (cdc.gov)
  • Gene Prospector is a component of HuGE Navigator, an integrated knowledge base for genetics association and human genome epidemiology [ 7 ]. (cdc.gov)
  • Gene Prospector was developed as a component of HuGE Navigator, an integrated, searchable, Web-based knowledge base of genetic associations and human genome epidemiology. (cdc.gov)
  • Published literature in human genome epidemiology is selected from PubMed and deposited in the HuGE Navigator database. (cdc.gov)
  • This novel method can pave the way for more accurate and efficient ontology-based methods, which can have significant implications for various semantic web applications. (edu.sa)
  • It is also a powerful learning tool that allows you to interact with the anatomy plates, listen to the audio pronunciations of every label, image title and image subtitle, zoom in and out of any anatomy plate with a movable magnifying window, search for specific terms or regions in the atlas, and print or export the images in gray-scale or color. (soulshednz.com)
  • You can also access online resources and tools that enhance your understanding of the human anatomy, such as the Online Application for Web-based Learning (OWL), the Ontology Lookup Service (OLS), the graph database of relations between terms, and the Semantic Web Rule Language (SWRL). (soulshednz.com)
  • Essentially, we're coming up with an agreed-upon set of terms that researchers will use when refer to amphibian anatomy," says Dr. Anne Maglia, assistant professor of biological sciences at UMR, who is working on the project with Dr. Jennifer Leopold, assistant professor of computer sciences at UMR, and AnalĂ­a Pugener, a postdoctoral researcher in biological sciences at UMR. (mst.edu)
  • The ontology could contain as many as 100,000 terms, and also will include ancillary information for the terms, such as cited literature, dates of the terms' publication and pictures. (mst.edu)
  • Clinical annotations within the HPO are sought from the medical and genetics community to improve the ontology. (wikipedia.org)
  • Mouse Models of Human Cancer Consortium (MMHCC) was established by NCI in 1999 to accelerate the development and validation of mouse models by the scientific community. (nih.gov)
  • This community page organizes different OBO anatomy ontologies and describes how they relate to one another. (obofoundry.org)
  • Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where multipotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. (biomedcentral.com)
  • First, research indicates that the majority (numerically) of the genes and cells contained within the human body belong to microbes. (christianscholars.com)
  • The first group describes a canonical or idealized view on a domain, such as an ontology of canonical anatomy. (biomedcentral.com)
  • Conclusion - Summarize the main points and benefits of Netter Interactive Atlas Of Human Anatomy 30iso - Provide some tips and recommendations for using Netter Interactive Atlas Of Human Anatomy 30iso effectively - Include a call to action for the readers to download and try Netter Interactive Atlas Of Human Anatomy 30iso - FAQs - What are the system requirements for Netter Interactive Atlas Of Human Anatomy 30iso? (soulshednz.com)
  • These findings have "profound implications…for our philosophical" and theological "comprehension of the human self. (christianscholars.com)
  • Hematopathology subcommittee of the Mouse Models of Human Cancers Consortium. (nih.gov)
  • This Funding Opportunity Announcement requests applications for a Human Tissue Core for the GenitoUrinary Development Molecular Anatomy Project (GUDMAP) consortium. (nih.gov)
  • The GUDMAP consortium has established a molecular anatomy atlas of the developing murine kidney and the lower urinary tract. (nih.gov)
  • The focus of this task is to confront existing alignment technology with real world ontologies. (ontologymatching.org)
  • The task is to find alignment between classes in the two ontologies. (ontologymatching.org)
  • In addition, it is allowed to use background knowledge, that has not specifically been created for the alignment tasks (ie no hand-made mappings between parts of the ontologies). (ontologymatching.org)
  • 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 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 applications that systematize the conceptual structure of cancer biology. (tu-dortmund.de)
  • This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. (biomedcentral.com)