The Sci2 Tool is an 'empty shell' filled with plugins. Some plugins run on the core architecture, OSGi and CIShell (see Section 7. Extending the Sci2 Tool). Others convert loaded data into in-memory objects, formatted for different algorithms to read it. The algorithm plugins themselves can be divided into different menus, in this case data preparation, preprocessing, analysis, modeling and visualization. Users are not limited to using pre-packaged plugins; instead, they can create, download, share, and import their own.
There are two ways plugins can be added to the menu. First, if an algorithm is listed in the default_menu.xml file, which is found in the configuration/ directory of a CIShell tool, it is added in the place specified by the default_menu.xml file. Secondly, if an algorithm is not listed in this file, but has specified a menu_path property in the algorithm.properties file, the menu manager CIShell service will add it to the appropriate menu, as described in the by the menu_path property's value (for example, Analysis/additions will place an algorithm on the bottom of the Analysis menu).
It is possible to extend Sci2 Tool, by adding plugins related to database functionalities and Cytoscape tool (open source software platform for visualizing networks).
To add Database and Cytoscape plugins to Sci2
- Download these files that contain additional plugins to add Database and Cytoscape plugins to Sci2:
- DatabasePlugins.zip (unzip to obtain the jar files that will be inside a folder named DatabasePlugins)
- org.textrend.visualization.cytoscape_0.0.3.jar
- Copy these jar files to the directory /plugins of Sci2directory
- Download the file default_menu.xml and copy it to the directory configuration/ under Sci2 directory, replacing the older version of this file.
- The next time the Sci2 Tool is loaded after this modifications, this additional plugins will appear as new menu items.
Algorithms available at extended version
Database
ISI
- Merge Identical ISI People – Merges all people in an ISI database who have the same name
- Suggest ISI People Merges – Generates a pre-annotated merging table based on a user-selected threshold and string similarity metric.
- Merge Document Sources – Merge document sources of documents and references based upon known name variants and abbreviations.
- Create Document Source Merging Table –
- Match References to Papers – Matches references to papers if they have the same first author, source (journal), start page, volume, and year.
--------------------------------------------- - Extract Authors – Outputs a table containing one row per author in the database.
- Extract Documents – Outputs a table containing one row per document in the database.
- Extract Keywords – Outputs a table containing one row per keyword in the database.
- Extract Document Sources – Outputs a table containing one row per document source in the database.
--------------------------------------------- - Extract Authors by Year – Outputs a table containing the amount of publications per author per year.
- Extract References by Year – Outputs a table containing the amount of references to a publication per year.
- Extract Original Author Keywords by Year – Outputs a table containing one row per original author keyword per year.
- Extract New ISI Keywords by Year – Outputs a table containing one row per new ISI keyword per year.
--------------------------------------------- - Extract Authors by Year for Burst Detection – Used for author burst detection.
- Extract Documents by Year for Burst Detection – Used for word occurrence based burst detection.
- Extract Original Author Keywords by Year for Burst Detection –
- Extract New ISI Keywords by Year for Burst Detection –
- Extract References by Year for Burst Detection –
--------------------------------------------- - Extract Longitudinal Summary –
--------------------------------------------- - Extract Co-Author Network –
--------------------------------------------- - Extract Author Citation Network –
- Extract Document Citation Network (Core Only) –
- Extract Document Citation Network (Core and References) –
- Extract Document Source Citation Network (Core Only) –
- Extract Document Source Citation Network (Core and References) –
--------------------------------------------- - Extract Document Co-Citation Network (Core Only) –
- Extract Document Co-Citation Network (Core and References) –
- Extract Document Source Co-Citation Network (Core Only) –
- Extract Document Source Co-Citation Network (Core and References) –
- Extract Author Co-Citation Network
--------------------------------------------- - Extract Author Bibliographic Coupling Network –
- Extract Document Bibliographic Coupling Network –
- Extract Document Source Bibliographic Coupling Network –
Visualization
Networks
- Cytoscape
