Batch Access to Indexing Initiative Tools

The Batch facility provides access to some of the Natural Language Processing tools being developed in the Applied Clinical Informatics Branch of the Lister Hill National Center for Biomedical Communications, an Intramural Research Division of the National Library of Medicine.

Terms of Service    Batch MetaMap    Batch MTI    Batch SemRep    Batch Generic

Batch Access facilitates the processing of large sets of data using one of our tools once you have selected the appropriate tool and options for your work. It is generally better to submit a single large file instead of several smaller files if you are processing with the same tool and options.

The various submission forms allow you to specify an input file to be processed and select options relevant to the individual programs. Upon submission of a job, you will be provided with a reference number for checking on the status of your job. The scheduling program will automatically distribute the processing of the data across multiple workstations to help speed up processing and email you when the job has completed.

Yes! The Batch facility provides a Batch Job Status Window allowing you to monitor the progress of your batch while it is running. Note: A window will appear in the top left corner of your screen depicting the current status of all jobs in the queue.

The Batch facility processes your data using our Scheduler which distributes your batch across a large pool of clients. You will be notified via email with instructions on how to download your results when the batch finishes and will have a reasonable amount of time to download the results file after the batch completes before we remove the batch.

Yes! The Batch Job Status Window provides a "Suspend My Job" button for this purpose. If you happen to see your batch generating a large number of errors, please suspend it.

For Batch access to our tools, you must have activated a UMLS Terminology Services (UTS) account. For more information please visit our Help about UTS accounts Web page. This account is free with only the minor requirement of filing a brief annual report on your use of the UMLS.

Please Note: You must have an UTS Account to run any of the tools in Batch Mode. Please see the What are the requirements to use the Batch facility? question for more details and requirements.

The Generic Batch with Validation tool is mainly used to run command line options for the list of tools above, you also have the option of specifying a Generic program to be run using the Scheduler. If you choose to run your own Generic program, you will be prompted for the name of the command and any environment variables needed to run the command. Note: For security reasons, it is assumed the command originates in /nfsvol/nls/bin and "../" notation is not allowed in the pathing.

IMPORTANT: With this option, your Generic program MUST specify the following at the end of the resultant file: "<<< EOT >>>\n" without the quotes. This is less-than, less-than, less-than, space, EOT, space, greater-than, greater-than, greater-than. This is a single line with the marker starting at the beginning of the line and followed by a newline character. This marker line MUST also be the last line in the resultant file. This is normally accomplished by adding " -E" at the end of the argument list.

  • Batch Job Status Window: A window will appear in the top left corner of your screen depicting the current status of all jobs in the queue.

  • Suspend Submitted Job: Allows you to stop execution of any job currently running that you personally own. The current state of the job is saved for you upon suspension of execution

  • Resume Submitted Job: Allows you to resume execution of a Suspended Job exactly where it was when it was suspended.

  • Rerun Submitted Job: Allows you to rerun a batch job from the beginning of the batch.

Please review our Help Information Web page. This page describes what tools are available, and more importantly, details the various input file formats that are recognized by the tools. Please review the Help Information page prior to submitting your first request to ensure that there are as few problems as possible - your consideration is greatly appreciated.

If you still have questions or concerns after reviewing the Help Information page, please feel free to contact us at: and we will try to assist you.

  • Mega Batch: Special Access is required to run a Mega Batch.