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add annotation on PGDB

asked 2017-08-30 10:24:48 -0500

mikeaalv gravatar image

I have some PGDB and I need to add some annotation on the gene pages. I cannot change it by change genbank file, because it is already constructed PGDB with several "Refine" after build. In this situation, is there any methods to add some more information for each genes directly in the PGDB?

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Is modification on data file of PGDB possible in this situation? I am not quite sure which file is storing annotation information for individual genes. I have try update build for revised annotation, but the program just crash with error that I don't understand.

mikeaalv gravatar imagemikeaalv ( 2017-08-30 13:12:11 -0500 )edit

The error is: Error: #<"CPLX66-188" instance frame in HUMANBASE[F] @ #x107bd64362> must be a class frame in KB HUMANBASE

mikeaalv gravatar imagemikeaalv ( 2017-08-30 13:12:21 -0500 )edit

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answered 2017-08-30 16:49:13 -0500

Suzanne Paley gravatar image

If you just want to make changes to a handful of genes, you are probably best off using the regular editing tools and editing each gene/protein individually rather than editing the genbank file and going through PathoLogic. If you have large-scale changes to make across large numbers of entries, then yes, the Update Build for Revised Annotation is the correct command to use (although if the changes are fairly simple, and you know how to program a little bit, you might be able to make your changes programmatically through one of our APIs).

I also do not understand why you are getting the error you report (or why it is referring to a protein in HumanCyc at all -- I assume this is your own PGDB and you are not attempting to change our human database, correct?). Does your PGDB contain either the reaction RXN66-32 or the pathway PWY66-11? You can check for these using the Search by Name or Frame ID command under the Reaction and Pathway menus in the Navigator window. If they are present, delete them by right-clicking on the name and selecting Delete Frame from the Edit menu (I'm not sure how they would have gotten there, but they are human-specific, so don't belong in a PathoLogic-generated PGDB). Then try running the Update Build... command again. If they are not present, then I am even more baffled. I will need to ask you to send us a stack backtrace. I am assuming that you see the error because the software breaks into the debugger in your terminal window, correct? If so, at the debugger prompt, please type: :zoom :count :all and send the result to If instead of breaking into the debugger, you saw the error message in a popup window, then debugging info should have been saved to a file error.tmp in your home directory -- please send that file to

In general, if you get error messages like this, you will need to provide us with this debugging information, along with a description of how to reproduce the problem.

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It is actually C. elegans genome derived pathway and RXN66-32 or PWY66-11 are all not found. The PGDB were constructed by an earlier version of pathway-tools. Is that related? The error are in terminal(EC:) and the windows is not working. I will send there after reproduce it. I also find Import Frame and Export Frame. Could that be used for changing some gene related information?

mikeaalv gravatar imagemikeaalv ( 2017-08-30 20:20:25 -0500 )edit

Additionally, I am just curious where the information is storing in PGDB directory. Is it in /data? I only find fasta and graph there.

mikeaalv gravatar imagemikeaalv ( 2017-08-30 20:31:01 -0500 )edit

The pgdb data is all stored in the kb directory in the .ocelot file, which, if the PGDB has been updated and saved in the last year or so, will be a binary file, so not human-readable. I don't know what kinds of changes you are trying to make, but you can read about Frame Import/Export in section 5.6 of the user guide and decide whether or not it meets your needs. This might be a good way to go if you're just adding or modifying names, synonyms, gene start/end positions, comments, or other fields that just contain data rather than links to other database objects. It would not work for updating functional assignments.

Suzanne Paley gravatar imageSuzanne Paley ( 2017-08-30 23:39:32 -0500 )edit

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Asked: 2017-08-30 10:24:48 -0500

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Last updated: Aug 30 '17