KEfED + OoEVV

OoEVV Software

We have developed a command-line application for manipulating OoEVV components (and for extracting reporting statistics from our current prototype version of BioScholar's KEfED editor tool). 

Downloads

The system is at prototype level of development (alpha) and is available for download.

MacOS Installer - kefedAdmin_macos_0_0_2.dmg
Windows Installer - kefedAdmin_windows_0_0_2.exe
Linux/Unix Archive kefedAdmin_unix_0_0_2.tar.gz

These are quite large (~110MB) since they include unit-test data as they are prototypes, not trimmed release versions.

 

Installation

The installation should be a simple, one-click install. To use the Database functions, you must have MySQL pre-installed.

Running OoEVV Commands 

The system installs as a command line application providing functions that may be exectuted from the command line. Usage information can be obtained by running each command with no arguments.

1) Commands to generate KEfED & OoEVV components

generateOoevvSpreadsheet <Spreadsheet-file-path>

This generates a preformatted OoEVV spreadsheet in the location specified.

generateKefedDatabase <dbname> <login> <password>

This creates a MySQL database (with the specified name) with the appropriate underlying schema needed for the OoEVV applications. The schema also contains some tables related to future KEfED implementation. The <login> and<password> arguments must be a valid MySQL login with administrator permissions. The <dbname> argument denotes the desired name of a MySQL database that will be used in subsequent commands.

generateOoevvOdpOwl <owl-file-path>

This creates a base OWL file that contains only the OoEVV class definitions (this is the base ODP uploaded to the BioPortal system).

2) Commands to upload OoEVV elements to a database

ooevvSpreadsheetToDatabase <Spreadsheet-file-path> <dbName> <login> <dbPassword> [bioPortalLookup?]

The <Spreadsheet-file-path> is the full path to the spreadsheet to be uploaded. The <dbname><login>, and<password> are the same login details used to generate the underlying OoEVV/KEfED database. If the[bioPortalLookup?] flag is set to any value, the system will fully evaluate all external ontology linkages by querying Bioportal, potentially slowing down the program's execution.

ooevvDirToDatabase <xl-dir> <db-name> <db-login> <db-password> [ontology-lookup?]

The <xl-dir> is the full path to the directory containing a number of spreadsheets to be uploaded. The <db-name><db-login>, and <db-password> are the same login details used to generate the underlying OoEVV/KEfED database. If the[ontology-lookup?] flag is set to any value, the system will fully evaluate all external ontology linkages by querying Bioportal, potentially slowing down the program's execution.

3) Commands to generate OWL files

databaseToOoevvOwl <database-name> <login> <dbPassword> <owl-file>

The <database-name><login>, and <dbPassword> are the same login details used to generate the underlying OoEVV/KEfED database. The <owl-file> argument is the path to the output OWL file to be generated.

ooevvSpreadsheetToOwl <Spreadsheet-file-path> <Owl-file-name> [bioPortalLookup?]

The <Spreadsheet-file-path>, is the full path of the spreadsheet to be converted to OWL. The <owl-file-name>argument is the name of the output OWL file to be generated (if the file does not already exist), or added to if it exists already. If the [bioPortalLookup?] flag is set to any value, the system will fully evaluate all external ontology linkages by querying Bioportal, potentially slowing down the program's execution. Thus, this command may be used repeatedly over multiple input files to generate an OWL representation for several OoEVV element sets.

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