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How do I convert a PDF document to text using MedScan?

You can convert a Full-text article in PDF format to text format using the tool ‘PDF to Text Converter’ in MedScan.

Below are steps to follow:

1. Open...

06/16/2010 Category: MedScan Text Mining Tools

How do I create a new entity?

Select the “Add” button located within the bottom menu bar in the pathway pane, and from the drop-down menu, select “Entity”.

In the Add New Protein window...

08/05/2008 Category: Working with Pathways, ResNet Databases and Ontologies

How do I deactivate my license in Pathway Studio 6 Desktop and activate my license in Pathway Studio 7 Desktop?

Note:  Before upgrading your Pathway Studio 6 desktop installation to Pathway Studio 7, please read the Technical Support Bulletin that describes the...

12/10/2008 Category: Installation and Maintenance

How do I export all the information in a pathway, including the proteins in a functional class?

Description:

When using Pathway Studio Desktop version or PC Client, export of pathway in tab-delimited format is possible, however, if the pathway includes...

03/24/2010 Category: Working with Pathways

How do I export an image of a pathway?

Select the file for export and select Export. A menu box appears with 3 export options.  The first two options export the file as a *.gpp file that can...

08/05/2008 Category: ResNet Databases and Ontologies, Working with Pathways

How do I export an image of my pathway I have generated?

There are four options for exporting an image of your pathway:

- Copy Picture to clipboard…: the picture is copied to your clipboard and can be...

08/05/2008 Category: Working with Pathways

How do I find the intersection between the entities of a group and a pathway?

You can select the members of a pathway that overlap with a group by performing the following steps:

1.  Right-click on the group icon in the explorer...

08/17/2008 Category: Working with Pathways

How do I find the intersection between two lists of groups?

Follow these steps to find the intersection between two lists of groups: 

1.  Open both list of groups in the list pane (ex. the results of a GSEA...

10/06/2008 Category: Working with Pathways, ResNet Databases and Ontologies

How do I find the overlap between two groups?

Select the first group by navigating to the folder where the group resides.  (Figure 1).

Open the file to see the tabular view of all the entities in the...

08/05/2008 Category: Experimental Data Analysis

How do I find the overlap between two pathways?

Figure 1.

First, ensure both pathways are in the same folder. Select both pathways (hold the Ctrl button down while successively selecting both with the mouse). Next,...

08/05/2008 Category: Working with Pathways

How do I import a list of proteins?

In the database pane, select Import.  From the drop-down menu select “Gene List”. The following dialog box appears (Figure 1). 

Identifies such...

08/05/2008 Category: ResNet Databases and Ontologies, Experimental Data Analysis

How do I make a publication quality (high resolution) image of a pathway?

There is two options to obtain a publication quality image of a pathway:

Option 1:1. Open your pathway2. Place your mouse pointer in a white area of the...

08/05/2008 Category: Working with Pathways

How do I save the list of proteins/entities that are the results of my database search?

Figure 1.

You can save the result of a database query by performing the following steps:1. Open a New Group window by selecting “New Group” in the Home tab2. Select...

08/05/2008 Category: Experimental Data Analysis

How do I save the results of Gene Set Enrichment Analysis, Sub-Network Enrichment Analysis or Find Pathway/Groups Enriched with Selected Entities?

For each of these analysis, the results are displayed in the list pane. The options to save these results depends on the Pathway Studio Edition:

Pathway...

01/26/2009 Category: Experimental Data Analysis

How do I share a pathway with someone that doesn’t have Pathway Studio?

You can create a HTML image file of your pathway using the option 'Save Pathway as HTML…'

You can access to this option in two different ways:

- click on...

08/05/2008 Category: Working with Pathways

How do I share an object (for example a pathway) located in my private space with the other users of a remote ResNet database in Pathway Studio Enterprise?

This is a two-steps process. You have first to publish the pathway in the public space. Then a manager of the database has to accept your published pathway....

02/08/2010 Category: Working with Pathways, ResNet Databases and Ontologies

How do I sort the experimental data according to p-values, names or fold-change?

Open the experiment in the experiment folder. Click on the appropriate header cell with the LEFT mouse button to perform the desired sorting function.

 

08/05/2008 Category: Experimental Data Analysis

How Do I Upgrade from Pathway Studio Trial Version to Pathway Studio Full Version?

Description:You have completed your limited time trial of Pathway Studio and have purchased a subscription “full” license. You would like to upgrade your copy...

08/04/2010 Category: Installation and Maintenance

How do I use MedScan to read a document I have on my local drive?

You can use MedScan to extract relationships for an individual file or from all files found in a directory. Files can be html or text or *.pdf documents (note:...

08/05/2008 Category: MedScan Text Mining Tools

How do I zoom in or out on a pathway?

Figure 2

The Zoom function scrollbar can be found at the top right hand side above the graphic pane (Figure 1).  Zoom in by moving the scroll bar from the - to +...

08/01/2008 Category: Working with Pathways

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