NIH | National Cancer Institute | NCI Wiki  

Known Issues

The templates do not import correctly so there will be some broken (red) links on the concept pages.

Installation Process

The installation will take place in four separate steps.

  1. Use a bat file to extract the metadata about the concepts and write them as files into a directory.
  2. Run a php file to read the files and publish them to the Wiki.
  3. Edit the Main page to show the ontology hierarchy
  4. Import the templates into the Wiki

Setup and configuration

  1. Download and unzip the LexWikiPublisher 1.0 zip file.
  2. Open the lexWikiPublisher.prop file and enter the configuration information

The following are the configuration variables along with an example for each.

Required configuration information

logfile - location to store the published concepts

configpath - the path to the configuration file in the LexEVS installation

csn -the code system name to be published

ccd - the concept code at the root of the hierarchy

wiki - the name of the wiki
LexWiki test

template - SMW template name

formname - the name of the semantic mediawiki form

Optional configuration information

republishexistingpages - Republish existing pages?

propertiesonly - If you want to get properties and associations published only

vsformname - the name of the semantic mediawiki form for value sets

user - Wiki user name
Wiki user name

pwd - Wiki user password
Wiki user password

self - is the selected node to be published?

batch - will all the children of the selected node be published?

server - the server where the wiki is located

port - the port number where the wiki is setup

batchsize - number of concepts to process in each batch

namespace - the over riding namespace to use for pages
LexWiki master

startPage - the starting page where index.php is the default

Extracting concepts from LexEVS

  1. Be sure the directory configured for the logfile variable exists and is write enabled.
  2. Run the lexWikiPublisher file useing the bat file or shell script.

Publishing to the Wiki

  1. Open a command prompt in the lexwiki's maintenance directory
  2. Run the publish php using the directory location of the files created during the lexEVS as the only argument
    php publish.php /home/myhomedir/tobepublishedpages

Displaying the category tree

  1. Log in to the Wiki and display the Main Page.
  2. Click on the Edit tab at the top of the page.
  3. Update the information between the cateegorytree tags to match your onotology information
    Category BGT Gene Kind(B179) not found
    &nbsp:&nbsp:&nbsp:BGT - the coding scheme name
    &nbsp:&nbsp:&nbsp:Gene Kind - the root node for the Ontology
    (B179) - short name for the root node
    Category NPO_Entity(Entity) not found

Importing the templates

  1. From the wiki, select SpecialPages.
  2. On the SpecialPages, select import file.
  3. Import the templates which correspond to the ontology you created.