... community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions". BMC ... by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in ... Gene Ontology is being used by researchers to establish a disease-gene relationship, as GO helps in the identification of novel ... Gene Ontology analysis is of great importance in functional annotation, and specifically in bioremediation it can be applied to ...
He contributes to the development of a number of biological and biomedical ontologies, including the Protein Ontology, the ... Basic Formal Ontology, which serves as the top-level hub of the IOF, has been applied in the development of ontologies in many ... From the beginning of his career Smith has worked in the field of ontology, initially on the history of ontology as a sub- ... Building Ontologies with Basic Formal Ontology, with Robert Arp and Andrew Spear, Cambridge, MA: MIT Press, 2015. Chinese ...
For example, the gene ontology (GO) curates terms for biological processes, which are used to describe what we know about ... via ontologies). The role of a biocurator encompasses quality control of primary biological research data intended for ... controlled vocabularies that encompass many biological and medical knowledge domains, such as the Open Biomedical Ontologies. ... So, besides annotating biological sequences, biocurators also annotate texts, linking words to unique identifiers. This aids in ...
The primary focus of his work was to develop his own ontology of personhood derived from an extensive investigation of Greek ... He continues that man initially exists as a biological hypostasis, constrained as to the types of relationships one can have ( ... This rebirth 'from above' gives new ontological freedom as it is not constrained by the limits of biological existence. Such ... However, an essential component of the ontology of personhood is the freedom to self-affirm the participation in relationship. ...
"Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions ... Some approaches go further and try to apply contextualized relations, an approach also used by the Gene Ontology for their ... Terms are often reconciled to ontologies or other sources of unique identifiers, such as the Unified Medical Language System ( ... LBD systems often employ structured knowledge from biocurated biological resources, like the Online Mendelian Inheritance in ...
... allows users to visualize and analyze their data in the context of pathway collections and the Gene Ontology. Free and ... connecting gene-level datasets to biological processes and disease. First created in 2000, GenMAPP is developed by an open- ... a new tool for viewing and analyzing microarray data on biological pathways". Nature Genetics. 31 (1): 19-20. doi:10.1038/ ... open-source software portal Biology portal WikiPathways Cytoscape Ensembl KEGG Netpath Reactome Gene Ontology Dahlquist KD; ...
The database covers all types of drug classes and resistance mechanisms and structures its data based on an ontology. The CARD ... The Comprehensive Antibiotic Resistance Database (CARD) is a biological database that collects and organizes reference ... CARD's Model Ontology includes reference nucleotide and protein sequences, as well as additional search parameters including ... Each resistance determinant described by the CARD Antibiotic Resistance Ontology (ARO) must include a connection to each of ...
A simple example of concepts modeled in a frame language is the Friend of A Friend (FOAF) ontology defined as part of the ... facts about particular objects and event types and arrange the types into a large taxonomic hierarchy analogous to a biological ... With a Semantic Web it would be possible to specify the concept "Web Ontology Language" and the user would not need to worry ... An example is the Web Ontology Language (OWL) standard for describing information on the Internet. OWL is a standard to provide ...
Kloepper, J. W (1993). "Plant growth-promoting rhizobacteria as biological control agents". In Metting, F. B. Jr (ed.). Soil ... described by the Gene Ontology". BMC Microbiology. 9(Suppl 1) (Suppl 1): S6. doi:10.1186/1471-2180-9-S1-S6. PMC 2654666. PMID ... Journal of Biological Chemistry. 286 (10): 7737-7743. doi:10.1074/jbc.C110.209288. PMC 3048661. PMID 21257745. Maron, PA; ... has previously been associated with IBD and further it has been observed to be increased in non-responders to a biological drug ...
Gene product, gene expression, and phenotype data are annotated with terms from biomedical ontologies. ZFIN is based at the ... The Zebrafish Information Network (ZFIN) is an online biological database of information about the zebrafish (Danio rerio). The ... ZFIN's relational database interface provides query forms and display pages for the following biological data types: Genes, ... as well as biological resources such as laboratory protocols, a gene nomenclature guide, and anatomy information a relational ...
Stevens current research interests are the construction of biological ontologies, such as the Gene Ontology, and the ... Egaña Aranguren, Mikel (2009). Role and application of ontology design patterns in bio-ontologies (PhD thesis). University of ... Jupp, S.; Stevens, R.; Hoehndorf, R. (2012). "Logical Gene Ontology Annotations (GOAL): Exploring gene ontology annotations ... Wroe, C. J.; Stevens, R.; Goble, C. A.; Ashburner, M. (2003). "A methodology to migrate the gene ontology to a description ...
He has also conducted research on the physics of liquid foams, high-Reynolds number turbulence, on biological ontologies and in ... He has served as Chair of the Division of Biological Physics of the American Physical Society. In 2020, he co-founded the IMAG/ ... He has also been influential in promoting the use of computational modeling and simulation in the study of complex biological ... Glazier has played a significant role in the development and application of CompuCell3D for various biological systems. More ...
EC tree browser Taxonomy tree browser Ontologies for different biological domains (e.g., BRENDA tissue ontology, Gene Ontology ... M. Gremse, A. Chang, I. Schomburg, A. Grote, M. Scheer, C. Ebeling, D. Schomburg: The BRENDA Tissue Ontology (BTO): the first ... An in-house development of the BRENDA team is the BRENDA tissue ontology (BTO), a comprehensive, structured encyclopedia with ... In 2018 BRENDA was appointed to ELIXIR Core Data Resource with fundamental importance to biological and biomedical research and ...
The Infectious Disease Ontology is one of the ontologies in the Open Biological and Biomedical Ontologies Foundry, also known ... physical ontology), domain ontology, and upper ontology (also known as top-level or formal) ontology, and has attempted to ... Arp, R. (2010). Philosophical ontology, domain ontology, and formal ontology, in Key terms in logic (J. Williamson & F. Russo, ... Arp's book with Smith and Andrew Spear published in 2015 through MIT Press, Building Ontologies with Basic Formal Ontology, has ...
... and biological processes in which the putative proteins are involved. Blast2GO (B2G) enables Gene Ontology based data mining to ... of these organisms can thus reveal novel proteins and their isoforms that are implicated in such unique biological phenomena. A ...
... that the ontology of life constitutes an example of what Charles Taylor calls "implicit moral ontology", i.e. a set of ... Rather, he wants to engage with a less specifically biological, more metaphysical, articulation of Life and Modernity." Tarizzo ... Tarizzo's profile at International Summer School in Ontology. Davide Tarizzo, lecture: La vita come categoria biopolitica, ... decrypts the semantics of modern 'life' and widen the frame, which Foucault partially sketched, of the ontology of life. The ...
ER is practiced when certain biological terms are recognized (e.g. proteins or genes) for further processing. Applying text ... Doms A, Schroeder M (July 2005). "GoPubMed: exploring PubMed with the Gene Ontology". Nucleic Acids Research. 33 (Web Server ... Automatic extraction of protein interactions and associations of proteins to functional concepts (e.g. gene ontology terms) has ... McCray AT (2003). "An upper-level ontology for the biomedical domain". Comparative and Functional Genomics. 4 (1): 80-4. doi: ...
As a theoretical background of the modern Philosophical anthropology he researches the Critical ontology of the German ... explicating its significance for biological, sociological and philosophical debates in the 21st century. ...
May 2000). "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics. 25 (1): 25-9. ... Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological ... Gene Ontology Consortium (January 2015). "Gene Ontology Consortium: going forward". Nucleic Acids Research. 43 (Database issue ... Services provided to biological research communities include: Genome sequence annotations Location of genes and regulatory ...
Similarly, the gene ontology classifies both genes and proteins by their biological and biochemical function, but also by their ... Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and ... Proteins were recognized as a distinct class of biological molecules in the eighteenth century by Antoine Fourcroy and others, ... Protein is generally used to refer to the complete biological molecule in a stable conformation, whereas peptide is generally ...
Lopez argues it is best to see Buddhism as radically incompatible with science, as seeking to transcend all biological life, to ... Unno sees the ontology of David Bohm as being similar to the Mahayana Buddhist philosophy of the twofold truth (of form and ... In The Universe in a Single Atom (2005), the 14th Dalai Lama similarly points outs that while biological theories generally ... He attempts to harmonize biological theories of evolution with Buddhist views of the transformation of the mind. William S. ...
An SDA comprises a series of sentences each of which contains a relationship between two biological entities, mentioning the ... e.g. UniProtKB for proteins and the European Bioinformatics Institute ontology look up service for other entities. Calling ... A Structured Digital Abstract (SDA) is a method of describing relationships between biological entities in a structured, but ... to contain identifiers from other databases storing protein interactions or different types of relationships between biological ...
A Biositemap is a way for a biomedical research institution of organisation to show how biological information is distributed ... Official website Biomedical Resource Ontology Biositemaps online editor (Webarchive template wayback links, Domain-specific ... and Biomedical Resource Ontology (BRO). The IM is responsible for defining the data held in the metafields and the BRO controls ... Name Description URL Stage of development Organization Resource Ontology Label Keywords License Up-to-date documentation on the ...
Steckel, Richard H (1 February 2008). "Biological Measures of the Standard of Living". Journal of Economic Perspectives. 22 (1 ... Ansari, Iman (3 May 2016). "Nature Versus Denture: An Ontology of Dental Prostheses". Architectural Theory Review. 21 (2): 114- ...
SABIO-RK as part of MIRIAM Registry SABIO-RK homepage (Systems biology, Biochemistry, Molecular biology, Proteins, Biological ... Data are adapted, normalized and annotated to controlled vocabularies, ontologies and external data sources including KEGG, ... biological sources (organism, tissue, cellular location), environmental conditions (pH, temperature, buffer) and reference ...
This augmented ontology increases the explanatory power of this conception. Descriptive aspect Most descriptions of mechanisms ... For example, natural selection is a mechanism of biological evolution; other mechanisms of evolution include genetic drift, ... For example, one influential characterization of neuro- and molecular biological mechanisms by Peter K. Machamer, Lindley ... There are three distinguishable aspects of this characterization: Ontic aspect The ontic constituency of biological mechanisms ...
One of the uses of this ontology is to integrate data from different biological databases, and other species-specific ... The Uber-anatomy ontology (Uberon) is a comparative anatomy ontology representing a variety of structures found in animals, ... Biological databases, Comparative anatomy, Anatomical terminology, Ontology (information science), All stub articles, ... an integrative multi-species anatomy ontology". Genome Biol. England. 13 (1): R5. doi:10.1186/gb-2012-13-1-r5. PMC 3334586. ...
... biological ontology) or practical (ethics) perspective. They follow three main directions: Diagnostic reasoning, inductive ... Fagot-Largeault was a professor at the Collège de France, holding the Chair of Philosophy of Biological and Medical Sciences ... biological epistemology, bio-medical anthropology. Her research on the logic of medical reasoning and the nature of causal ... chair of philosophy of biological and medical sciences), psychiatrist at the Assistance publique - Hôpitaux de Paris, and a ...
Gene ontology analysis of both Hsp90A and Hsp90B interactomes indicate that each paralogs is associated with unique biological ... Jameel A, Skilton RA, Campbell TA, Chander SK, Coombes RC, Luqmani YA (Feb 1992). "Clinical and biological significance of ... Assembly of the reovirus cell attachment protein". The Journal of Biological Chemistry. 276 (35): 32822-7. doi:10.1074/jbc. ... The Journal of Biological Chemistry. 276 (18): 14649-57. doi:10.1074/jbc.M100200200. PMID 11297531. Peng Y, Chen L, Li C, Lu W ...
McWherter, The Problem of Critical Ontology (Palgrave, 2013), p 38: "Since Hume reduces objects of experience to ... Biological Sciences, 2005 Jun 29;360(1458):1259-69. Mattessich, Richard, ch 5 "The controversy around inductive logic", ... The Problem of Critical Ontology: Bhaskar Contra Kant (New York: Palgrave Macmillan, 2013). Lindberg, David C & Robert S ...