Jwoodlee Week 14

Milestone 3: Species Profile Creation

Majority of the procedure was from here.

Adding a Species Profile to GenMAPP Builder

In the Java perspective within Eclipse(change perspective on the top right), the following was executed.

Create the Species Profile

1. I exposed the contents of the src folder in my gmbuilder project.
2. Right-clicked on the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package and chose New > Class from the popup menu.
3. In the dialog that appears, I entered the following:
   • Name: ShigellaflexneriUniProtSpeciesProfile
   • Superclass: edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile
4. Clicked Finish. A new .java file within the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package was created.

Customize the Species Profile

• I opened the file that I just created.
• I added the following constructor block right below the public class line in the new file.

public ShigellaflexneriUniProtSpeciesProfile() {
    super("Shigella flexneri",
        623,
        "This profile customizes the GenMAPP Builder export for " +
            "Shigella flexneri" +
            " data loaded from a UniProt XML file.");
}

• I added the following method block right below the constructor block that I added above.

@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
    super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
    tableManager.submit("Systems", QueryType.update, new String[][] {
        { "SystemCode", "N" },
        { "Species", "|" + getSpeciesName() + "|" }
    });

    tableManager.submit("Systems", QueryType.update, new String[][] {
        { "SystemCode", "N" },
        { "Link", "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=~" }
    });

    return tableManager;
}

• I chose Organize Imports from the Source menu to make sure I had everything imported.

Add the Species Profile to the Catalog of Known Species Profiles

• Under edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles, I opened UniProtDatabaseProfile.java.
• Near the top of the file is a block that looks like this:

super("org.uniprot.uniprot.Uniprot",
    "This profile defines the requirements "
        + "for any UniProt centric gene database.",
    new SpeciesProfile[] {
    new EscherichiaColiUniProtSpeciesProfile(),
    new ArabidopsisThalianaUniProtSpeciesProfile(),
    new PlasmodiumFalciparumUniProtSpeciesProfile(),
    new VibrioCholeraeUniprotSpeciesProfile() });

• I added the species profile that I created to the block.

super("org.uniprot.uniprot.Uniprot",
    "This profile defines the requirements "
        + "for any UniProt centric gene database.",
    new SpeciesProfile[] {
    new EscherichiaColiUniProtSpeciesProfile(),
    new ArabidopsisThalianaUniProtSpeciesProfile(),
    new PlasmodiumFalciparumUniProtSpeciesProfile(),
    new VibrioCholeraeUniprotSpeciesProfile(),
    new ShigellaflexneriUniProtSpeciesProfile() });

• I saved changes and selected Organize Imports.

Build, Test, and Possibly Commit

1. I created a new distribution of GenMAPP Builder.
   • Expanded the custom project, scrolled down the build.xml and right clicked it. In the menu that appeared I clicked on Ant Build... (with ellipses). Now in the menu that appeared I deselected dist, and selected clean, dist in that order. The build order was now clean, dist so it will wipe the current version of genmappbuilder and create a new distribution. I clicked run.
2. With Trixie, we performed a new export run with this custom version of GenMAPP Builder. A new .gdb was created.
3. I checked the Systems table in the resulting .gdb with Microsoft Access and verified that it contained the custom information:
   • The record OrderedLocusNames was there with the species name under the Species column and our link URL under the Link column.
4. Opened up a gene in GenMAPP with the custom .gdb created to make sure the link that I inserted was working properly.
5. I then committed the custom version of GenMAPP builder to our GitHub branch.

Milestone 4: Species Export Customization

1. Trixie noticed that the microarray data has IDs that have CP#### and SF####.# not the typical SF####, which will need to accounted for.