Updating GMBuilder to work GO's OBO XML Files - lmu-bioinformatics/xmlpipedb GitHub Wiki

Occasionally, the Gene Ontology obo-xml file schema will change, rendering GMBuilder unable to process GO's obo-xml files. When this occurs, the dtd file for obo-xml will need to be manually edited. The error message produced by GMBuilder will state which new relations are necessary.

1. XSD2DB

After the DTD file has been completed, it needs to be uploaded, as xsd2db only works on files on the internet, not locally. Currently, the manually edited dtd files are located in the code in godb/xsd. Then, run xsd2db on the file. Documentation on how to run xsd2db can be found on the wiki here.

2. GODBPostProcessor

xsd2db will produce a series of files that need to be further processed by godbpostprocessor. GodbPostProcessor can be found in the code in godb/tools. Build and run GODBPostProcessor. It will prompt you to select a specified .sql and .hbm file. Select those files. They will then be processed so that GMBuilder is capable of utilizing them. Rename the .sql file that was specified to "godb.sql". In your GMBuilder directory, replace godb.sql with the .sql file that was edited by godbpostprocessor.

3. Building

Once post processing is complete, the folder created by xsd2db can now be safely built. Build it to produce a .jar file, and name that jar "godb.jar". In your GMBuilder directory, replace godb.jar with the new .jar file that was created.

4. SQL editing

There is one last step that needs to be performed before GMBuilder can be fully run. gmbuilder.sql combines the contents of several .sql files, including godb.sql. Find the section in gmbuilder.sql that corresponds to the contents of godb.sql. Then, replace the section in gmbuilder.sql with the contents of godb.sql, excluding the sections at the beginning that alter the tables.

5. Test

Now, create a new database and run the new gmbuilder.sql. Then, run GMBuilder. Test to see if GO Obo-xml processing completes successfully. The following error is expected:

Should everything complete successfully, GMBuilder is now configured to use the new format of the obo-xml file.