{"id":183,"date":"2012-11-25T15:52:14","date_gmt":"2012-11-25T15:52:14","guid":{"rendered":"https:\/\/www.nactem.ac.uk\/ucompare\/?page_id=183"},"modified":"2012-11-27T12:02:20","modified_gmt":"2012-11-27T12:02:20","slug":"example-workflow","status":"publish","type":"page","link":"https:\/\/www.nactem.ac.uk\/ucompare\/?page_id=183","title":{"rendered":"Example Workflow"},"content":{"rendered":"

In this example, we will develop a NLP workflow that identifies biomedical named entities (e.g., gene and protein names) in 100 abstracts retrieved from PubMed.<\/p>\n

Step 1: Adding a collection reader<\/h2>\n

The first NLP component in every UIMA\/U-Compare workflow is a collection reader. A collection reader is responsible for retrieving documents from a collection (e.g., online libraries like PubMed) and preparing the input for further processing by subsequent components. In this example, we will use Kleio Search<\/em>, which can be found in the component library, under Collection readers<\/em> category.<\/p>\n

\"Kleio<\/a>
\nKleio Search<\/em><\/a> is a semantic search engine, developed by NaCTeM<\/a>, which fetches MEDLINE abstracts matching a specific query. In our case, we use the query “content:CAT AND PROTEIN:”cat”<\/em>“, which retrieves documents that are relevant to the protein<\/strong> cat<\/em>.<\/p>\n

Step 2: Adding processing components<\/h2>\n

In this step, we need to add a biomedical Named Entity Recogniser (NER) component. From the available ones, we choose NeMine, which identifies genes and proteins in free text (ABNER, NLPBA<\/em> or Genia Tagger with Tokenisation<\/em> are also applicable NERs for this case).
\n
\n\"NeMine<\/a>
\nOnce we have placed NeMine in the workflow design panel<\/em>, we immediately observe that this component expects sentences as input. Hence, we first need to split the documents retrieved by Kleio Search<\/em> into sentences. To do so, we need to place a Sentence Splitter component before NeMine.
\n
\n\"Valid<\/a>
\nOur workflow is now valid (i.e., the input of components is compatible with the output of subsequent components).<\/p>\n

Step 3: Executing the workflow<\/h2>\n

We can execute a pipeline by simply clicking the play<\/em> button (it can be found under the workflow design panel). U-Compare will then start executing the components in our workflow, sequentially. Once U-Compare has finished processing the documents, a Session Results<\/em> window will pop up, as illustrated in the following screenshot.
\n\"Session<\/a>
\nA Session Results<\/em> window contains two tabs:<\/p>\n

\n