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About this document
This is an official Request for Comment (RFC) for Add your text here.
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Status
(6/28/2006) This page is still under construction.##Put the date and the status. Status can be e.g. "Not yet completely written", "Open for public comment", "Closed for public comment". There could be some explanation of the status
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Proposal
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:
- File format used in the manifest file is out-of-date.
- New file formats (OBO and Gene Association) are converted into old format before loading.
- Many entries in the new file formats are lost in the file format conversion process.
- The imported ontologies are stored in a huge map, not in a DAG which is the original data structure of GO.
- Because GO terms are imported as a huge map, it makes no sense for many biologists.
- Name mapping service is not sophisticated.
GO Annotations are mapped based on levels, which does not make sense for biologists.
To solve problems above, new BioDataServer should supports the following:
- Import everything in the OBO and Gene Association files.
Use CyNetwork class to store GO's DAG (like BinGO plugin)
- Import more general attribute files, not only GO.
Supports more general attributes. (Probably we should change the name to AttributeServer)
Directly convert attibutes into CyAttributes data structure, and avoid redundant data.
- Support for MySQL (popular DB in lifescience projects) connection.
- Support for XML attribute import based on XQuery or other light weight library
- Remote and local data source support.
Biological Questions / Use Cases
General Notes
There are several open-source applications/libraries which can be used in this project:
[http://www.cb.k.u-tokyo.ac.jp/aritalab/oka/software.html GO Viewer]
[http://www.psb.ugent.be/cbd/papers/BiNGO/ BiNGO Plugin]
Requirements
Deferred Items
Open Issues
Backward Compatibility
Expected growth and plan for growth
References
Implementation Plan
[:BioDataServerRFC/Implementation Plan:/Implementation Plan]