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Open Biomedical Ontologies
The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles. The OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in bioinformatics. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a phenotype in a mouse model and its related phenotype in zebrafish). Introduction The Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using controlled vocabularies. Ideally, such controlled vocabularies take the form of ontologies, which su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Suzanna Lewis
Suzanna (Suzi) E. Lewis was a scientist and Principal investigator at the Berkeley Bioinformatics Open-source Project based at Lawrence Berkeley National Laboratory until her retirement in 2019. Lewis led the development of open standards and software for genome annotation and ontologies. Education Lewis has Master of Science degrees in Biology and Computer science. Research She led the team responsible for the systematic annotation of the ''Drosophila melanogaster'' genome, which included development of the Gadfly annotation pipeline and database framework, and the annotation curation tool Apollo. Lewis' work in genome annotation also includes playing instrumental roles in the GASP community assessment exercises to evaluate the state of the art in genome annotation, development of the Gbrowse genome browser, and the data coordination center for the modENCODE project. In addition to her work in genome annotation, Lewis has been a leader in the development of Open Biomedical Ontolog ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Eagle-i
The eagle-i network (or just eagle-i) was a tool developed by a set of institutions from the United States that enables users to locate scientific resources around their country. It was retired November 4, 2021 after more than a decade in service. It used an ontology to map the resources (such as scientific equipment A scientific instrument is a device or tool used for scientific purposes, including the study of both natural phenomena and theoretical research. History Historically, the definition of a scientific instrument has varied, based on usage, laws, an ...) to their location, facilitating reuse and collaboration. The eagle-i team has produced ontologies that take care of different kinds of resources, such as the Reagent Application Ontology. External links eagle-i info page * https://www.eagle-i.net/ - former web site References {{Searchengine-website-stub Science websites ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Plant Ontology
Plant ontology (PO) is a collection of ontologies developed by the Plant Ontology Consortium. These ontologies describe anatomical structures and growth and developmental stages across Viridiplantae. The PO is intended for multiple applications, including genetics, genomics, phenomics, and development, taxonomy and systematics, semantic applications and education. Project Members *Oregon State University *New York Botanical Garden * L. H. Bailey Hortorium at Cornell University *Ensembl * SoyBase * SSWAP * SGN * Gramene *The Arabidopsis Information Resource (TAIR) * MaizeGDB *University of Missouri at St. Louis *Missouri Botanical Garden See also *Generic Model Organism Database *Open Biomedical OntologiesOBO Foundry References External linksPlant Ontology Consortium [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Disease Ontology
The Disease Ontology (DO) is a formal ontology of human disease. ThDisease Ontology projectis hosted at thInstitute for Genome Sciencesat the University of Maryland School of Medicine. The Disease Ontology project was initially developed in 2003 at Northwestern University to address the need for a purpose-built ontology that covers the full spectrum of disease concepts annotated within biomedical repositories within an ontological framework that is extensible to meet community needs. The Disease Ontology is an OBO ( Open Biomedical Ontologies) Foundry ontology. Disease Ontology Identifiers (DOIDs) consist of the prefix DOID: followed by number, for example, Alzheimer's disease has the stable identifieDOID:10652 DO is cross-referenced in several resources such as UniProt. Example term The Disease Ontology entry for motor neuron disease in OBO format is given below, showing the links to other classification schemes, including ICD-9, ICD-10, MeSH, SNOMED and UMLS. :id: DOID:231 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChEBI
Chemical Entities of Biological Interest, also known as ChEBI, is a chemical database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinformatics Institute (EBI). The term "molecular entity" refers to any "constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity". The molecular entities in question are either products of nature or synthetic products which have potential bioactivity. Molecules directly encoded by the genome, such as nucleic acids, proteins and peptides derived from proteins by proteolytic cleavage, are not as a rule included in ChEBI. ChEBI uses nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and nomenclature committee of the International Union of Biochemistry and Molecular Biology ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Zebrafish Information Network
The Zebrafish Information NetworkZFIN is an online biological database of information about the zebrafish (''Danio rerio''). The zebrafish is a widely used model organism for Genetics, genetic, Genomics, genomic, and Developmental biology, developmental studies, and ZFIN provides an integrated interface for querying and displaying the large volume of data generated by this research. To facilitate use of the zebrafish as a model of human biology, ZFIN links these data to corresponding information about other model organisms (e.g., Mus musculus, mouse) and to human disease databases. Abundant links to external DNA sequence, sequence databases (e.g., GenBank) and to genome browsers are included. Gene product, gene expression, and phenotype data are annotated with terms from biomedical Ontology (computer science), ontologies. ZFIN is based at the University of Oregon in the United States, with funding provided by the National Institutes of Health (NIH). Contents ZFIN consists of two prin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Foundational Model Of Anatomy
The Foundational Model of Anatomy Ontology (FMA) is a reference ontology for the domain of Human anatomy. It is a symbolic representation of the canonical, phenotypic structure of an organism; a spatial-structural ontology of anatomical entities and relations which form the physical organization of an organism at all salient levels of granularity. FMA is developed and maintained by the Structural Informatics Group at the University of Washington. Description FMA ontology contains approximately 75,000 classes and over 120,000 terms, over 2.1 million relationship instances from over 168 relationship types. – The Foundational Model of Anatomy (retrieved 2012-11-06). See also * |
Gene Ontology Consortium
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry. Whereas gene nomenclature focuses on gene and gene products, the Gene Ontology focuses on the function of the genes and gene products. The GO also extends the effort by using markup language to make the data (not only of the genes and their products but also of curated attributes) machine readab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java Virtual Machine
A Java virtual machine (JVM) is a virtual machine that enables a computer to run Java programs as well as programs written in other languages that are also compiled to Java bytecode. The JVM is detailed by a specification that formally describes what is required in a JVM implementation. Having a specification ensures interoperability of Java programs across different implementations so that program authors using the Java Development Kit (JDK) need not worry about idiosyncrasies of the underlying hardware platform. The JVM reference implementation is developed by the OpenJDK project as open source code and includes a JIT compiler called HotSpot. The commercially supported Java releases available from Oracle are based on the OpenJDK runtime. Eclipse OpenJ9 is another open source JVM for OpenJDK. JVM specification The Java virtual machine is an abstract (virtual) computer defined by a specification. It is a part of java runtime environment. The garbage-collection algorithm u ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source Software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open-source software may be developed in a collaborative public manner. Open-source software is a prominent example of open collaboration, meaning any capable user is able to participate online in development, making the number of possible contributors indefinite. The ability to examine the code facilitates public trust in the software. Open-source software development can bring in diverse perspectives beyond those of a single company. A 2008 report by the Standish Group stated that adoption of open-source software models has resulted in savings of about $60 billion per year for consumers. Open source code can be used for studying and allows capable end users to adapt software to their personal needs in a similar way user scripts an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Command-line Interface
A command-line interpreter or command-line processor uses a command-line interface (CLI) to receive commands from a user in the form of lines of text. This provides a means of setting parameters for the environment, invoking executables and providing information to them as to what actions they are to perform. In some cases the invocation is conditional based on conditions established by the user or previous executables. Such access was first provided by computer terminals starting in the mid-1960s. This provided an interactive environment not available with punched cards or other input methods. Today, many users rely upon graphical user interfaces and menu-driven interactions. However, some programming and maintenance tasks may not have a graphical user interface and use a command line. Alternatives to the command-line interface include text-based user interface menus (for example, IBM AIX SMIT), keyboard shortcuts, and various desktop metaphors centered on the pointer (usual ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
