• 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)
  • 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)
  • For example, the AntibodyRegistry combines data from 200+ vendors, the NIF Integrated BrainGeneExpression combines gene expression data from Gensat, Alan Brain, and Mouse Genome Informatics, the Connectivity view combines six databases that have statements about nervous system connectivity, the Integrated Animal view combines data about experimental animal catalogs available to researchers from transgenic or inbred worms, zebrafish, mice and rats. (wikipedia.org)
  • In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
  • 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)
  • 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)
  • 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 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)
  • This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. (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. (biomedcentral.com)
  • 10,000) and affected by historical, demographic and selective constraints, providing a framework for the partitioning of variation in gene expression within and among populations. (biomedcentral.com)
  • Tools like the TIGR Gene index [ 35 ] and Unigene [ 36 ] provide significant information on many species, yet these databases do not meet the needs of functional genomics projects for many non-model species. (biomedcentral.com)
  • To solve this problem, we have designed and implemented a tool named Key2Ann, which replaces in multiple fasta files the database keys with short terms indicating the taxonomic position or other features like the gene name or the EC-number. (degruyter.com)
  • U. Consortium, The Gene Ontology (GO) Project in 2006. (org.pk)
  • In turn, these hypotheses, which provide reasonable explanations for the biological phenomenon, lead to an enhanced understanding of the gene regulatory network. (hindawi.com)
  • aliases2entrez converts human gene symbols to curated gene entrezID from NCBI database. (osuosl.org)
  • babelgene converts between human and non-human gene orthologs/homologs from multiple databases. (osuosl.org)
  • GOxploreR provides a method to explore the gene ontology. (osuosl.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)
  • Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. (biomedcentral.com)
  • We are currently working on broad Phospho-site database in partnership with SHENZHEN University China, we almost collected 36,00,000+ non-redundant phosphor-sites of 1,50,000+ proteins from the latest published scientific literature, our database will be superior in both the number of Phospho-sites and Protein globally. (habdsk.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)
  • a map is constructed that shows interactions among molecular entities (such as genes, proteins and RNAs), using information from literature and databases. (hindawi.com)
  • The specific function of these "A-type" ISC proteins within the framework of mitochondrial and bacterial Fe/S protein biogenesis is still unresolved. (yeastgenome.org)
  • 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)
  • In particular, we investigated the use of a Semantic Web-based model to foster integration and interoperability of interinstitutional and cross-border microbiology laboratory databases. (jmir.org)
  • For an exhaustive and up to date list of Databases and Datasets registered to NIF please check this page www.neurolex.org. (wikipedia.org)
  • As a result, these biological datasets exist in fragments that do not "talk" to each other, thereby reducing its value. (elucidata.io)
  • Brain Analysis Library of Spatial maps and Atlases (BALSA) is a database for hosting and sharing neuroimaging and neuroanatomical datasets for human and primate species. (biokeanos.com)
  • The NIF is a dynamic inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology (i.e. (wikipedia.org)
  • Ethnopharmacological findings are scattered over a multitude of publications and databases and are not well connected to other biomedical databases. (biomedcentral.com)
  • Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. (oregonstate.edu)
  • Instead, PathCase-SB relies on (a) freely available (and curated-only) models in BioModels Database and CellML model repository to populate its model database, and (b) pathways from KEGG pathways data source [ 6 ], obtained via a license, to populate its pathways database. (biomedcentral.com)
  • A PPI network provides crucial information on how biological pathways are structured and coordinated from individual protein functions. (nature.com)
  • 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)
  • 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)
  • It provides unique identifiers, names and synonyms, list of complex members with their unique identifiers (UniProt, ChEBI, RNAcentral), function, binding and stoichiometry annotations, descriptions of their topology, assembly structure, ligands and associated diseases as well as cross-references to the same complex in other databases (e.g. (stanford.edu)
  • 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)
  • Annotations of images in a relational database are confined by the number of columns used for the descriptions of the images. (biomedcentral.com)
  • 2016). Example of Anti-Microbial Resistance (AMR) Databases is CARD(McArthur, Waglechner et al. (habdsk.org)
  • In this paper we propose a semantic representation of these images in the form of a Monogenean Haptoral Bar Image (MHBI) ontology, which are annotated with taxonomic classification, diagnostic hard part and image properties. (biomedcentral.com)
  • 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)
  • 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)
  • This will enable linking of information from the monogenean ontology to the host species found in the fish ontology without changing the underlying schema for either of the ontologies. (biomedcentral.com)
  • 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)
  • Figure 1: Neo4j Graph Schema for 7 biological entities. (elucidata.io)
  • EAV is also known as object-attribute-value model , vertical database model , and open schema . (wikipedia.org)
  • 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)
  • In this paper, we describe the current functionality (i.e., the currently available user interfaces) of PathCase-SB which provides a database-enabled integrative framework and tools towards effective and efficient systems biology model development and simulation for mechanistic understanding of the behavior of complex biological systems. (biomedcentral.com)
  • 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 addition many databases that have very similar types of data have been integrated into 'virtual databases', which combine many databases into one table. (wikipedia.org)
  • We discuss the general utility of this approach for other databases that capture data from the research literature. (stanford.edu)
  • 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)
  • The group will also work with other Semantic Web groups to gather suggestions for future development, and will support and encourage the use of Semantic Web technologies and foster the growth of interoperable, policy-aware data and databases in the health care and life sciences industries. (w3.org)
  • We have provided wide-ranging open data sharing of COVID-19 Knowledge for both global research communities and local people on the name of EDBCO-19, C0-19 PDB, CRDB and other biological databases with timely updates. (habdsk.org)
  • PathCase-SB aims to integrate systems biology models data and metabolic network data of selected biological data sources on the web (currently, BioModels Database and KEGG, respectively), and to provide more powerful and/or new capabilities via the new web-based integrative framework. (biomedcentral.com)
  • Local databases are wrapped into semantic data repositories that automatically expose local computing-formalized laboratory information in the Web. (jmir.org)
  • ISO 15926 http://en.wikipedia.org/wiki/ISO_15926 is titled: "Industrial automation systems and integration---Integration of life-cycle data for process plants including oil and gas production facilities" is a standard for data integration, sharing, exchange, and hand-over between computer systems. (w3.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)
  • An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (biomedcentral.com)
  • The data we used are basically of the monogenean species found in fish, thus we built a simple Fish ontology to demonstrate how the host (fish) ontology can be linked to the MHBI ontology. (biomedcentral.com)
  • In this paper, we utilized the Taxonomic Data Working Group Life Sciences Identifier (TDWG LSID) vocabulary to represent our data and defined a new vocabulary which is specific for annotating monogenean haptoral bar images to develop the MHBI ontology and a merged MHBI-Fish ontologies. (biomedcentral.com)
  • Contemporary approaches to organizing image data and its corresponding textual descriptions are by using either the relational database technologies or the XML technologies. (biomedcentral.com)
  • Storing images outside the database file in a directory and linking them via identifiers in the database column was a possible solution but here again any new inclusion of data will required a change in identifiers [ 7 , 8 ]. (biomedcentral.com)
  • However, within that period, extreme diversity in physical hardware, operating systems, databases, software and immature networking protocols hampered the sharing of data. (mkbergman.com)
  • 2017). Repositories differ from databases in that users can add information to the dataset in order to obtain an accession number for the data. (gr.jp)
  • In GlyCosmos, each dataset listed below is displayed in their own subsection, annotated as either "Database" or "Standard" to differentiate between data and standards for representing the data. (gr.jp)
  • There are several examples where, the relationships between biological entities can change depending on the how the data is being modelled. (elucidata.io)
  • Neo4j is a graph-native database which performs fast, dynamic and transactional queries over graph data. (elucidata.io)
  • Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. (hindawi.com)
  • 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 values of parameters in this model can be determind from literature, databases or they are directly estimated from quantitative experimental data using optimization methods. (hindawi.com)
  • OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. (biokeanos.com)
  • Its development will provide data archiving services to the broader bioimaging database community. (biokeanos.com)
  • SSBD is a database that collects and shares quantitative biological dynamics data, microscopy images, and software tools. (biokeanos.com)
  • In recent years, relevant databases have been converted their data into the RDF/OWL format. (biomedcentral.com)
  • In this task view, we focus on the most-important CRAN packages dedicated to omics data analysis including those related to annotation and databases. (osuosl.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)
  • 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)
  • However, sequences extracted from databases are most often annotated with identifiers which only implicitly contain the desired information. (degruyter.com)
  • BED is an interface for the Neo4j database providing a mapping between different identifiers of biological entities. (osuosl.org)
  • More specifically, riceidconverter can be used to convert rice biological identifiers. (osuosl.org)
  • The Neuroscience Information Framework is a repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources and provides many authoritative links throughout the neuroscience portal of Wikipedia. (wikipedia.org)
  • These and many other functional genomics studies rely on full genomic sequence to establish well-annotated databases. (biomedcentral.com)
  • This FOA encourages applications to establish partnerships between researchers interested in a biological problem of significant scope and researchers providing high-throughput structure determination capabilities through the NIGMS PSI:Biology network. (nih.gov)
  • The AMR databases incorporates diverse molecular and sequencing details, offers a basic guiding framework in the form of the Antibiotic Resistance Ontology and can easily classify putative antibiotic resistance genes in new unannotated genome sequences(McArthur, Waglechner et al. (habdsk.org)
  • Figure 7: Illustration of steps to determine a network in Homo sapiens using the metagraph concept, where each metanode represents a set of orthologous eukaryotic genes from the COG database 53 . (nature.com)
  • Multiple miRNA-mRNA prediction databases were searched by differentially expressed genes (DEGs) to obtain pairs of a miRNA-DEG regulatory network. (frontiersin.org)
  • Final W3C approval earlier this month of two key Semantic Web technologies, the Web Ontology Language (OWL) and the revised Resource Description Framework (RDF), is "a huge step forward" for the Semantic Web, said W3C's Eric Miller. (preferisco.com)
  • Resource Description Framework (RDF) is a set of rules for providing simple descriptive information in XML for implementation in library catalogs and worldwide directories, as well as for syndication and aggregation of software, news and other content. (preferisco.com)
  • FoodOn is based largely on LanguaLâ„¢ and is being further developed in the ontology environment. (langual.org)
  • Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. (biomedcentral.com)
  • The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. (biomedcentral.com)
  • The main purpose of a bioinformatics platform within SWEGENE should be to provide com- putational facilities and logistical support [databases & infrastructure] for scientists whose primary research in biology and medicine benefit from computational approaches. (lu.se)
  • The purpose of a bioinformatics platform within SWEGENE is to provide computational facilities and logistical support [databases, algorithms & infrastructure] for problem oriented scientists in an optimal way. (lu.se)
  • Table 1 shows the statistics of experimentally identified PPIs in representative plant species taken from the BioGRID database 29 . (nature.com)
  • Menke J, Roelandse M, Ozyurt B, Martone M , Bandrowski A . The Rigor and Transparency Index Quality Metric for Assessing Biological and Medical Science Methods. (neurotree.org)
  • Each food is described by a set of standard, controlled terms chosen from facets characteristic of the nutritional and/or hygienic quality of a food, as for example the biological origin, the methods of cooking and conservation, and technological treatments. (langual.org)
  • We integrate the ontology within the probabilistic framework of Bayesian networks which enables reasoning and prediction of protein function. (sunderland.ac.uk)
  • Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database. (hmdb.ca)
  • Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. (degruyter.com)
  • 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)
  • 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)
  • 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)
  • 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)
  • By putting semantic web into practice, a new framework is being presented for knowledge engineering, querying and information sharing. (org.pk)
  • 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)
  • Representation of design information using causal ontologies is very effective for creative ideation in product design. (designsociety.org)
  • 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)
  • Consider how one would try to represent a general-purpose clinical record in a relational database. (wikipedia.org)
  • Below is an example of a linked view of 7 molecular entities linked into a consolidated ontology. (elucidata.io)
  • The term omics concerns various biological disciplines ending with the suffix -omics, such as genomics, proteomics, metabolomics, transcriptomics. (osuosl.org)
  • PRO is a unique database resource for species-specific protein complexes. (biomedcentral.com)
  • The system interlinks three ontologies, comprising anatomical, developmental and taxonomical information, and includes instances of structures for different species. (degruyter.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)
  • The ontology is populated with the entities and relationships from protein-to-protein interactions. (sunderland.ac.uk)
  • 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)
  • 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)
  • The architecture uses an ontology-driven approach to promote the integration of a network of sentinel hospitals or laboratories. (jmir.org)
  • We will outline use of the ontology for immune assay integration and statistical enrichment analysis. (bioontology.org)
  • We can automatically generate a biological ontology by text mining the type II diabetes research literature. (sunderland.ac.uk)
  • The project is headed by Maryann Martone, co-director of the National Center for Microscopy and Imaging Research (NCMIR), part of the multi-disciplinary Center for Research in Biological Systems (CRBS), headquartered at UC San Diego. (wikipedia.org)
  • Many published models of the biomimicry process include steps to identify, understand, and translate function of biological systems. (mdpi.com)
  • The database currently holds approximately 2000 complexes with the majority from Saccharomyces cerevisiae, human and mouse. (stanford.edu)
  • The Neuroscience Information Framework (NIF) is an initiative of the NIH Blueprint for Neuroscience Research, which was established in 2004 by the National Institutes of Health. (wikipedia.org)
  • 9th International Conference on Bioinformatics & Biosciences (BIOS 2023) is a forum for presenting new advances and research results in the field of biology to increase the understanding of all biological process. (ourglocal.com)
  • The Hydraulic Instrumentation Section (HIS) of the International Association of Hydraulic Engineering and Research (IAHR) initiates an ambitious project for the benefit of the world-wide hydraulic engineering community and instrument manufacturers: The Instrumentation Database. (w3.org)
  • 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)
  • 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)
  • The idea was also to propose a framework where the SWEGENE platform users would get computerised support for their research projects. (lu.se)
  • 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)
  • Various software resources are also required to enable users to conveniently connect their experimental results with publicly, and application specific, bioinformatics databases and tools. (lu.se)
  • In chapter 2, Empusa is described as an infrastructure that bridges the gap between the intended and actual content of a database. (wur.nl)
  • This infrastructure was used in chapters 3 and 4 to develop the framework. (wur.nl)
  • The framework is constructed for comparative analyses in the field of evolutionary development. (degruyter.com)
  • Map2NCBI provides information on markers described by their positions by querying the NCBI database. (osuosl.org)
  • A "native" graph database means that Neo4j implements a true graph model till the storage level, as in it is not stored as a "graph abstraction" over another technology. (elucidata.io)
  • Most of the platforms are expected to be connected to resources for handling various types of user interactions, conceivably with a back-end database management system and a front-end web based technique to handle user interactions. (lu.se)
  • 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)
  • The proposed monogenean image ontology will form the basis of a monogenean knowledge base to assist researchers in retrieving information for their analysis. (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)
  • sponsoring of algorithm knowledge, database building for specific applications, some computer related acquisitions such as software and databases. (lu.se)
  • 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)