Glossary

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Reactome Glossary

A

Accession – A code usually composed of letters and numbers that can be used to refer to an entry in a database, e.g. P49597 is a Uniprot database accession. Often considered to by the same as database ID, and for some databases this would be correct as accession and ID are synonymous, but it is not correct for Uniprot where the ID is a different value (for the example above the ID is P2C56_ARATH).

Advanced Search – A powerful tool for searching Reactome by database field.

Analyze, Annotate & Upload - A button at the top of the Pathway Browser sidebar that launches a control panel allowing configuration of the tools embedded in the browser, such as molecular interaction overlay.

API – Reactome has a SOAP-based API – for details please see the Download tab.

ArrayExpress – A database of microarray experiment results.

Attributes – Used in BioMart to determine the information types that are returned by a query.

Author – An expert biologist who contributes the details used to create new pathways in Reactome.

Author Tool – a software package available to biologists who wish to contribute to Reactome.

B

BioMart - The name of a project and the corresponding software that allows rapid bulk searches of large databases, and the ability to link between databases so that a single query can retrieve data from more than one database source.

BioPax - A collaborative effort to create a data exchange format for biological pathway data, see http://www.biopax.org/. Reactome data can be downloaded in several formats including BioPax level 2 and level 3.

Color –Within Reactome Pathway Diagrams objects represent molecules or groups of molecules participating in the reaction. The color and shape of these indicates the type of participant:

  • Blue – complexes (more than one molecule)
  • Green – proteins or sets of proteins
  • Grey – compounds (small molecules) or Genome-encoded entities

C

Candidate Set – A set of molecules that contains at least one member that might be anticipated to be functionally equivalent to the other members of the set but this has yet to be experimentally verified. Candidate sets are often used in Reactome when some members of a protein family have been demonstrated to participate in a reaction (defined as Members of the set) and other related proteins are anticipated to have similar properties but have not been proven to do so (Candidates).

ChEBI – A database of compound information. ChEBI IDs are the primary identifiers for chemicals and small compounds in Reactome.

Compartment - the subcellular location of molecules. All molecules in Reactome belong to a compartment, defined by an equivalent Gene Ontology term. Molecules that exist in more than one compartment are distinct in Reactome and have their own internal identifiers - this distinction is made because molecules that are separated by compartment within the cell may not be able to interact. This also explains why a protein with one external identifier (e.g. Uniprot accession) can have several identifiers in Reactome.

Complex – Two or more molecules that are bound to each other. Complexes may have functional properties that none of the member molecules have individually.

Contributors – Reactome content is contributed by expert biologists. If your area of interest is not represented please help us by contributing as a Reactome author.

Curated – Maintained by Reactome curators, specialists who convert information provided by an expert biologist author into records in the Reactome database.

Curator Tool – a software package intended for use by Reactome curators to annotate biological pathways based on the Reactome schema.

D

Database schema – Reactome data is stored in a MySQL framework with a schema detailed under the Contents tab on the Homepage.

Defined Set – A set of molecules that are functionally equivalent, i.e. all proven to be capable of participating in the same reaction.

Detail Panel - the bottom panel of the Pathway Browser, contains detailed information about the last object (pathway, reaction, complex, protein, set or small molecule) selected in the Pathway Diagram or Pathway Hierarchy. This panel can be opened by clicking the blue triange on the bottom edge of the Pathway Diagram.

Diagram - See Pathway Diagram.

Display Interactors - A context-sensitive option that is listed when a protein is right-clicked in a Pathway Diagram, if that protein has interactors in the currently selected external interaction source (by default this is IntAct). Generates an overlay of the interactors on the Pathway Diagram.

DOI – Digital Object Identifier – is used within a standardised system for identifying electronic publications. Reactome can issue DOIs for significant contributions to the database.

E

Editorial Calendar – Details our plans to add content to Reactome. Reactome is updated quarterly.

Ensembl – A database of annotations on genomes, Ensembl IDs are the primary identifiers for genes in Reactome.

Entity – A molecule or group of molecules that participate in a reaction.

Event – A change of state for a molecule, e.g. movement between compartments of the cell, phosphorylation, binding to another molecule.

Event Hierarchy – An outdated term for the Pathway Hierarchy.

Expression analysis – A Reactome tool that overlays user-supplied expression measurements onto pathways, giving a visualisation that is colored by expression level. If more than one expression data set is supplied, e.g. to represent a time course, or disease progression, the visualisation cycles through these generating a 'movie' of the expression changes.

Experiment Browser toolbar - a toolbar superimposed onto the Pathway Diagram following Expression Analysis. Used to step through multiple data sets if supplied by the user.

F

G

GO – Gene Ontology, a set of pre-defined categories that can be used to describe genes and their derived proteins.

Go To Pathway - Menu item displayed when a Subpathway Icon is right-clicked in a Pathway Diagram, if selected opens the appropriate Pathway Diagram

H

Help – see Contact Us (to ask for help via email) or the Reactome User Guide (online documentation).

Heat-map – A graphic where the spectrum of colours from blue to red is used to represent increasing numeric values.

Hierarchy – A system of organisation based on levels. In Reactome all reactions and pathways are associated with a 'top-level' pathway that is the highest level of the hierarchy. These top-level pathways often have sub-pathways and these can also have sub-pathways, there is no limit to the number of levels. Reactions can be at any level and not necessarily within a pathway (though this is the norm).

Home - Button at the top left of all Reactome pages, takes you to the Homepage.

Homepage – the first page you see when accessing www.reactome.org

I

Identifiers – See Accession

Inferred - Deduced from evidence. In Reactome events can be inferred to exist. Manually inferred reactions are human reactions that are believed to occur based on evidence from model organisms – these reactions have an Inferred From flag that identifies the details of the reaction in the model organism. Reactome also contains computationally inferred reactions for 19 model organism species, these are based on EnsEMBL Compara orthology predictions.

Instance – one item of something, in computing an instance is one of a type of object, a specific meaning from the realm of object-oriented programming.

Installing Reactome – Reactome database, code and content can all be downloaded from the website. Instructions for making a local installation are available via the Download tab on the homepage.

Interactor – A broad term used to define a molecule that can physically associate with another (pre-defined) molecule. Interactions are defined using a huge range of experimental methods, some more reliable than others. Reacome is not an interactions database, but Reactome makes available several different classes of interactor inferred from Reaction data.


J

K

L

Linking to Reactome – This can be achieved by creating URLs containing the name of and an identifier from an 'external' database, for more details see the Documentation tab on the homepage.


M

Molecular Interaction Overlay - A tool available in the Pathway Browser that allows the overlay of protein-protein interactions data from external databases such as IntAct or protein-compound data from ChEBI onto Reactome pathways.

N

Navigation Bar – Toolbar or Menu across the top of most Reactome pages


O

Objects - Symbols used to represent reactions or the molecules that take part in them in pathway diagrams. Green rectangles (boxes) are used for proteins and sets. Blue reactangles are complexes. Green ovals are simple molecules. These objects are connected by lines to a central Reaction Node, that can be one of several symbols, indicating the reaction subclass. See the Reactome User Guide for more detail.

Open Source - software that is available for use and modification by anyone, such as Reactome. Use of Reactome code is covered by a Creative Commons License, for details see the Licence Agreement under About on the Reactome Homepage

Other Pathways - A context-sensitive option listed when a protein is right-clicked on the pathway diagram, if it is represented in other pathways.

Output – see Product

Over-representation analysis – One of the analysis types available with the Pathway Analysis tool. A statistical approach based on Fisher's Exact test that determines whether a user-supplied set of identifiers contains a higher proportion of the proteins in a Reactome pathway than would be expected by chance.

P

Paint – Represent numeric information as coloration of pathway objects.

Participating Molecules - a context sensitive menu option displayed when a complex or set is right-clicked in a pathway diagram. Generates a list of the molecules within the complex or set.

PathFinder – Tool for identifying the shortest set of connections (path) between two molecules or reactions.

Pathway – Generally used to mean a series of events leading to a biological outcome, in Reactome pathway has a second, more specific meaning: a series of reactions that are connected by their participants.

Pathway Analysis - Reactome tool that has two functions, can be used to Map user-supplied identifiers to pathways or to perform over-representation analysis.

Pathway Browser - Reactome tool for viewing and interacting with pathways.

Pathway Diagram - The right-hand panel of the Pathway Browser, containing a diagram that represents pathways as connected reactions, and reactions as their inputs, outputs, catalysts and regulators, all represented as objects (boxes and ovals) joined by lines. The color and shape of objects and lines have meaning - see Objects. Molecules are represented in their subcellular compartment. Compartments are represented as pink boxes, their boundaries represent the membrane that encloses the subcellular space, e.g. the boundary of the cytosol is the plasma membrane.

Pathway Hierarchy - A representation of Reactome pathways, subpathways and the reactions they contain, present as the left side panel in the Pathway Browser. Within the pathway hierarchy pathways are represented by a 'dots joined by lines' symbol. Reactions are represented by 2 dots joined to one by an arrowed line. A third symbol with two dots joined by a broken line represents 'black-box' reactions, where the full set of participants has not been represented for the sake of brevity, or for reactions where some details of the reaction are established but believed to be incomplete.

Pathways Tab - one of three tabs in the Pathway Brower sidebar, contains the Pathway Hierarchy.

Product – Molecule(s) produced by a reaction, in the same sense as used for biochemical reactions.

Protege – a standard (http://protege.stanford.edu/) used to define the Reactome data model i.e. classes, their hierarchy, attributes and constraints on them.

PSI-MI(TAB) – PSI is the Protein Standards Initiative, an effort to define community standards for data representation in proteomics. Within this effort is a group concerned with Molecular Interaction (MI) which has created a standard format PSI-MITAB. Reactome data is available in this format, see http://wiki.reactome.org/index.php/PSI-MITAB_interactions for details.

PubMed – A database of scientific literature. PubMed IDs are the primary accession for literature in Reactome.

Q

R

Reactant – See Substrate

Reaction – A biological event that changes the state of a molecule. Reactions are the units of Reactome pathways.

Reaction Diagram - Now obsolete - A graphical representation of a reaction using boxes to denote participants.

Reaction Map – Now obsolete - A graphical overview of all Reactome reactions, clustered into pathways.

Reaction Node - A symbol used in Reaction diagrams to represent the reaction and allow it's selection. There are several types of symbol that denote the type of reaction, e.g. solid black circles are association (binding) events. See the Reactome User Guide for more details.

Reviewer – New Reactome content is reviewed by an independent expert biologist, to ensure that a) No errors were introduced at the curation stage, b) the reactions and pathways represent consensus knowledge, not fringe or contentious opinions.

S

SBML – Systems Biology Markup Language, a machine-readable format for representing biological models. Reactome data can be downloaded in this format.

Schema – see Database schema

Search Panel – Tool for performing text searches of Reactome, available near the top of most pages.

Sidebar - The left side of the Reactome homepage

SkyPainter – obsolete term, replaced by Pathway Analysis.

Small Molecule Search – Tool for searching Reactome using structures which can be generated with a simple drawing tool.

SOAP - A SOAP based Web Services API is available to access Reactome data. For details please see the Download tab.

Species Comparison – Tool used to compare Reactome human pathways to the equivalent predicted for model organisms.

Species selector – Dropdown list for choosing a species.

Starry Sky or Sky - obsolete - See Reaction Map.

Sub-pathway - Part of a pathway. Sub-pathways are frequently used in Reactome to split pathways that would otherwise be unmanageable.

Subpathway Icon - used in Pathway Diagrams to represent the existence of a diagram for a sub-pathway, in effect a visualization that identifies that there is a Pathway Diagram available but it is not displayed.

Substrate – Molecules that are the input to a reaction, in the same sense as used for biochemical reactions.

T

Top-level pathways – The highest level in our hierarchical view of biological topics.

Type Selector Box – Used to select specific subsets of results following a text search


U

Uniprot – A database of protein sequences. Uniprot accessions are the primary identifiers for peptides in Reactome.

User Guide – Available online, see the Documentation tab on the homepage.


V

W

Wiki – Reactome has a user-Wiki. Use as a reference is open-access, contributors are required to register. See the Documentation tab.


X

Y

Z

Zoom/Move toolbar - Located in the top left corner of the Pathway Diagram, these tools allow navigation of the diagram. Most browsers support zooming with the mouse wheel.