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Open Reaction Database ORD consortium Organic reactions machine-readable reaction schemes "ORD" [8] 2,000,000 OrgSyn Organic Syntheses: Organic Syntheses, Inc. Reliable chemical reactions Searchable experimental procedures Peer reviewed "OrgSyn search". PDB PDBe Protein Data Bank in Europe EMBL-EBI: has some chemicals as well as proteins "PDBe".
Meta databases are databases of databases that collect data about data to generate new data. They are capable of merging information from different sources and making it available in a new and more convenient form, or with an emphasis on a particular disease or organism.
Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for ...
EmBiology (formerly EMBiology) is a web-based Software as a service tool from Elsevier in which researchers can view biological relationships between entities, such as genes, proteins, and cells.
Most data visualization in systems biology is done using mathematically generated models. Researchers will diagram all of the protein, gene, or metabolic pathways in a given biological system, then determine the speed of the reactions in that system using mass action kinetics or enzyme kinetics .
Biological data has also been difficult to define, as bioinformatics is a wide-encompassing field. Further, the question of what constitutes as being a living organism has been contentious, as "alive" represents a nebulous term that encompasses molecular evolution, biological modeling, biophysics, and systems biology.
This table is edited from a version that was originally published in the Encyclopedia of Computational Neuroscience. [48] System boundaries codes: R = reflecting, A = absorbing, T = transmitting, P = periodic, and I = interacting. * Algorithm is exact but software produced incorrect results at the time of original table compilation.
For example, a chemical database might store a molecule with stereochemistry unspecified, whereas a chemical registry system requires the registrar to specify whether the stereo configuration is unknown, a specific (known) mixture, or racemic. Each of these would be considered a different record in a chemical registry system.