Ontology framework biological ontologies. Medical search. Frequent questions

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)

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 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)
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)

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)
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)
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)
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)

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)
Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. (philpapers.org)

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

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 isnâ€™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)
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)
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)

U. Consortium, The Gene Ontology (GO) Project in 2006. (org.pk)

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

We will outline use of the ontology for immune assay integration and statistical enrichment analysis. (bioontology.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)

This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. (philpapers.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)

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)
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)
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)
Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. (philpapers.org)
Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. (philpapers.org)
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)
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)
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)
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)

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)

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)

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)

Integration of gene expression and methylation to unravel biological networks in glioblastoma patients: Gadaleta et al. (researchgate.net)
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 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)

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)
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 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)

By putting semantic web into practice, a new framework is being presented for knowledge engineering, querying and information sharing. (org.pk)

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)
The ontology is populated with the entities and relationships from protein-to-protein interactions. (sunderland.ac.uk)

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)

We can automatically generate a biological ontology by text mining the type II diabetes research literature. (sunderland.ac.uk)

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)

We had, in fact, built our own, small scale laboratory ontology that maps onto what we actually do in our laboratory. (cameronneylon.net)

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)
Thesauri are often limited to tasks such as information retrieval, whereas ontologies support reasoning. (nih.gov)

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)

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)
Where I differ with many is that assumption that because an ontology exists it provides the best means of recording my research. (cameronneylon.net)

References to protein records in UniProtKB are made through entries in the ProForm sub-ontology within PRO (Figure 1 ). (biomedcentral.com)
We integrate the ontology within the probabilistic framework of Bayesian networks which enables reasoning and prediction of protein function. (sunderland.ac.uk)

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)
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)

We present a novel approach to modelling biological information using ontologies. (degruyter.com)

Both can be shared, but ontologies lend themselves to reuse, sometimes in widely differing applications from the ones for which they were originally designed. (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)

One particular difficulty in making these ontologies interoperable results from the existence of two particular types of biomedical ontologies. (biomedcentral.com)
Key results: Ontologies can advance plant science in four keys areas: 1. (philpapers.org)
This improvement results from a direct relationship between also allows for rapid identification of needed model modifications to internal dosimetry to biological response. (cdc.gov)

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)
Although more than sixty terminological systems exist in the biomedical domain, few actually qualify as an ontology. (nih.gov)

Ontologies as Integrative Tools for Plant Science. (philpapers.org)

Diseases1

Chemicals and Drugs2

Analytical, Diagnostic and Therapeutic Techniques and Equipment15

Phenomena and Processes16

Disciplines and Occupations13

Technology, Industry, Agriculture1

Humanities2

Information Science49

Health Care8

Biomedical ontology3

Controlled vocabularies3

Sequence Ontology1

Foundry5

Annotation4

Informatics4

Phenotype2

Genomic2

Anatomical1

Mammalian1

Vocabulary3

Interoperability4

Consortium1

Ontological framework1

Semantics2

Classification1

Assay2

Metadata1

Formally1

Data16

Processes1

Consistent3

Conclusions1

Philosophy1

Gene2

Comparative1

Anatomy2

Context1

Structures2

Integration1

Principles2

Semantic Web1

Entities5

Cellular1

Tend1

Generate1

Provide1

Laboratory1

Support2

Immune2

Research4

Protein2

Knowledge2

Approach1

Applications1

Multiple1

Results3

Systems3

Tools1