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You are here: Home Documentation Previous versions OME Server Conceptual Framework Analysis Modules

Analysis Modules

An important aspect of the data in OME is the description of where that data came from. Was it generated by the microscope at the time of acquisition, or during a post-processing step? Was it typed in by the user as a description or annotation? Was it the result of a computation? Which one? What were its parameters?

OME defines an entity called an analysis module which encodes this information. An analysis module represents any process which can create attributes. The act of creating new data is encoded as a transformation which generates or distills new information from existing data. This is represented by a module's formal inputs and formal outputs; a module receives input attributes for each of its formal inputs, performs its transformation or computation, and generates new output attributes for each of its formal outputs. Each formal input and output is semantically typed, which places a constraint on which attributes will be accepted as inputs or creates as outputs.

It's helpful to think of the module being the driving process behind this transformation; the inputs arrive, the module does something, and new outputs appear. However, it is important to realize that this is not always the case: modules can also be used to describe a transformation which has already happened, and which may be difficult or impossible to repeat. If the module does represent a repeatable algorithm (i.e., a computer program), OME can handle that, and can be the driving force behind controlling when and how the module gets executed. However, this is not required.

As their names suggest, analysis modules usually represent computational algorithms, but the data acquisition and annotation stages are also represented in OME as analysis modules. Since these processes are the means through which data first gets into OME, these stages are the only modules which do not define any formal inputs. These modules represent the user's almost "magical" ability to bring data in from the black hole, about which OME knows nothing and can make no assumptions.

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