• Several piper files are included in cTAKES that are capable of running typical pipelines, including the Default Clinical Pipeline.
• Create your own piper files to build custom pipelines.
• Run piper files using a GUI, from the command line(Shell-Scripts#runpiperfilesh), or programmatically.

Basic Pipelines
Partial Pipelines
Pipelines with Sectionizer

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Thread-Safe Basic Pipelines
Thread-Safe Partial Pipelines
Thread-Safe Pipelines with Sectionizer

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Piper files containing pipelines that do not detect Sections or Lists.

Name	Description
Cnlpt Negation	This is an example piper file that will spin up a complete pbj pipeline.
Default Advanced Pipeline	Pipeline with degree-of and location-of relations, events, times, temporal relations, document creation time relations and coreferences.
Default Coref Pipeline	Pipeline with coreference resolution.
Default Fast Pipeline	Commands and parameters to create a plaintext document processing pipeline with UMLS entity lookup.
Default Relation Coref Pipeline	Pipeline with degree-of and location-of relations and coreference resolution.
Default Relation Pipeline	Clinical Pipeline with degree-of and location-of relations.
Default Relation Temporal Pipeline	Clinical Pipeline with degree-of, location-of, events, times, temporal and event-doc creation time relations.
Default Temporal Coref Pipeline	Pipeline with events, times, temporal relations, document creation time relations and coreferences.
Default Temporal Pipeline	Clinical Pipeline with events, times, event-event and event-time relations plus event-document creation time relations.
Default Tokenizer Pipeline	Commands and parameters for a small tokenization pipeline.
Full Tokenizer Pipeline	Commands and parameters for a small tokenization pipeline with sections, paragraphs and lists.
Pbj Starter	This is a piper file that will perform initial steps required for running a ctakes-pbj pipeline.
Pbj Stopper	This is a piper file that will perform final steps required for stopping a ctakes-pbj pipeline.

Piper files containing partial pipelines that cannot run alone, but are intended to be included in full pipelines using the piper load command.

Name	Description
Assertion Sub Pipe	Commands and parameters to create a default entity attributes processing sub-pipeline.
Attribute Cleartk Sub Pipe	Commands and parameters to create a default entity attributes processing sub-pipeline.
Chunker Sub Pipe	Commands and parameters to create a default chunker processing sub-pipeline.
Coref Sub Pipe	Commands and parameters to create a default coreference processing sub-pipeline.
Dictionary Sub Pipe	Commands and parameters to create a dictionary lookup sub-pipeline.
Ne Contexts Sub Pipe	Partial pipeline to add assertion (e.g. negation, uncertainty) attributes based upon context.
Relation Sub Pipe	Commands and parameters to create a default relation extraction sub-pipeline.
Temporal Sub Pipe	Commands and parameters to create a temporal processing sub-pipeline.
Windowed Attribute Cleartk Sub Pipe	Commands and parameters to create a default entity attributes processing sub-pipeline for large files. This is not a full pipeline.

Piper files containing pipelines that detect Sections and Lists.

Name	Description
Sectioned Advanced Pipeline	Pipeline with section, paragraph and list detection, degree-of and location-of relations ...
Sectioned Coref Pipeline	Pipeline with section, paragraph and list detection and coreference resolution.
Sectioned Fast Pipeline	Commands and parameters to create a plaintext document processing pipeline with Sections, paragraphs and lists.
Sectioned Relation Coref Pipeline	Pipeline with section, paragraph and list detection, degree-of and location-of relations and coreferences.
Sectioned Relation Pipeline	Clinical Pipeline with section, paragraph and list detection and degree-of and location-of relations
Sectioned Relation Temporal Pipeline	Clinical Pipeline with sections, paragraphs, lists, degree-of, location-of, events, times, temporal and event-doc creation time relations.
Sectioned Temporal Coref Pipeline	Pipeline with section, paragraph and list detection, events, times, temporal relations and document creation time relations.
Sectioned Temporal Pipeline	Clinical Pipeline with sections, paragraphs, lists, events, times, temporal and event-doc creation time relations.

Piper files containing pipelines that do not detect Sections or Lists. Thread-Safe Annotation Engines and Writers are used in these pipelines.

Name	Description
Ts Default Advanced Pipeline	Thread-safe Pipeline with degree-of and location-of relations, events, times, temporal relations, document creation time relations and coreferences.
Ts Default Coref Pipeline	Thread-safe Pipeline with coreference resolution.
Ts Default Fast Pipeline	Commands and parameters to create a thread-safe plaintext document processing pipeline with UMLS lookup.
Ts Default Relation Coref Pipeline	Thread-safe Pipeline with degree-of and location-of relations and coreference resolution.
Ts Default Relation Pipeline	Thread Safe Default Clinical Pipeline with degree-of and location-of relations
Ts Default Relation Temporal Pipeline	Thread Safe Clinical Pipeline with degree-of and location-of relations, events, times, temporal abd event-doc creation time relations.
Ts Default Temporal Coref Pipeline	Thread-safe Pipeline with events, times, temporal relations, document creation time relations and coreferences.
Ts Default Temporal Pipeline	Thread Safe Default Clinical Pipeline with events, times, event-event and event-time relations plus event-document creation time relations
Ts Default Tokenizer Pipeline	Commands and parameters for a small thread-safe tokenization pipeline.
Ts Full Tokenizer Pipeline	Commands and parameters for a small thread-safe tokenization pipeline with sections, paragraphs and lists.

Piper files containing partial pipelines that cannot run alone, but are intended to be included in full pipelines using the piper load command. Thread-Safe Annotation Engines and Writers are used in these partial pipelines.

Name	Description
Ts Attribute Cleartk Sub Pipe	Commands and parameters to create a thread-safe default entity attributes processing sub-pipeline.
Ts Chunker Sub Pipe	Commands and parameters to create a thread-safe default chunker processing sub-pipeline.
Ts Coref Sub Pipe	Commands and parameters to create a thread-safe default coreference processing sub-pipeline.
Ts Dictionary Sub Pipe	Commands and parameters to create a default dictionary lookup sub-pipeline.
Ts Relation Sub Pipe	Commands and parameters to create a relation extraction sub-pipeline.
Ts Temporal Sub Pipe	Commands and parameters to create a thread safe temporal processing sub-pipeline.

Piper files containing pipelines that detect Sections and Lists. Thread-Safe Annotation Engines and Writers are used in these pipelines.

Name	Description
Ts Sectioned Advanced Pipeline	Thread-safe Pipeline with section, paragraph and list detection, degree-of and location-of relations ...
Ts Sectioned Coref Pipeline	Thread-safe Pipeline with section, paragraph and list detection and coreference resolution.
Ts Sectioned Fast Pipeline	Commands and parameters to create a thread-safe plaintext document processing pipeline with Sections, paragraphs and lists.
Ts Sectioned Relation Coref Pipeline	Thread-safe Pipeline with section, paragraph and list detection, degree-of and location-of relations and coreferences.
Ts Sectioned Relation Pipeline	Thread Safe Clinical Pipeline with section, paragraph and list detection and degree-of and location-of relations.
Ts Sectioned Relation Temporal Pipeline	Thread safe Clinical Pipeline with sections, paragraphs, lists, degree-of, location-of, events, times, temporal and event-doc creation time relations.
Ts Sectioned Temporal Coref Pipeline	Thread-safe Pipeline with section, paragraph and list detection, events, times, temporal relations and document creation time relations.
Ts Sectioned Temporal Pipeline	Thread safe Clinical Pipeline with sections, paragraphs, lists, events, times, temporal and event-doc creation time relations.