This is a utility to update the contents of the protein lists which make up the different ontology views of proteins.
This script is not usable by external users of GPMDB; instead, this is a script used by maintainers of an installation to assist with curation of one set of data displays. As such, it is designed to run from the command line on a node of a GPMDB installation. This was done to facilitate automated updating of the ontology files.
There are two required arguments: the first is an ontology identifier such as BTO:0000131 (blood plasma proteins), GO:0005886 (plasma membrane proteins) or HS_CHR1 (proteins expressed from the genes of human chromosome 1); and the requested output type, which is either html, csv or txt.
If the html output type is specified, all three file types will be created, as the csv and txt versions of the information are linked to in the HTML generated by the script. Specifying either csv or txt will generate only the requested type.
The script will attempt to open an XML configuration file which is located in a directory specified within the script itself. The XML file contains details regarding the ontology name, identifier, location for the output file, and the list of protein accession numbers that makes up the collection. The script will then query the best_expect table and map tables in the GPMDB installation for information regarding the protein, and write the results out according to the given file type.
As this is a command-line script, the only output to the console is status updates (start and end time, number of proteins written to the requested file) and error messages from the database server or filesystem.
This script uses the following tables in GPMDB: best_expect. From EnspMapDB, map.