A Uniform Resource Identifier (URI) is a unique sequence of characters that identifies a logical or physical resource used by web technologies. URIs may be used to identify anything, including real-world objects, such as people and places, concepts, or information resources such as web pages and books. Some URIs provide a means of locating and retrieving information resources on a network ; these are Uniform Resource Locators (URLs). A URL provides the location of the resource. A URI identifies the resource by name at the specified location or URL. Other URIs provide only a unique name, without a means of locating or retrieving the resource or information about it; these are Uniform Resource Names (URNs). The web technologies that use URIs are not limited to web browsers. URIs are used to identify anything described using the Resource Description Framework (RDF), for example, concepts that are part of an ontology defined using the Web Ontology Language (OWL), and people who are described using the Friend of a Friend vocabulary would each have an individual URI.
A Uniform Resource Name (URN) is a Uniform Resource Identifier (URI) that uses the urn scheme. URNs are globally unique persistent identifiers assigned within defined namespaces so they will be available for a long period of time, even after the resource which they identify ceases to exist or becomes unavailable. URNs cannot be used to directly locate an item and need not be resolvable, as they are simply templates that another parser may use to find an item.
A digital object identifier (DOI) is a persistent identifier or handle used to uniquely identify various objects, standardized by the International Organization for Standardization (ISO). DOIs are an implementation of the Handle System; they also fit within the URI system. They are widely used to identify academic, professional, and government information, such as journal articles, research reports, data sets, and official publications. DOIs have also been used to identify other types of information resources, like commercial videos.
The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.
Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.
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.
Life Science Identifiers are a way to name and locate pieces of information on the web. Essentially, an LSID is a unique identifier for some data, and the LSID protocol specifies a standard way to locate the data. They are a little like DOIs used by many publishers.
BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. All the models in the curated section of BioModels Database have been described in peer-reviewed scientific literature.
The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational modeling.
MIRIAM is a community-level effort to standardize the annotation and curation processes of quantitative models of biological systems. It consists of a set of guidelines suitable for use with any structured format, allowing different groups to collaborate and share resulting models. Adherence to these guidelines also facilitates the sharing of software and service infrastructures built upon modeling activities.
BioPAX is a RDF/OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.
The Handle System is the Corporation for National Research Initiatives's proprietary registry assigning persistent identifiers, or handles, to information resources, and for resolving "those handles into the information necessary to locate, access, and otherwise make use of the resources".
The minimum information about a simulation experiment (MIASE) is a list of the common set of information a modeller needs to enable the execution and reproduction of a numerical simulation experiment, derived from a given set of quantitative models.
SABIO-RK is a web-accessible database storing information about biochemical reactions and their kinetic properties.
Signaling Gateway is a web portal dedicated to signaling pathways powered by the San Diego Supercomputer Center at the University of California, San Diego. It was initiated by a collaboration between the Alliance for Cellular Signaling and Nature. A primary feature is the Molecule Pages database.
LibSBML is an open-source software library that provides an application programming interface (API) for the SBML format. The libSBML library can be embedded in a software application or used in a web servlet as part of the application or servlet's implementation of support for reading, writing, and manipulating SBML documents and data streams. The core of libSBML is written in ISO standard C++; the library provides API for many programming languages via interfaces generated with the help of SWIG.
JSBML is an open-source Java (API) for the SBML format. Its API strives to attain a strong similarity to the Java binding of the corresponding library libSBML, but is entirely implemented in Java and therefore platform independent. JSBML provides an elaborated abstract type hierarchy, whose data types implement or extend many interfaces and abstract classes from the standard Java library. In this way, JSBML integrates smoothly into existing Java projects, and provides methods to read, write, evaluate, and manipulate the content of SBML documents.
Identifiers.org is a project providing stable and perennial identifiers for data records used in the Life Sciences. The identifiers are provided in the form of Uniform Resource Identifiers (URIs). Identifiers.org is also a resolving system, that relies on collections listed in the MIRIAM Registry to provide direct access to different instances of the identified records.
Experimental factor ontology, also known as EFO, is an open-access ontology of experimental variables particularly those used in molecular biology. The ontology covers variables which include aspects of disease, anatomy, cell type, cell lines, chemical compounds and assay information. EFO is developed and maintained at the EMBL-EBI as a cross-cutting resource for the purposes of curation, querying and data integration in resources such as Ensembl, ChEMBL and Expression Atlas.
Nicolas Le Novère is a British and French biologist. His research focuses on modeling signaling pathways and developing tools to share mathematical models.
