Workflow : Information Extraction From Query

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Operation

The Information Extraction From Query Workflow allows you to set up some tasks over the results of a query, including Corpus creation (mandatory) and NER and RE Processes (optionally).

To run the workflow, you must select a Query object on the Clipboard and right click Workflow -> Information Extraction (From query) or click on the Workflow Information Extraction button in the Query View.


Workflow Syngenta1.png


Select Query Publications

The first step of the workflow is to select candidate publications to create a Corpus. If you have already selected publications using the Query View this information will already be present. After selecting the desired publications, press Next.


Workflow Syngenta2.png


Select Steps

The next step is to determine the tasks that will be executed by the workflow. The Corpus creation is mandatory but NER and RE processes can also be applied to this Corpus in subsequent operations. After selecting the tasks, press Next to continue.


Workflow Syngenta3.png


Create Corpus

(Mandatory)

The next step is to configure the corpus creation, where you have to select the name of the Corpus and its type.

Corpus Type

Abstract : : Only publications with abstracts will be considered.

Full Text : Only publications with full Text / PDF will be considered.

Retrieve PDF : Only publications with full Text / PDF will be considered, and a Journal Retrieval Process will be launched to collect all selected documents


Workflow Syngenta4.png


Workflow Syngenta4b.png


If you have selected only the task of corpus creation, the processing of your data will start after clicking ok. When this process finishes, you can see the results in the Workflow_Report

Otherwise, if other steps are included, press next to proceed to NER configuration.

Select NER Process

(Optional)

The next step is the configuration of an NER Process. Using the combo box (in blue), select the NER process configuration that is more suitable. For each NER Process, the specific settings appear under the combo box (area in orange)


Workflow NER Selection.png


NER - Based in Lexical Resources

You can select an NER process based in lexical resources. The configuration has two panels: Basic and Advanced:

Basic

Here, you can select one or more dictionaries to use as resources in the NER. For each dictionary, you can filter for classes, i.e. select which classes will be associated to the dictionary.


Workflow Syngenta5.png


Advanced Option

Expert users can configure some advanced options. These options are based in the operation NER - Lexical Resources: check details in NER - Lexical Resources


Workflow Syngenta5b.png


ABNER

Chemical Tagger

Linnaeus Tagger

If your workflow terminates in the NER process, the data processing will start after clicking ok. When the process finishes, you can see results the in the Workflow_Report

Otherwise, if an RE process will be conducted, press next to proceed to its configuration.

Select RE Process

(Optional)

The next step is the configuration of an REProcess. Using the combo box select the RE process that best serves your needs (in blue). For each RE Process, the specific settings appear under combo box (area in the orange box)


Workflow RE Selection.png


RE Based in POS-Tagging

You can select an RE Based in Natural Language processing. The configuration has two panels: Basic an Advanced.

Basic

Here, you can select the relation model


Workflow Syngenta6.png


Advanced

Expert users can configure some advanced options. These options are based in the RE operation detailed in: Relation Extraction


Workflow Syngenta6b.png


RE Cooccurrence

Bio Event Extraction

Processing

As the process proceeds you can check the status of activity looking at the progress bar


Workflow Syngenta7.png


Workflow Report

As a result of the process, a Workflow_report is shown.

Pre-Configuration

Default settings can be changed using the option Preferences in the Settings Menu and selecting Workflow -> Query Node


Workflow Query Preconfiguration.png