|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. |
|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. |
|Extracellular||The part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. |
|FlyBase||The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), and Indiana University and is a database of the Drosophila Genome.
You can find out more about FlyBase on the WikiPedia page: http://en.wikipedia.org/wiki/FlyBase |
|Gene ontology||Gene Ontology (GO) is a controlled vocabulary used to describe the biology of a gene product in any organism. There are 3 independent sets of vocabularies, or ontologies, that describe: the molecular function of a gene product, the biological process in which the gene product participates and the cellular component where the gene product can be found (http://www.geneontology.org). |
|Glycolysis||A metabolic pathway that converts glucose into pyruvate. The free energy released in this process is used to form the high-energy compounds ATP, FADH2 and NADH. |
|MySQL||My Structured Query Language (MySQL) is a software program for the design, population and provision of access to databases, conceptually similar to Oracle. http://www.mysql.com/ |
|NHGRI||National Human Genome Research Institute. An NIH institution developing research and technology to understand the structure and function of the human genome, promoting genomic research and applications to human health.
|Ontology||Is a formal representation of knowledge as a set of concepts within a domain, and the relationships between those concepts |
|Subcellular||A component of the cell, for example the mitochondrion, the nucleus or plasma membrane. |
|UniProt||UniProt – Universal Protein Resource: The world's most comprehensive catalogue of information on proteins and a central repository of protein sequence and function, created by joining the information contained in UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and PIR http://www.ebi.ac.uk/uniprot/ |
|UniProt-GOA||The UniProt-Gene Ontology Annotation database provides high-quality manual and electronic GO annotations to proteins within UniProtKB. UniProt-GOA is the largest and most comprehensive open-source contributor of annotations to the GO Consortium annotation effort. |
|XML||Extensible Markup Language (XML) defines a set of rules for encoding documents in a format that is both human-readable and machine-readable.
You can find out more about XML on the Wikipedia page: http://en.wikipedia.org/wiki/XML |
|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. |
|flat files||A file that contains one record per line. Individual fields within such a record are typically separated by delimiters such as commas or tabs. |
|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. |