genomemap Files

Release notes for genomemap application version 1.0.0

Date: June 26, 2011

Project website: http://genomemap.sourceforge.net

This is the first release of the of the netbeans platform application for this project called as genomemap application. It can dynamically discover computations from multiple job modules. Currently, there is only one such module, Genomemap Jobs- OrganismData which installs the following features.


The following features are supported:


1. ProcessComplData: (Category: Organism Data)

From an unorganized assignment data format (known as complementation data) create the assignment.xml file. The complementation data has the Java properties file format, where the key is a gene label and the value is the assigned clone labels, separated by comma. The feature organizes the complementation data into the format assignment.xsd and creates an instance. The format of assignment.xsd uses an instance of OrganismData for this purpose. The feature only recognizes the genes and clones present in the instance of OrganismData and ignores the rest while processing the complementation data.

This feature has been used as a part of the process of creating the assignment data for data 1.0. Version 1.0 indicates a specific collection of raw data in a certain format. Some complementation data was available from Dr. Arnold (arnold_compl_data.txt) and some was generated using data from the Broad website (broad_compl_data.txt). These two were merged manually in a file (all_compl_data.txt) and the file was run with this feature to produce the global assignment data (assignment.xml). The instance of OrganismData used was created by the provider 'impl1'. Note that a the result of a provider is always reproducible i.e., it uses onyl deterministic steps (no probabilistic missing value algorithms are used). A provider uses a certain  format of the data and uses specific algorithms to clean the data. However, the specific version of the data (i.e., the URL of the data 1.0) and its linkage groups to be used are configurable. The linkage groups to be used can be specified by a comma separated list of the available linkage groups. For our analysis we used the URL 'organism_data_impl1' and all the available linkage groups (1,...,7).



2. ClassifyGenes: (Category: Organism Data)

This feature was used as a part of the process of creating the assignment data for data 1.0. To collect the complementation data from Broad, we needed to manually collect the clone assignments for all the genes in data 1.0. From all the genes available on the Broad website we needed to find the genes available in data 1.0, organized by the linkage groups. This feature was used exactly for this purpose. We created a list of all the gene names and ran it through this feature to find the desired genes. 

Clone labels have different formats in Broad and Arnold data and this feature does not recognize gene and clone labels in the complementation data if they do not match to that of the OrganismData instance used. To that end, we needed to check (check_broad_clone_names.groovy) and convert (convert_broad_clone_names.groovy) the clone labels.