Terms in Experiment Designer:

  • Experiment Design: This is the design created by the user and stored in the workspace under {project}/experiments directory, the same level as samples and ms. The file name is closely tied with the corresponding sample file, i.e. if the sample is named "sample12345.xml", the corresponding experiment design is named "experiment12345.xml". Experiment Design contains protocol instances (with a reference to their corresponding protocols), their connections, their parameters with values and selected unit-of-measurement, their location and size within the graph.
  • Experiment Design Template: This has practically the same content as any experiment design created by the user but additionally it contains a user provided name, description, creator and a generated uri (generated from the name). Templates are stored in the configuration directory under {configuration_directory}/org.grits.toolbox.editor.experimentdesign/experimentTemplates/.
  • Protocol: Each experiment design created contains one or more protocols connected to each other. Protocol has a name, description, creator, a list of parameter groups, a list of parameters and a list of paper references. Protocols are defined in the ontology and they are instantiated and become part of the experiment design when they are added as nodes of the experiment design graph. The populated values for the parameters then becomes part of the Experiment Design and stored as described above. Protocols can also be added into the ontology by the user by saving a protocol instance as a template.
  • Parameter and Parameter Group: Parameters and Parameter Groups are also defined in the ontology together with their unit of measurement, if any, their namespaces and data types. Parameter Group is the grouping of two or more parameters that practically make up another parameter.
  • Protocol Category: Protocols are assigned categories that define their placement in the graphical editor's palette. Protocol Category is stored in the ontology with its name, description and its order in the palette.
  • Protocol Variant: Protocol variants are protocol instances which are explicitly saved by the user with a name to be used later in other experiment designs or to be shared with other scientists. They contain all the information filled by the user such as parameter values, paper references etc. They are stored in the configuration directory under {configuration_directory}/org.grits.toolbox.editor.experimentdesign/protocols. This directory contains an index file named "protocols.xml" to list all the protocol variant names with their corresponding file names.

Ontologies "experimentdesignontology.owl" and "localexperimentdesignontology.owl" are stored under {configuration_directory}/org.grits.toolbox.editor.experimentdesign/ directory.

Mappings of Terms to GlycoVault

Grits Experiment Designer GlycoVault
Protocol ProtocolDesign
ProtocolVariant Protocol
Parameter Parameter
Parameter (instantiated) ParameterValue
Experiment Design Template ExperimentDesign
Protocol (instantiated) ExperimentStep + Protocol
ExperimentDesign ExperimentDesign
Last modified 7 years ago Last modified on 12/10/2014 06:51:34 PM