en Author: Ravi Shankar, Stanford Medical Informatics <table border="1"> <tr> <td> <b><i>Version</i></b> </td> <td> 0.97 </td> </tr> <tr> <td> <b><i>Date</i></b> </td> <td> 3/2/2007<br> </td> </tr> </table> <br> blood-draw priorityfor an activity. Typicaly, the blood draws for clinical activities has higher priorities over the blood draws for mechanistic studies. the volume of specimen that will be drawn from the participant. The specimen volume can be conditional on the visit. So, for now, we specify the volume, and ay conditions, as text. AND XOR AND XOR asyont:Assay ClinicalTrial ClinicalTrial specifies the study id, the title, the protocol and the operational plan of a clinical trial..<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasStudyId </td> <td> a unique identifier for the clinical trial typically assigned by the study sponsor </td> </tr> <tr> <td> hasBriefTitle </td> <td> clinical trial title intended for the lay public </td> </tr> <tr> <td> hasOfficialTitle </td> <td> Official name of the clinical trial as provided by the study principal investigator or sponsor </td> </tr> <tr> <td> hasProtocol </td> <td> the protocol that includes planned clinical trial activities and the schedule of these activities </td> </tr> <tr> <td> hasOperationalPlan </td> <td> the operational plan that includes the facilities plan and the specimen processing plan </td> </tr> </table> ClinicalTrialEntity true An abstract class that is the superclass of all classes relevant to clinical trial DeviationCode A deviaiton code is used to record a deviation from planned specimen workflow activities. It includes a standard code and reason for the deviation. <br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasShortCode </td> <td> a standard code that is a unique identifier for the deviation </td> </tr> <tr> <td> hasDescription </td> <td> a brief description of the reason for the deviation </td> </tr> <tr> <td> requiresComment </td> <td> during implementation of the protocol, if this deviaiton occurs, whether the study personnel should make additional comments regarding this deviation </td> </tr> </table> DeviationCodeGroup A grouping of deviation codes by specimen work flow activities where the associated deviations can occur.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasName </td> <td> name of the deviation codes group </td> </tr> <tr> <td> hasDeviationCodes </td> <td> a set of deviation codes in this group </td> </tr> <tr> <td> hasDescription </td> <td> a brief description of the deviation group </td> </tr> </table> EncounterFlowTransition Information on transition from one node (encounter, context) to another node in the encounter flow diagram. It mainly specifies the temporal sequence of the nodes in the diagram.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> :FROM </td> <td> the <i><b>from</b></i> node (encounter, context) in the transition </td> </tr> <tr> <td> :TO </td> <td> the <i><b>to</b></i> node (encounter, context) in the transition </td> </tr> <tr> <td> transition_condition </td> <td> the condition under which the transition happens </td> </tr> </table> FacilitiesPlan A facilities plan enumerates clincal, laboratory and bio-repository facilities that are involved in the implementation of the protocol.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasStudySites </td> <td> a set of clinical sites where the protocol is implemented. A study coordinator at each site oversees the protocol. Participants are recruited for the protocol at the sites. Enrolled participants visit the sites as per the protocol plan. </td> </tr> <tr> <td> hasClinicalLaboratories </td> <td> a set of laboratories used for clinical assessments, and for pre-processing biological specimens for mechanistic studies. Typically these laboratories are part of the study sites. </td> </tr> <tr> <td> hasCoreLaboratories </td> <td> a set of core laboratories where complex assays are performed on the biological specimens collected at the study sites. </td> </tr> <tr> <td> hasBioRepositories </td> <td> a set of bio-repositires where biological specimens are temporarily stored before shipping them to the core laboratories, and also, where specimens are archived for future use. </td> </tr> </table> FacilitiesPlanEntity true An abstract class that is the superclass of all classes relevant to facilities plan OperationalPlan OperationalPlan includes information on participating facilities and on specimen processing.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasSpecimenProcessingPlan </td> <td> specifies specimen workflows and associated specimen containers. </td> </tr> <tr> <td> hasFacilitiesPlan </td> <td> enumerates the study sites, bio-repositories and laboratories involved in the protocol implementation </td> </tr> </table> OperationalPlanEntity true An abstract class that is the superclass of all classes relevant to the operational plan. Primary-SecondaryContainerRelation Information on specimen containers involved when aliquoting specimens<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasPrimaryContainer </td> <td> the source container that will contain the specimen collected from the participant </td> </tr> <tr> <td> hasSecondaryContainers </td> <td> a set of target containers that will contain the aliquoted specimens </td> </tr> </table> ProtocolSchemaTransition Information on transition from one node (period, context) to another node in the protocol schema diagram. It mainly specifies the temporal sequence of the nodes in the diagram.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> :FROM </td> <td> the <i><b>from</b></i> node (period, context) in the transition </td> </tr> <tr> <td> :TO </td> <td> the <i><b>to</b></i> node (period, context) in the transition </td> </tr> <tr> <td> transition_condition </td> <td> the condition under which the transition happens </td> </tr> </table> 1 1 SpecimenAliquot Information on the activity of processing and aliquoting specimens to prepare them for assaying.<br><br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasLabel </td> <td> display label </td> </tr> <tr> <td> hasTransitionRestriction </td> <td> specifies the collective split/join transition constraint on a set of transitions from or to an event. </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of specific planned activities that involve specimen processing and where the node is part of the processing workflow. </td> </tr> <tr> <td> hasStorageInstructions </td> <td> specimen container and specimen (short-term) storage instructions </td> </tr> <tr> <td> hasProcessingInstructions </td> <td> specimen processing instructions including aliquoting instructions </td> </tr> <tr> <td> hasContainersAliquoted </td> <td> specifies a set of primary containers, and, for each primary container, a set of associated secondary containers. Basically the specimen in the primary container will be processed and aliquoted into the associated set of secondary containers </td> </tr> <tr> <td> isPerformedAtFacilities </td> <td> Clinical laboratory sites where the specimens are aliquoted </td> </tr> </table> 1 1 SpecimenArchival Information on the specimen archiving activity<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasLabel </td> <td> display label </td> </tr> <tr> <td> hasTransitionRestriction </td> <td> specifies the collective split/join transition constraint on a set of transitions from or to an event. </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of specific planned activities that involve specimen processing and where the node is part of the processing workflow. </td> </tr> <tr> <td> hasArchivalInstructions </td> <td> specimen archival (long-term storage) instructions </td> </tr> <tr> <td> hasContainersArchived </td> <td> list of specimen containers that contain the specimens to be archived </td> </tr> <tr> <td> isPerformedAtFacilities </td> <td> Bio-repository where the specimens are archived </td> </tr> </table> 1 1 SpecimenAssaying Information on the activity of performing assays on specimens<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasLabel </td> <td> display label </td> </tr> <tr> <td> hasTransitionRestriction </td> <td> specifies the collective split/join transition constraint on a set of transitions from or to an event. </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of specific planned activities that involve specimen processing and where the node is part of the processing workflow. </td> </tr> <tr> <td> hasStorageInstructions </td> <td> specimen container and specimen (short-term) storage instructions </td> </tr> <tr> <td> hasAssayInstructions </td> <td> assay instructions </td> </tr> <tr> <td> hasAssaysPerformed </td> <td> list of assays that will be performed on the specimens </td> </tr> <tr> <td> hasContainersAssayed </td> <td> list of specimen containers that contain specimens that are assayed </td> </tr> <tr> <td> isPerformedAtFacilities </td> <td> Core laboratory sites where the specimens will be assayed </td> </tr> </table> 1 1 SpecimenCollection Information on the specimen collection activity<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasLabel </td> <td> display label </td> </tr> <tr> <td> hasTransitionRestriction </td> <td> specifies the collective split/join transition constraint on a set of transitions from or to an event. </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of specific planned activities that involve specimen processing and where the node is part of the processing workflow. </td> </tr> <tr> <td> hasStorageInstructions </td> <td> specimen container and specimen (short-term) storage instructions </td> </tr> <tr> <td> hasProcessingInstructions </td> <td> specimen processing instructions </td> </tr> <tr> <td> hasCollectionInstructions </td> <td> specimen collection instructions including blood draw priorities </td> </tr> <tr> <td> hasContainersCollected </td> <td> list of specimen containers that are used to collect the specimens into </td> </tr> <tr> <td> hasCollectedSpecimenType </td> <td> type of specimen that is collected </td> </tr> <tr> <td> hasSpecimenVolume </td> <td> volume of specimen that is collected </td> </tr> <tr> <td> hasBloodDrawPriority </td> <td> numerical priority (1=highest) in relation to other blood collection activities at a single clinical encounter. It allows site coordinators to prioritize blood draws when complying with guidelines on volume of participant's blood draw during a clinical encounter. </td> </tr> <tr> <td> isPerformedAtSites </td> <td> Clinical sites where the specimens are collected </td> </tr> </table> SpecimenContainerSet An set of primary and secondary containers aggregated across specimen collection activities for the purposes of creating physical specimen container kits used at specific encounters<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasName </td> <td> name of the container set </td> </tr> <tr> <td> hasDescription </td> <td> a brief description of the container set </td> </tr> <tr> <td> hasPrimarySecondaryContainers </td> <td> sets of primary and secondary containers </td> </tr> <tr> <td> hasEncountersWhenNeeded </td> <td> protocol encounter such as visits when the container is used </td> </tr> </table> SpecimenContainerSpecification Information on the specimen containers used to store biological specimens, after collection and during the processing of the specimens. This class is used to specify, for a particular protocol activity, the number and type of specimen containers based on <b>when</b> that activity is planned.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasContainerCount </td> <td> the number of specimen containers </td> </tr> <tr> <td> hasContainerType </td> <td> the type of specimen container </td> </tr> <tr> <td> hasSpecimenType </td> <td> the type of specimen that is stored in the container </td> </tr> <tr> <td> hasContainerLabelText </td> <td> the label that will be affixed on the physical container </td> </tr> <tr> <td> hasConditionalTimings </td> <td> the protocol timings (such as visits) when the container is used </td> </tr> </table> SpecimenProcessingPlan SpecimenProcessingPlan lists the specimen workflows associated with processing specimens that are collected as part of specfic planned protocol activities. Typically there will be one specimen workflow associated with a planned activity. Transitions between specimen workflows are facilitated using router nodes in the workflow diagrams. The plan also enumerates the specimen containers used in all the specimen workflows, and the deviation codes used when recording any execution-time deviations from the specimen workflow specifications.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasSpecimeWorkflows </td> <td> list of specimen workflows specified in the protocol </td> </tr> <tr> <td> hasSpecimenContainerSets </td> <td> an aggregated list of specimen container sets used at different encounters associated with specimen processing (see hasAssociatedEncounters) </td> </tr> <tr> <td> hasDeviationCodeGroups </td> <td> a list of deviation code groups associated with the specimen workflow activities </td> </tr> <tr> <td> hasAssociatedEncounters </td> <td> a list of encounters that are the timings of specific planned activities associated with the specimen processing plan. </td> </tr> </table> SpecimenProcessingPlanEntity true An abstract class that is the superclass of all classes relevant to specimen processing plan. 1 1 SpecimenReceiving Information on the specimen receiving activity<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasLabel </td> <td> display label </td> </tr> <tr> <td> hasTransitionRestriction </td> <td> specifies the collective split/join transition constraint on a set of transitions from or to an event. </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of specific planned activities that involve specimen processing and where the node is part of the processing workflow. </td> </tr> <tr> <td> hasContainersReceived </td> <td> list of specimen containers that are received at facilities </td> </tr> <tr> <td> isPerformedAtFacilities </td> <td> Facilities where the specimens are received </td> </tr> </table> 1 1 1 SpecimenShipping Information on the specimen shipping activity<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasLabel </td> <td> display label </td> </tr> <tr> <td> hasTransitionRestriction </td> <td> specifies the collective split/join transition constraint on a set of transitions from or to an event. </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of specific planned activities that involve specimen processing and where the node is part of the processing workflow. </td> </tr> <tr> <td> hasShippingInstructions </td> <td> specimen shipping instructions </td> </tr> <tr> <td> hasContainersArchived </td> <td> list of specimen containers that are shipped </td> </tr> <tr> <td> hasShippingDestinations </td> <td> facilities where the specimens are shipped to </td> </tr> <tr> <td> isPerformedAtFacilities </td> <td> facilities where the specimens are shipped from </td> </tr> </table> 1 SpecimenWorkflow SpecimenWorkflow is the workflow of a specimen collection and processing activity. The workflow is specified as an activity diagram with activity nodes, and with conditional transitions between nodes.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasSpecimenWorkflowIdentifier </td> <td> unique identifier of the specimen workflow </td> </tr> <tr> <td> hasSpecimenWorkflowDescription </td> <td> brief description of the specimen workflow </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of planned activities that invlove specimen processing that is captured in this workflow </td> </tr> <tr> <td> hasSpecimeWorkflowNodes </td> <td> activity nodes in the specimen workflow diagram </td> </tr> <tr> <td> hasSpecimenWorkflowTransitions </td> <td> a transition connects two nodes on the specimen workflow diagram to indicate the temporal sequence of the two nodes; it also contains any conditions on the transition. </td> </tr> </table> SpecimenWorkflowEntity true An abstract class that is the superclass of all classes relevant to specimen workflow SpecimenWorkflowNode An abstract node on the specimen workflow diagram.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasLabel </td> <td> display label </td> </tr> <tr> <td> hasTransitionRestriction </td> <td> specifies the collective split/join transition constraint on a set of transitions from or to a node. </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of specific planned activities that involve specimen processing and where the node is part of the processing workflow. </td> </tr> </table> SpecimenWorkflowTransition Information on transition from one node to another node in the specimen workflow diagram. It specifies the temporal sequence of the nodes in the diagram.<br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> :FROM </td> <td> the <b><i>from</i></b> node in the transition </td> </tr> <tr> <td> :TO </td> <td> the <b><i>to</i></b> node in the transition </td> </tr> <tr> <td> transition_condition </td> <td> the condition under which the transition happens </td> </tr> </table> StartActivity Start activity of the specimen workflow.<br><br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> hasLabel </td> <td> display label </td> </tr> <tr> <td> hasTransitionRestriction </td> <td> specifies the collective split/join transition constraint on a set of transitions from or to a node. </td> </tr> <tr> <td> hasAssociatedPlannedActivities </td> <td> list of specific planned activities that involve specimen processing and where the node is part of the processing workflow. </td> </tr> </table> Transition TransitionRestriction specifies the collective split/join transition constraint on a set of transitions from or to an event. <br><br> <table border="1"> <tr> <th> Attribute </th> <th> Comment </th> </tr> <tr> <td> label </td> <td> </td> </tr> <tr> <td> split_constraint </td> <td> specifies the transition restriction when there are more than one outgoing transitions from an event. It takes the values AND or XOR. If the value is AND, then all the transitions are evaluated for possible transition, and all possible (transition condition evaluates to true) transitions are taken. If the value is XOR, then the outgoing transitions are evaluated in order, and the first transition that is possible is taken. The AND constraint allows concurrent transitions from the <i><b>from</b></i> event. </td> </tr> <tr> <td> join_constraint </td> <td> specifies the transition restriction when there are more than one incoming transitions to an event. It takes the values AND or XOR. If the value is AND, then all the transitions are evaluated for possible transition, and the transition is taken only when all transitions are possible. If the value is XOR, then the outgoing transitions are evaluated for possible transition, and the transition is taken when one of the transitions is possible. The AND constraint allows sychronizing multiple paths at a <i><b>to</b></i> event. </td> </tr> </table> orgont:Bio-Repository orgont:ClinicalLaboratory orgont:CoreLaboratory orgont:Facility orgont:StudySite prtont:Encounter prtont:PlannedActivity prtont:Protocol DIRECTED-BINARY-RELATION protege:DIRECTED-BINARY-RELATION PAL-CONSTRAINT owl:Thing <table border="1"> <tr> <td> <b><i>Version</i></b> </td> <td> 0.97 </td> </tr> <tr> <td> <b><i>Date</i></b> </td> <td> 3/2/2007<br> </td> </tr> </table> <br> en Author: Ravi Shankar, Stanford Medical Informatics <table border="1"> <tr> <td> <b><i>Version</i></b> </td> <td> 0.97 </td> </tr> <tr> <td> <b><i>Date</i></b> </td> <td> 3/2/2007<br> </td> </tr> </table> <br>