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About this document

This is an official Request for Comment (RFC) for Add your text here.

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7/20/2006: Open for public comment.

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BioDataServer class was used to import Ontologies, annotations, and synonyms. Basically, the constructor takes manifest file location and load data from individual data sources (annotation files, ontology file, and synonym file) specified in the manifest file. Current problems are the following:

  1. File format used in the manifest file is out-of-date.
  2. New file formats (OBO and Gene Association) are converted into old format before loading.
  3. Many entries in the new file formats are lost in the file format conversion process.
  4. The imported ontologies are stored in a huge map, not in a DAG which is the original data structure of GO.
  5. Because GO terms are imported as a huge map, it makes no sense for many biologists.
  6. Name mapping service is not sophisticated.
  7. GO Annotations are mapped based on levels, which does not make sense for biologists.

To solve problems above, new BioDataServer should supports the following:

Biological Questions / Use Cases

General Notes

There are several open-source applications/libraries which can be used in this project:


Deferred Items

Open Issues

Backward Compatibility

Expected growth and plan for growth


Implementation Plan

Current Implementation

User Interface

The following is a temporary GUI for the new classes. This may be changed.




GaryBader - 2006-08-07 17:48:48

The BioJava Ontology class seems overly complex.  I use BioJava a lot and find it difficult to work with.  A simple Ontology class, similar to the current one, which allows searching by terms and traversing the DAG (get parents, children, all ancestors), etc. may be more useful.

KeiichiroOno - 2006-09-19 16:50:40

Although BioJava interface is implemented in this version, users still can use old style methods like "get parent/chindren."  (not yet implemented, but will be available soon).

Internally, this implementation of Ontology is simply a CyNetwork, all functionality in the older versions can be implemented easily in the new one.

Scooter - 2007-01-28 06:35:23

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BioDataServerRFC (last edited 2009-02-12 01:03:40 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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