|Annotation||The process of attaching additional information to biological entities. Annotation can be structural (i.e. identification of the elements from a sequence, such as protein coding regions or the location of regulatory motifs) or functional (i.e. adding biological information to the identified elements, such as the biological function of a protein domain or an entire protein, or the molecular interactions or regulatory role of a nucleotide sequence). Annotation can either be applied automatically or can be manually added (in a process called 'curation') from various sources, such as the scientific literature. At EMBL-EBI, we use a combination of automatic and manual annotation to enrich our databases. Annotation can either be applied automatically or it can be curated (manually) from the scientific literature. At EMBL-EBI, we use a combination of automatic and manual annotation to enrich our databases. |
|BioModels Database||BioModels Database is a repository of computational models of biological interest, sourced primarily, but not exclusively, from the field of systems biology. A large number of those mathematical models have been published in the peer reviewed literature. This resource allows biologists to store, search and retrieve mathematical models. In addition, users can generate sub-models, launch online simulations of the stored models, or convert them into different representational formats. www.ebi.ac.uk/biomodels/ |
|BioPAX||BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its main aim is to facilitate the exchange of pathway data. www.biopax.org |
|CellML||An XML model description format. Its purpose is to store computer-based mathematical models. CellML is developed by the Auckland Bioengineering Institute at the University of Auckland and affiliated research groups. http://www.cellml.org/ |
|Computational model||Describes a system with mathematical concepts and languages, and allows the study of its behaviour via computer simulations. A model is made up of variables, functions and constraints. Different types of models exists, such as dynamic models, logical models, rule-based models, multi-agent models, statistical models and many more. |
|Controlled vocabulary||A controlled vocabulary makes a database easier to search by drawing together all of the different words and phrases used to describe a concept under a single word or phrase. Synonyms are also listed and searchable so that you do not need to know the selceted word or phrase in advance. |
|MIRIAM||The Minimum Information Required In the Annotation of Models (MIRIAM), is a set of guidelines that helps researchers to re-use, modify and combine computer models of biochemical processes. MIRIAM has two parts: (1) a ‘reference correspondence’ that matches each model to its description (often a journal publication), and (2) a set of annotation schemes. The first of these documents the model’s provenance and provides a stable link to its full description; the second links the components of the model to relevant bioinformatics resources. These links rely on perennial URIs generated and resolved by MIRIAM Resources. www.ebi.ac.uk/miriam/ |
|Octave||A language primarily intended for numerical computations. It can be used for solving numerical problems and experiments, as well as providing extensive graphics capabilities for data visualisation and manipulation. The Octave language is quite similar to Matlab®, so most programs are easily portable. http://www.gnu.org/software/octave/ |
|SciLab||SciLab is a free open source software for numerical computation, similar to MatLab®, created by INRIA (the French national institute for research in computer science and control). http://www.scilab.org/ |
|Systems Biology Graphical Notation||The Systems Biology Graphical Notation (SBGN, http://sbgn.org) is a set of standard graphical languages for representing biological processes and interactions. SBGN defines comprehensive sets of symbols with precise semantics, together with detailed syntactic rules defining their use. It also describes the manner in which such graphical information should be interpreted. SBGN is made up of three different and complementary languages: the Process Descriptions, the Entity Relationships, and the Activity Flows. |
|Systems Biology Markup Language||Systems Biology Markup Language (SBML) is a standard format based on XML for communicating and storing computational models of biological processes. It is a free and open standard with widespread usage and software support. SBML represents many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks and infectious diseases. www.sbml.org |
|VCML||The Virtual Cell Markup Language (VCML) is an XML document format for describing biological and mathematical models and specifications for analysis (e.g. simulations), created by the Virtual Cell. http://vcell.org/ |
|Web Services||Web Services ( www.w3.org/ws ) are software systems designed to support interoperable machine-to-machine interaction over a network. To ensure that software systems from different sources work well together, they are built using open standards such as SOAP. |
|XPPAUT||A general numerical tool for simulating, animating, and analysing dynamic systems. http://www.math.pitt.edu/~bard/xpp/xpp.html |
|accession number||A unique, relatively stable, identifier given to database record which allows you to track different versions of that record over time in a single data repository.
For example, in in the ArrayExpress Archive, experiments and array designs are given unique accession numbers in the format of E-XXXX-n for experiments and A-XXXX-n for array designs. XXXX is a four letter code indicating the course of submission and n is a number e.g. E-MEXP-568. Some experiments also have secondary accession numbers.
In the UniProt database, proteins have unique UniProt Accession Numbers (e.g. P04637) and UniProt Protein ID's (e.g. P53_HUMAN). Uniprot accessions are unique to specific protein isoforms in specific species, and are used as the standard method for uniquely referencing a protein in EBI resources. Uniprot accessions cross-link the entries in various UniProt databases. Most often, researchers will find it useful to follow the Uniprot accession back to an entry in UniProtKB/Swiss-Prot to view a curated summary of known information about that protein.
There is a 'ID Mapping' Tool on the UniProt homepage which can be useful for converting Accession Numbers to corresponding idenfiers in other databases.
|curator||A professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases. The role of a biocurator encompasses quality control of primary biological research data intended for publication, extracting and organizing data from original scientific literature, and describing the data with standard annotation protocols and vocabularies that enable powerful queries and biological database inter-operability. Curators communicate with researchers to ensure the accuracy of curated information and to foster data exchanges with research laboratories. |
|gene||A molecular unit of heredity of a living organism. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring. All organisms have many genes corresponding to various biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type or increased risk for specific diseases, or the thousands of basic biochemical processes that comprise life. |