• Ontologies are typically represented using semantic web languages such as RDF (Resource Description Framework) or OWL (Web Ontology Language). (leger.ca)
  • He was among the first researchers to utilize description logic -based ontologies for schema and information integration (a decade before W3C adopted a DL-based ontology representation standard), and he was the first to deliver a keynote about Semantic Web applications in search. (wikipedia.org)
  • Within the framework of Semantic Web, in this work we implement a XML / OWL ontology for mammals of Virunga National Park in DRC. (likrdc.net)
  • The Semantic Web provides a common framework that allows data to be shared and reused across application, enterprise, and community boundaries. (findatwiki.com)
  • 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 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)
  • By leveraging ontologies, generative AI models can generate content that aligns with the underlying structure and semantics defined by the ontology. (leger.ca)
  • With the help of ontologies, automated content creation systems can generate high-quality content that aligns with the underlying semantics and structure defined by the ontology. (leger.ca)
  • In simple terms, an ontology is a formal representation of knowledge that captures the relationships between concepts within a specific domain. (leger.ca)
  • Since ontologies provide a shared vocabulary and standardized representation, they enable seamless integration of data from various sources. (leger.ca)
  • In summary, ontologies form the foundation for automated content creation by providing a structured representation of knowledge within a specific domain. (leger.ca)
  • 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)
  • The Web Ontology Language ( OWL ) is a family of knowledge representation languages for authoring ontologies . (findatwiki.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)
  • 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)
  • recently, he has pioneered ontology-driven approaches to metadata extraction and semantic analytics. (wikipedia.org)
  • 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)
  • We will introduce users to the Open Biological and Biomedical Ontologies (OBO) foundry community and their founding principles, as well as explore practical examples and applications using the Genomic Epidemiology Ontology (GenEpiO) and the Food Ontology (FoodOn). (osf.io)
  • That being said, this course is not limited to individuals who work within genomic and epidemiological frameworks - our aim is to support users in solving practical data-quality problems using open access ontologies across disciplines. (osf.io)
  • Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. (biomedcentral.com)
  • Audience:** Researchers, Data Curators **Original Course Dates:** July 26th-28th, 2022 **Total Length:** 3 hours (1 hr/session) + optional exercises --- **Level:** Beginner **Requirements:** This course is for beginners with no prior experience in ontologies, but basic computer skills are expected. (osf.io)
  • One key advantage of using ontologies is their ability to facilitate interoperability between different systems and applications. (leger.ca)
  • The best approach for enhancing interoperability of the BMRB would be to convert the archive into standard web formats, XML and RDF, using a data structure that corresponds closely to the NMR-STAR ontology described by an XML schema and OWL. (biomedcentral.com)
  • Ontologies are a formal way to describe taxonomies and classification networks, essentially defining the structure of knowledge for various domains: the nouns representing classes of objects and the verbs representing relations between the objects. (findatwiki.com)
  • They are built upon the World Wide Web Consortium 's (W3C) standard for objects called the Resource Description Framework (RDF). (findatwiki.com)
  • Along with the RDF, we also provide its ontology written in RDF/RDFS/OWL syntax as BMRB/OWL [ 10 , 11 ], which is a direct translation of the BMRB/XML schema. (biomedcentral.com)
  • Additionally, the annotated biological data must be maintained and new annotations created. (biomedcentral.com)
  • The rise of Systems Biology, seeking to comprehend biological processes as a whole, highlighted the need to not only develop corresponding quantitative models, but also to create standards allowing their exchange and integration. (wikipedia.org)
  • Functional annotation of gene models suggested that many overlapping biological processes are associated with cancer outcomes in RT treated and non-RT treated patients, including proliferation and immune responses. (bvsalud.org)
  • Biological processes influencing outcome overlapped for patients treated with or without radiation suggest that existing signatures may lack specificity. (bvsalud.org)
  • This reasoning capability enhances the quality and coherence of generated content by ensuring logical consistency across different pieces of information. (leger.ca)
  • Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. (biomedcentral.com)
  • These ontologies are increasingly being applied to annotate and classify biological data. (biomedcentral.com)
  • Welcome** ### Introduction to Data Curation using Ontologies - FAIR Datasets and Community Collaboration The ways in which people encode meaning into text are complex. (osf.io)
  • Ontologies are data structures that are composed of controlled vocabularies, and the relations between them, that represent a piece of knowledge in a subject area. (osf.io)
  • This is a course not on how to develop an ontology, nor on the underlying data models, but rather on how a data curator can engage in ontology practices to support their FAIR data objectives. (osf.io)
  • Over three sessions we will cover what ontologies are, how to access and explore ontologies, finding and evaluating appropriate ontology terms, annotating spreadsheet data, and how to make new term requests. (osf.io)
  • Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. (biomedcentral.com)
  • As knowledge and understanding of living systems expands, biological network databases are becoming increasingly sophisticated, in terms of data complexity and overall functionality. (biomedcentral.com)
  • Pharmaceutical research has a wealth of available data sources to help elucidate the complex biological mechanisms that lead to the development of diseases. (biomedcentral.com)
  • In a novel, automated machine learning framework, we use sequence as well as diverse functional annotations to train models on multiple organisms using experimentally validated data. (frontiersin.org)
  • The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. (biomedcentral.com)
  • However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. (biomedcentral.com)
  • The NMR-STAR Dictionary, acting as ontology for NMR-STAR data, continues to be improved and expanded to keep up with the needs of the biomolecular NMR community. (biomedcentral.com)
  • This growing biological data archive has raised researchers' interest in integrating the diverse biological information resources to form new hypotheses for understanding biological functions and phenomena. (biomedcentral.com)
  • To automate the XML conversion of BMRB entries, we have developed a software suite (the BMRBxTool) that generates XML documents and validates their format and data consistency according to the BMRB/XML schema. (biomedcentral.com)
  • Similarly, ontologies are typically far more flexible as they are meant to represent information on the Internet coming from all sorts of heterogeneous data sources. (findatwiki.com)
  • One important task in biomedical text mining is relation extraction, which aims to identify designated relations among biological entities reported in literature. (springer.com)
  • Here, we report a novel framework to facilitate the development of a pattern-based biomedical relation extraction system. (springer.com)
  • In his work, semantic metadata extracted from biological text is made up of complex knowledge structures (complex entities and relationships) that reflect complex interactions in biomedical knowledge. (wikipedia.org)
  • Developing and maintaining these ontologies requires manual creation, deletion and correction of concepts and their definitions within the ontology. (biomedcentral.com)
  • Chapter 3 describes the development of the Genome Biology Ontology Language and the GBOL stack of supporting tools enforcing consistency within and between the GBOL definitions in the ontology (OWL) and the Shape Expressions (ShEx) language describing the graph structure. (wur.nl)
  • In this paper, we present a novel framework for fast development of relation extraction systems. (springer.com)
  • We present a novel framework to systematically quantify the suitability of yeast as a model organism for different human tissues. (biomedcentral.com)
  • The Web Ontology Language ( OWL , [ 4 ]) makes it possible to do complex logical reasoning and consistency checking of RDF/OWL resources. (biomedcentral.com)
  • A diversity score for a given drug was calculated by measuring how "diverse" a drug is calculated using various biological entities (regardless of the cardinality of actual instances in each category). (jmir.org)
  • His work on using ontologies for information processing encompassed the approach for searching for an ontology-automated [14] reasoning for schema integration, semantic search, other applications, and semantic query processing. (wikipedia.org)
  • The development of the ontology was announced more officially in a message from Le Novère to Michael Hucka and Andrew Finney on October 19. (wikipedia.org)
  • NICEATM and NC3Rs are partnering with the National Institute of Allergy and Infectious Diseases, the U.S. Army Combat Capabilities Development Command Chemical Biological Center, and NCATS to direct the MPS for COVID Research (MPSCoRe) working group. (nih.gov)
  • Such development pattern shares an overlapping biological behavior with the growth plate, which is a process of mesenchymal stem cells differentiating into chondrogenic cells and then sequentially into fibrocartilage cells ( Killian, 2022 ). (elifesciences.org)
  • Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. (biomedcentral.com)
  • The information represented in the wiki should adhere to particular quality criteria, such as internal consistency (the wiki content does not contain contradictory information) and consistency with biological background knowledge (the wiki content should be factually accurate). (biomedcentral.com)
  • We have developed the BOWiki, a wiki system that uses a core ontology together with an automated reasoner to maintain a consistent knowledge base. (biomedcentral.com)
  • To address these questions, I developed a semantic systems biology framework capable of extracting knowledge, biological concepts and emergent system properties, from a vast array of publicly available genome information. (wur.nl)
  • Ontologies play a crucial role in automated content creation by providing a structured framework for organizing and representing knowledge. (leger.ca)
  • By capturing explicit relationships through properties like 'is-a' or 'part-of,' ontologies allow machines to infer new knowledge based on existing information. (leger.ca)
  • Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. (biomedcentral.com)
  • A relation extraction system derived using the proposed framework achieved overall F-scores of 72.66% for the Simple events and 55.57% for the Binding events on the BioNLP-ST 2011 GE test set, comparing favorably with the top performing systems that participated in the BioNLP-ST 2011 GE task. (springer.com)
  • 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)
  • References to protein records in UniProtKB are made through entries in the ProForm sub-ontology within PRO (Figure 1 ). (biomedcentral.com)
  • Proteomics is a new science direction that explores biological activity related to protein expression [ 28 ]. (hindawi.com)
  • A practical implementation of a semantic systems biology framework for FAIR ( de novo ) genome annotation is provided in chapter 4. (wur.nl)
  • The semantic framework and genome annotation tool described in this chapter has been used throughout this thesis to consistently, structurally and functionally annotate and mine microbial genomes used in chapter 5-10. (wur.nl)
  • This paper argues that some of the strong beliefs held by humans have deep biological roots in our evolutionary past, and the neuronal pathways and structures that support them can be found in other species. (bvsalud.org)
  • Simulation tools can check the consistency of a rate law, convert reaction from one modelling framework to another (e.g., continuous to discrete), or distinguish between identical mathematical expressions based on different assumptions (e.g. (wikipedia.org)
  • Several free and/or open-source tools will be introduced throughout the course, including but not limited to: Ontobee, EMBL-EBI Ontology Lookup Service, Protégé, and OntoMaton. (osf.io)
  • 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)
  • Furthermore, ontologies enable automated content creation systems to reason about the relationships between different concepts. (leger.ca)
  • The latter involved query transformations using different ontologies for user queries and resources and federated queries-a concept with associated measures and techniques for computing information loss when traversing taxonomic relationships. (wikipedia.org)
  • It abstracts, captures and retains operations away from a biological network repository and website. (biomedcentral.com)
  • The purpose of ontologies in automated content creation is to provide machines with a common understanding of the concepts and their relationships within a particular domain. (leger.ca)
  • This system allows a continuous update of the ontology with immediate availability and suppress merging problems. (wikipedia.org)
  • We have developed the BOWiki, a web-based system that includes a biological core ontology. (biomedcentral.com)
  • We demonstrate how our framework is used to develop a system which achieves state-of-the-art performance on a public benchmark corpus. (springer.com)
  • We also suggest that the study of religious belief has discouraged the adoption of an overarching framework for understanding our belief system in all its breadth. (bvsalud.org)
  • Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. (kb.se)
  • This infrastructure was used in chapters 3 and 4 to develop the framework. (wur.nl)
  • The ten essays in this collection approach the philosophy of Thomas Aquinas not merely as an object of scholarly interest but also as a framework for addressing perennial philosophical questions, even as they are raised and debated in our own times. (edu.au)
  • This course covers how we can use ontologies to improve the consistency and communication of ideas. (osf.io)
  • In Computer and Information Science, ontology is a structured set of concepts that allow providing meaning to various pieces of information. (likrdc.net)
  • Arguments that could have direct bearing on questions in medical ethics are examined in William A. Wallace's essay, in which he appeals to principles of Thomistic natural philosophy to argue that personal death may well precede the biological death of the human body. (edu.au)
  • We further study each of these subspaces in detail, and shed light on their unique biological roles in the human tissues. (biomedcentral.com)
  • The framework requires only a list of triggers as input, and does not need information from an annotated corpus. (springer.com)