Access framework biological ontologies. Medical search. Frequent questions

The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. (biomedcentral.com)
As a Semantic Web application domain, Gene Ontology Consortium provides a RDF-XML data file http://archive.geneontology.org/full/2007-08-01/go_200708-assocdb.rdf-xml.gz . (biomedcentral.com)
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)
The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. (philpapers.org)
We consider approaches for representing the role of protein complexes in the cell cycle, displaying modules of metabolism in a hierarchical format, integrating experimental interaction data with structured vocabularies such as Gene Ontology categories and representing conserved interactions among orthologous groups of genes. (nature.com)

W3C Takes Step in Uniting Area Specialists with Web Technologies to Improve Communication, Information Sharing The HCLSIG will develop use cases that demonstrate the value to business of adopting Semantic Web technology, core vocabularies and ontologies, guidelines and best practices for unique identifiers. (w3.org)
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)
Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. (philpapers.org)
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)

The growing need for integration of diverse and heterogeneous data sets from distinct communities of scientists in separate biological research fields has thus been the major driving force to migrate from traditional XML to Semantic Web [ 2 ]. (biomedcentral.com)
Semantic Web Technologies Can Provide Bridge Between Chemists, Biologists, Clinicians and other Researchers Health care and life sciences research are rapidly evolving, and a critical key to their success is the implementation of new informatics models that will bridge many forms of biological and medical information across institutions. (w3.org)
OilEd: a Reason-able Ontology Editor for the Semantic Web. (auth.gr)
Ontologies are typically represented using semantic web languages such as RDF (Resource Description Framework) or OWL (Web Ontology Language). (leger.ca)

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)
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)
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)
In this study, we report a Vaccination Informed Consent Ontology (VICO) that extends the Informed Consent Ontology and integrates related OBO foundry ontologies, such as the Vaccine Ontology, with a focus on vaccination screening questionnaire in the vaccination informed consent domain. (biomedcentral.com)
Current VICO contains 993 terms, including 248 VICO specific terms and 709 terms imported from 17 OBO Foundry ontologies. (biomedcentral.com)

The nanotechnologies (nano) tab-delimited (TAB) format is a general purpose framework that provides a standard means to communicate metadata ( i.e. , study details, material characteristics, assay measurements etc. ), data on nanomaterial physicochemical properties, as well as data from in vitro and in vivo experiments of nanomaterials. (nih.gov)
Moreover, most APIs are documented in isolation because it is not straightforward to access metadata used in existing relevant APIs. (stanford.edu)
To facilitate the creation of such metadata, and also to provide instant access to the metadata elements and values used by other API providers, we developed smartAPI editor by extending the existing Swagger editor. (stanford.edu)
This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. (philpapers.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)
By embedding semantics into medical and research information, researchers will have better access to the knowledge required to effectively find cures to diseases, make drugs safer and more affordable, and enable health-care providers to offer individualized clinical management to patients. (w3.org)
Semantics in Support of Biodiversity: An Introduction to the Biological Collections Ontology and Related Ontologies. (philpapers.org)
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)

As a result, these biological datasets exist in fragments that do not "talk" to each other, thereby reducing its value. (elucidata.io)
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)
This interoperability allows generative AI models to access diverse datasets and combine information from multiple domains, resulting in more comprehensive and accurate content generation. (leger.ca)

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)

More simply, an ontology is a way of showing the properties of a subject area and how they are related, by defining a set of terms and relational expressions that represent the entities in that subject area. (wikipedia.org)
What ontologies in both information science and philosophy have in common is the attempt to represent entities, including both objects and events, with all their interdependent properties and relations, according to a system of categories. (wikipedia.org)
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)
But, not all relationships that exist between multiple biological entities are well-defined or "universally" accepted. (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 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)
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)
Figure 1: Neo4j Graph Schema for 7 biological entities. (elucidata.io)
depending on the biological problem investigated and experimental data available, the interaction map can be translated into a detailed mechanistic model that can simulate the temporal evolution of molecular entities. (hindawi.com)
The Vaccination Informed Consent Ontology (VICO) represents entities related to vaccination informed consents with a special focus on vaccination informed consent forms, and questionnaires and questions in the forms. (biomedcentral.com)

The US National Cancer Institute defines biomedicine as synonymous with "allopathic medicine, conventional medicine, mainstream medicine, orthodox medicine, and Western medicine" (NCI Other Internet Resources , accessed 12 March 2020). (stanford.edu)
Applied Ontology , 2020, 15(3): 361-384. (meteck.org)

This problem arises in part because of systemic inequalities in dataset curation, unequal opportunity to participate in research and inequalities of access. (cdc.gov)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. (philpapers.org)

However, there are shortcomings in the Resource Description Framework (RDF) data file provided by the GO consortium: 1) Lack of sufficient semantic relationships between pairs of terms coming from the three independent GO sub-ontologies, that limit the power to provide complex semantic queries and inference services based on it. (biomedcentral.com)

Every academic discipline or field creates ontologies to limit complexity and organize data into information and knowledge. (wikipedia.org)
Improved ontologies may improve problem solving within that domain, interoperability of data systems, and discoverability of data. (wikipedia.org)
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)
We propose a RDF model, GORouter , which encodes heterogeneous original data in a uniform RDF format, creates additional ontology mappings between GO terms, and introduces a set of inference rulebases. (biomedcentral.com)
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)
Our facility includes a state-of-the-art molecular laboratory for microbial sample processing and omics data generation and access to high-performance computing clusters and cloud computing (courtesy of Compute Ca nada) to provide a "one-stop-shop" for research and collaboration. (sfu.ca)
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)
An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (umsystem.edu)
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)
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)
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)
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)
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)
As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. (biomedcentral.com)
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)
Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. (hindawi.com)
Data to UK10K samples are available from the European Genome-Phenome Archive through the UK10K Data Access Committee ( [email protected] , https://www.uk10k.org/data_access.html ) for researchers who meet the criteria for access to confidential data. (plos.org)
Fillottrani, P.R., Keet, C.M. KnowID: An architecture for efficient Knowledge-driven Information and Data access . (meteck.org)
Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. (philpapers.org)
We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (philpapers.org)
Since ontologies provide a shared vocabulary and standardized representation, they enable seamless integration of data from various sources. (leger.ca)
Ethical issues must be considered when machines and researchers have access to large amounts of data , in many cases attached to personal information. (psychologicalscience.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)

The system interlinks three ontologies, comprising anatomical, developmental and taxonomical information, and includes instances of structures for different species. (degruyter.com)

Ontology is a branch of philosophy and intersects areas such as metaphysics, epistemology, and philosophy of language, as it considers how knowledge, language, and perception relate to the nature of reality. (wikipedia.org)

Pertinent to the development of promising biomedical nanotechnologies and to the safety of nanoscale materials in general, is a thorough understanding of nanomaterial-biological interactions. (nih.gov)
However, a rational approach must be employed early on in nanotechnology evolution to direct the safe development of novel nanotechnologies and provide accurate predictions of nanomaterial-biological interactions based on weight-of-the-evidence (Dahl et al. (nih.gov)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. (philpapers.org)

Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. (philpapers.org)

The first occurrence in English of ontology as recorded by the OED (Oxford English Dictionary, online edition, 2008) came in Archeologia Philosophica Nova or New Principles of Philosophy by Gideon Harvey. (wikipedia.org)
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)
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)
The design principles can be used as a template to build programmable interfaces for other biological databases. (biomedcentral.com)
This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. (philpapers.org)

Artificial intelligence has retained considerable attention regarding applied ontology in subfields like natural language processing within machine translation and knowledge representation, but ontology editors are being used often in a range of fields, including biomedical informatics, industry. (wikipedia.org)
This entry will review the philosophical literature (and some literature in allied fields, such as history of medicine) that scrutinizes the biomedical framework itself, in whole or in part. (stanford.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)
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)
One particular difficulty in making these ontologies interoperable results from the existence of two particular types of biomedical ontologies. (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)
To create an infrastructure that connects and serves these diverse communities, there is a need to both bring together the people, and ground this work in a framework that supports semantically-rich system, process and information interoperability. (w3.org)
One key advantage of using ontologies is their ability to facilitate interoperability between different systems and applications. (leger.ca)

Keet, C.M., Grütter, R. Toward a systematic conflict resolution framework for ontologies . (meteck.org)

In simple terms, an ontology is a formal representation of knowledge that captures the relationships between concepts within a specific domain. (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)

However, a systems biological analysis of the lipidome, by incorporating pathway information remains challenging, leaving lipidomics behind compared to other omics disciplines. (mdpi.com)
WikiPathways (wikipathways.org) is an open-source biological pathway database. (bvsalud.org)

Quine and Kripke in philosophy, Sowa and Guarino in information science), and debates concerning to what extent normative ontology is possible (e.g., foundationalism and coherentism in philosophy, BFO and Cyc in artificial intelligence). (wikipedia.org)
Applied ontology is considered by some as a successor to prior work in philosophy. (wikipedia.org)
Most of the "medicine" examined in "philosophy of biomedicine" is medicine pursued within a biomedicine framework, so there is much overlap. (stanford.edu)
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)

Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. (oregonstate.edu)
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)

This creates a Catch-22 because to get access to exculpation one needs to admit to some level of abnormality. (lu.se)

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)

Tools or resources must also account for socio-behavioral cultural context in vocabulary/ontology development. (nih.gov)

AI researchers argued that they could create new ontologies as computational models that enable certain kinds of automated reasoning, which was only marginally successful. (wikipedia.org)

If model predictions are in agreement with the experiments, the model justifies the biological hypotheses behind it. (hindawi.com)
In turn, these hypotheses, which provide reasonable explanations for the biological phenomenon, lead to an enhanced understanding of the gene regulatory network. (hindawi.com)

Khan, Z.C., Keet, C.M. Structuring Abstraction to Achieve Ontology Modularisation . (meteck.org)

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)

Biomedicine is the umbrella theoretical framework for most health science and health technology work done in academic and government settings. (stanford.edu)
Biomedicine, in other words, is the name for how most powerful global institutions envision the relations between biological sciences and medicine. (stanford.edu)

Currently, there is no support for a correct and consistent integration of such ontologies. (biomedcentral.com)

For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. (mdpi.com)
Open Access articles citing this article. (nature.com)

It is a framework, a set of philosophical commitments, a global institution woven into Western culture and its power dynamics, and more. (stanford.edu)
This concern with meaning has an obvious application in connection with Husserl's theory of language, but it is no less a focus for his philosophical logic, ontology, phenomenology and what Husserl himself called 'axiology' (value theory). (nd.edu)

With a standard set of taxonomies and ontologies for equipment, measurements and analysis, there is an opportunity to streamline the way companies manage test execution, samples and results so that they can predict stability issues early. (pharmamanufacturing.com)

Their integration into a common ontological framework is an indispensible step towards the development of expressive knowledge bases. (biomedcentral.com)

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. (philpapers.org)

All articles published by MDPI are made immediately available worldwide under an open access license. (mdpi.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)

Advances in lipidomics allow identification of hundreds of lipid species from biological samples. (mdpi.com)
access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. (philpapers.org)
The Plant Ontology facilitates comparisons of plant development stages across species. (philpapers.org)

This course covers how we can use ontologies to improve the consistency and communication of ideas. (osf.io)

Such efforts often use ontology editing tools such as Protégé. (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)
Ontologies as Integrative Tools for Plant Science. (philpapers.org)
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)

In the context of generative AI, ontologies serve as a backbone that enables machines to understand and generate meaningful content. (leger.ca)

We are interested in solving practical health problems using multidisciplinary approaches and in a One Health framework. (sfu.ca)
However, experimental approaches have limitations when dealing with complex biological systems composed of multiple layers of regulation such as the transcriptional and post-transcriptional regulation by transcription factors (TFs) and miRNAs [ 2 ]. (hindawi.com)

In the 1980s, the AI community began to use the term ontology to refer to both a theory of a modeled world and a component of knowledge-based systems. (wikipedia.org)
He is attempting to develop a body of theory applicable to several levels of biological organization from cells to social systems, unifying concepts of life, information and knowledge across the paradigmatic disciplines of epistemology, biology, and the sciences of cognition, organization, information and knowledge management. (evodevouniverse.com)
Keet, C.M., Khan, Z.C. Foundational Ontologies: From Theory to Practice and Back . (meteck.org)

Key results: Ontologies can advance plant science in four keys areas: 1. (philpapers.org)

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)
PAR-23-181 ) and the other funded projects in a Behavioral and Social Science Ontology Development U01 Research Network. (nih.gov)
Source code developed for this project is available at https://github.com/bio-ontology-research-group/phenomenet-vp , and analysis results at http://www.cbrc.kaust.edu.sa/onto/pvp/ . (plos.org)
The idea was also to propose a framework where the SWEGENE platform users would get computerised support for their research projects. (lu.se)

This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. (umsystem.edu)

Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. (biomedcentral.com)
Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts. (hindawi.com)

Some philosophers have also proposed alternative frameworks for understanding the relations between biology and medicine. (stanford.edu)

Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. (degruyter.com)
Many published models of the biomimicry process include steps to identify, understand, and translate function of biological systems. (mdpi.com)
Lipids play an important role in biological systems and have the potential to serve as biomarkers in medical applications. (mdpi.com)
Furthermore, ontologies enable automated content creation systems to reason about the relationships between different concepts. (leger.ca)

The framework is constructed for comparative analyses in the field of evolutionary development. (degruyter.com)
The development of nano-TAB is being facilitated through the use of knowledge that is represented in the NanoParticle Ontology (NPO). (nih.gov)

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)

Chemicals and Drugs1

Analytical, Diagnostic and Therapeutic Techniques and Equipment7

Phenomena and Processes5

Disciplines and Occupations6

Anthropology, Education, Sociology and Social Phenomena1

Humanities1

Information Science33

Health Care3

Gene Ontology5

Vocabularies4

Semantic Web4

Foundry8

Metadata4

Semantics5

Datasets3

Phenotype2

Entities11

20202

Curation1

Genes1

Resource Descripti1

Data28

Anatomical1

Metaphysics1

Nanomaterial-biological interactions2

Genomic1

Conclusions1

Principles6

Biomedical5

Interoperability4

Systematic1

Representation2

Pathway2

Philosophy4

Pathways2

Creates1

Informatics1

Vocabulary1

Computational1

Hypotheses2

Abstraction1

Researchers1

Biomedicine2

Consistent1

Article2

Philosophical2

Taxonomies1

Ontological1

Genomics1

Open Access1

Provide1

Species3

Consistency1

Tools4

Context1

Approaches2

Theory3

Plant science1

Research4

Analysis1

Different biological2

Biology1

Systems4

Development2

Multiple1