• The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. (bioontology.org)
  • ProComp leverages, and cross references, entries in existing protein-centric informatics resources, including the protein complexes that are represented in the Cellular Component branch of the Gene Ontology. (biomedcentral.com)
  • Specifically, the network uses hierarchical graph convolution that mimic the organization of a well-established gene ontology to track the convergence of genetic risk across biological pathways. (stanford.edu)
  • U. Consortium, The Gene Ontology (GO) Project in 2006. (org.pk)
  • Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. (umsystem.edu)
  • This paper describes how high level biological knowledge obtained from ontologies such as the Gene Ontology (GO) can be integrated with low level information extracted from a Bayesian net- work trained on protein interaction data. (sunderland.ac.uk)
  • New, previously unrelated information is extracted from the growing body of research literature and in- corporated with knowledge already known on this subject from the gene ontology and databases such as BIND and BioGRID. (sunderland.ac.uk)
  • The National Center for Biomedical Ontology (NCBO) in collaboration with the Protein Ontology (PRO) and the Infectious Disease Ontology (IDO) will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012. (bioontology.org)
  • Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. (biomedcentral.com)
  • International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016). (oregonstate.edu)
  • Projects should address health-related behavioral and social science problems not easily solved without improvement in semantic knowledge structures (e.g., controlled vocabularies, taxonomies, and ontologies). (nih.gov)
  • How much confidence do you have that the researchers and stakeholders will indeed use the common terms and controlled vocabularies developed in your ontology? (videohall.com)
  • It may surprise many to know that I am a great believer in ontologies and controlled vocabularies. (cameronneylon.net)
  • Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. (oregonstate.edu)
  • As a result, translating a statement or transferring an annotation from one ontology to another may not always yield the correct results. (biomedcentral.com)
  • As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (philpapers.org)
  • To support the selection of the databases suitable for a particular application, the 'Task specific information' tabs within 'Lipid Oriented Databases' section provide an overview of the database functionalities, including the number of included lipid structures, structural ontology, covered lipid (sub)classes, levels of curation and annotation. (analisedeseo.com)
  • I also provide, and in reference to the normative goals described above, several arguments for preferring a social ontology of natural kinds with historical essences. (degruyter.com)
  • Research: I am interested in the philosophy of action, broadly conceived, as well as the philosophy of psychology/cognitive science and social ontology. (lu.se)
  • The example I used in the talk was the Sequence Ontology terms relating to categories of DNA. (cameronneylon.net)
  • 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)
  • OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies. (philpapers.org)
  • The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. (philpapers.org)
  • The research projects must include multi-disciplinary teams of subject matter experts in one or more BSSR fields, as well as ontology related informatics and computational approaches. (nih.gov)
  • Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. (oregonstate.edu)
  • The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. (biomedcentral.com)
  • A major contribution of PRO as a protein biology community informatics resource is that it provides a formal ontological structure with foundation in Basic Formal Ontology http://www.ifomis.org/bfo/ to describe types of protein complexes and gives these types unique, permanent identifiers http://www.obofoundry.org/id-policy.shtml . (biomedcentral.com)
  • 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)
  • We call the former group canonical ontologies and the latter phenotype ontologies . (biomedcentral.com)
  • Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science. (bioontology.org)
  • In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. (bioontology.org)
  • In regards to semantic data mining and semantic pre-processing, ontologies are a way to conceptualize and formally define semantic knowledge and data. (wikipedia.org)
  • citation needed] In general, the use of ontologies bridges the gaps between data, applications, algorithms, and results that occur from semantic mismatches. (wikipedia.org)
  • As a result, semantic data mining combined with ontology has many applications where semantic ambiguity can impact the usefulness and efficiency of data systems. (wikipedia.org)
  • Data will be consecutively integrated in physiological maps, quantitative adverse outcome pathway networks and ontology frameworks. (fhi.no)
  • Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. (biomedcentral.com)
  • The precise capture of biological data and knowledge and their correct and consistent representation in computational form is a basic pre-requisite for achieving these goals. (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)
  • First, I will showcase an end-to-end deep learning framework that fuses neuroimaging, genetic, and phenotypic data, while maintaining interpretability of the extracted biomarkers. (stanford.edu)
  • Given the diversity of microorganisms (bacteria, viruses, parasites) and the complex of biological phenomena that we seek to understand, data-driven research in microbiology requires researchers to collaborate and to share data. (sfu.ca)
  • Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. (philpapers.org)
  • Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. (philpapers.org)
  • Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. (philpapers.org)
  • This standard (ISA-TAB-Nano) specifies the format for representing and sharing information about nanomaterials, small molecules and biological specimens along with their assay characterization data (including metadata, and summary data) using spreadsheet or TAB-delimited files. (nih.gov)
  • Furthermore, there has been very limited success in using non-standardized data to represent or derive structure-activity-relationships (SARs) that are critical for understanding the effects of nanomaterial structure on biological activity in nanomedicine. (nih.gov)
  • An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (umsystem.edu)
  • In order to represent linked biological entities, we tend to utilise a schema or a structure that is a result of how the data is being modelled. (elucidata.io)
  • There are several examples where, the relationships between biological entities can change depending on the how the data is being modelled. (elucidata.io)
  • In this research, we are developing ontologies to facilitate disparate data integration, dissemination and comparison for Hg monitoring in freshwater ecosystems. (videohall.com)
  • The developed ontologies will allow Hg data to be placed in the context of the Hg biogeochemical cycle and linked to contextual characteristics of the observation settings. (videohall.com)
  • The OWL Web Ontology Language provides a standard way to define Web-based ontologies so data can be described as what it is -- an enzyme in a biological application or a hotel in a travel industry application -- instead of as a document in a tree structure or other database abstraction. (preferisco.com)
  • and (3) approaches to ally, understanding ADME leads to a more complete use of integrating PBPK model outputs with other HHRA tools, including biological and toxicological data to support route-to-route and benchmark dose modeling. (cdc.gov)
  • Logical and semantic access to related protein forms is critical for advancing bioinformatics approaches to representing, modeling, and reasoning about complex biological systems at the genomic and cellular level [ 1 ]. (biomedcentral.com)
  • The system interlinks three ontologies, comprising anatomical, developmental and taxonomical information, and includes instances of structures for different species. (degruyter.com)
  • This type of diversity in materials raises questions about the meaning of obsolescence and potential values of material engagement with biological processes and trajectories. (iiconservation.org)
  • Biomedical ontologies provide an organizational framework of the concepts involved in biological entities and processes in a system of hierarchical and associative relations that allows reasoning about biomedical knowledge. (nih.gov)
  • These processes reflect intimate interactions between physical, chemical, and biological states on multiple scales. (copernicus.org)
  • This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. (umsystem.edu)
  • We apply the formalism to ontologies of mouse anatomy and mammalian phenotypes in order to demonstrate the approach. (biomedcentral.com)
  • Tools or resources must also account for socio-behavioral cultural context in vocabulary/ontology development. (nih.gov)
  • Ontology (information science) In computer science and information science, an ontology formally represents knowledge as a hierarchy of concepts within a domain, using a shared vocabulary to denote the types, properties and interrelationships of those concepts. (pearltrees.com)
  • Very often the fit isn’t very good, and more seriously, it is rarely clear why or how to go about adapting or choosing the right ontology or vocabulary. (cameronneylon.net)
  • 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)
  • 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)
  • Semantics in Support of Biodiversity: An Introduction to the Biological Collections Ontology and Related Ontologies. (philpapers.org)
  • Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification. (bioontology.org)
  • Artworks that utilise tissue engineering and biotechnical tools endure a lack of historical classification of partially living systems that acknowledge the growth part of a material's trajectory, confirming that current archival ontologies simply do not recognise the environmental phenomenon of biodegradable artworks. (iiconservation.org)
  • Most of the "medicine" examined in "philosophy of biomedicine" is medicine pursued within a biomedicine framework, so there is much overlap. (stanford.edu)
  • We will outline use of the ontology for immune assay integration and statistical enrichment analysis. (bioontology.org)
  • This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. (philpapers.org)
  • The explicit representation of protein complexes in PRO--defining each member of the complex at the level of its isoform, variant, or modified form--provides the ability to represent complex biological knowledge as it is emerging in the experimental research community in structures that are both human readable and accessible to algorithmic approaches. (biomedcentral.com)
  • References to protein records in UniProtKB are made through entries in the ProForm sub-ontology within PRO (Figure 1 ). (biomedcentral.com)
  • The ontology is populated with the entities and relationships from protein-to-protein interactions. (sunderland.ac.uk)
  • We integrate the ontology within the probabilistic framework of Bayesian networks which enables reasoning and prediction of protein function. (sunderland.ac.uk)
  • Currently, there is no support for a correct and consistent integration of such ontologies. (biomedcentral.com)
  • The relationships depicted between the entities are consistent with the universally accepted ontologies linked to each of the entities (Details in next section). (elucidata.io)
  • A Hg Research Ontology will provide a way to explicitly capture knowledge about the specific domain, and support consistent and unambiguous representations of entities and relationships within the field. (videohall.com)
  • Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. (philpapers.org)
  • The framework is constructed for comparative analyses in the field of evolutionary development. (degruyter.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)
  • We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver. (bioontology.org)
  • This publication is the first on conserving bio-based materials making it significant in appropriating ethical and archival protocols for biological artworks (Biological artworks are objects that are made with materials that have non-static properties and qualities, introducing different types of material-object interaction within a museum and educational context). (iiconservation.org)
  • Databases that curate individual lipid structures, both from historical and new publications into organized repositories are essential for researchers who aim to identify the specific molecules present in their biological samples. (analisedeseo.com)
  • The framework of mad studies is used to investigate how both the works and personas of Plath and Swift have been received and interpreted through the lens of modernist, sanist social structures. (lu.se)
  • Biomedicine is the umbrella theoretical framework for most health science and health technology work done in academic and government settings. (stanford.edu)
  • An e-learning theoretical framework. (cedtech.net)
  • I begin with representation, and outline a model of representation as a fundamental solution to the biological problem of action selection. (lehigh.edu)
  • Integration of gene expression and methylation to unravel biological networks in glioblastoma patients: Gadaleta et al. (researchgate.net)
  • The architecture uses an ontology-driven approach to promote the integration of a network of sentinel hospitals or laboratories. (jmir.org)
  • We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. (philpapers.org)
  • This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. (philpapers.org)
  • Biomedicine, in other words, is the name for how most powerful global institutions envision the relations between biological sciences and medicine. (stanford.edu)
  • This Notice of Funding Opportunity (NOFO) invites applications to support research projects focused on the expansion of existing or development of new ontologies for behavioral or social science research (BSSR). (nih.gov)
  • Harren's paper highlights the issues of "managing material indeterminacy" in the Fluxus art movement, which calls for theoretical frameworks to support artworks beyond traditional points of reference within museum collections. (iiconservation.org)
  • Thesauri are often limited to tasks such as information retrieval, whereas ontologies support reasoning. (nih.gov)
  • The idea was also to propose a framework where the SWEGENE platform users would get computerised support for their research projects. (lu.se)
  • But, not all relationships that exist between multiple biological entities are well-defined or "universally" accepted. (elucidata.io)
  • In order to model the "universal" relationships, we utilise relationships between entities using existing ontologies ( O ) . (elucidata.io)
  • Below is an example of a linked view of 7 molecular entities linked into a consolidated ontology. (elucidata.io)
  • Figure 1: Neo4j Graph Schema for 7 biological entities. (elucidata.io)
  • Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. (bioontology.org)
  • Interestingly, the most recent systems tend to be ontologies, developed either from the top down (e.g. (nih.gov)
  • Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field. (bioontology.org)
  • PAR-23-181 ) and the other funded projects in a Behavioral and Social Science Ontology Development U01 Research Network. (nih.gov)
  • The ontology will be constructed and tested using my current database, followed by a series of research community workshops to further test and refine the ontology. (videohall.com)
  • She is now a professor at Soka University, where she currently teaches and continues to do research to develop useful glycoinformatics tools for the community and to apply them to the understanding of glycan function in biological system. (gr.jp)
  • We can automatically generate a biological ontology by text mining the type II diabetes research literature. (sunderland.ac.uk)
  • Where I differ with many is that assumption that because an ontology exists it provides the best means of recording my research. (cameronneylon.net)
  • Thus, our framework stratified relevant functional loci and helped identify TPM1 manipulation as a novel strategy to enhance in vitro hematopoiesis. (biomedcentral.com)
  • To focus our studies on credible functional follow-up candidates, we utilized a penalized logistic regression framework, i.e., the least absolute shrinkage and selection operator (LASSO) [ 23 , 24 ]. (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)
  • By putting semantic web into practice, a new framework is being presented for knowledge engineering, querying and information sharing. (org.pk)
  • In present paper, we presented an ontology based effort for the development of a knowledge that would allow for semantically querying bacteria knowledge base. (org.pk)
  • 2009). On the other hand, emergence of Jung's conception of a complex according to Brooke (2009) the emergence of a psyche that cannot be explained only in physi- poetic thought in Jung would never have been ological, biological, neurological and/or ana- systematically exposed in a clear theoretical/ tomical terms. (bvsalud.org)
  • We had, in fact, built our own, small scale laboratory ontology that maps onto what we actually do in our laboratory. (cameronneylon.net)
  • An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. (bioontology.org)
  • In-depth biological analysis of connected genes in ANDnet and XORnet revealed genes that are related to energy metabolism, cell cycle control (AATF), immune system response, and several cancer types. (researchgate.net)
  • However, the ICC analyses performed in some of those studies suffer from several limitations, as they rely on tools designed to detect interactions rather than to investigate how the interactions change between two biological conditions (for example, young/old and healthy/sick). (nature.com)
  • The Centre for Infectious Disease Genomics and One Health at SFU is an interdisciplinary group of researchers interested in solving practical health problems using multidisciplinary approaches and in a One Health framework. (sfu.ca)
  • We are interested in solving practical health problems using multidisciplinary approaches and in a One Health framework. (sfu.ca)
  • We present a novel approach to modelling biological information using ontologies. (degruyter.com)
  • While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. (philpapers.org)