BioRAT Documentation

Running BioRAT from the command line

Most aspects of BioRAT can be accessed from the command line. This may be more convenient for batch-driven high-throughput processes. Some examples are included in the software distribution (biorat_cl_windows.bat and biorat_cl_unix.sh). Consider this example:
java -Xmx1000m frontend.command -t data\templates\new_template.xml -a tmp\rat_doc_list.txt Reading from left to right, this starts Java, requests 1000Mb of memory, runs the BioRAT commannd interface, and specifies two options. The "-t" option specifies which set of templates to apply, and the "-a" option specifies an index file, which lists the locations of a set of text files which will be analysed. A full list of options is given below. These assume that the Java classpath has been specified to include the required library files. The "-Xmx1000m" option, which reserves memory, may not be needed for some commands, especially file downloading commands. Template processing tends to require more memory, and so this option may be required then.
Here are some more examples:
java -Xmx1000m frontend.command -p 9920921
java -Xmx1000m frontend.command -f data/papers/9920921_abs.txt -t data\templates\fish.xml
The first of these commands instructs BioRAT to download an abstract from PubMed with the given PubMed id nunber. By default, this will have "_abs.txt" appended to the PubMed id to form a filename, and then saved into the data/papers directory. Hence the second command specifies that file, and instructs BioRAT to apply the "fish" templates to that directory.

General settings:
-h Display this help message
-ver Display version information
-i Use specified file as BioRAT initialisation file
Template processing:
-f Analyse specified file
-d Analyse all text files (*.txt) in specified directory
-a Analyse all text files listed in given file
-t Specify location of template index file (.xml)
-o Specify filename root to store results in
-g Specify location of gazetteer index file (.lst)
-r Specify target directory in which to store results
File downloading:
-p Download abstract with given PubMed ID
-w Download full length paper from web with corresponding PubMed ID
-l Download all abstracts with PMIDs listed in given file (comma- or newline-separated)
-b Download full length papers with PMIDs listed in given file (comma- or newline-separated)
-m Specify maximum number of simultaneous download operations (default=5)
-u Specify username and password (e.g. for firewall access)

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