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[locrefdev] Re: Proposal for new GO Flat File format (fwd) [NCBI tracking system #15018423]

Michael Ovetsky ovetsky at ncbi.nlm.nih.gov
Thu May 29 07:47:47 PDT 2003


Hi All,

After reviewing new GO Flat File format proposal, I have an impression that
the best format to satisfy the stated design goals (Human readability, Ease
of parsing, Extensibility, Minimal redundancy) would be XML. 

1) Human readability
XML is humanly readable and self-explanatory 

2) Ease of parsing
There are plenty XML parsers for all possible platforms, so there will be no
need to write a new low-level parser.

3) Extensibility
New tags can always be added to the document definition

4) Minimal redundancy
Since XML describes tree-type data structures, it is easy to avoid
relational database-type redundancy.

Michael Ovetsky


On Fri, 25 Apr 2003, John Richter wrote:

>
> Hello, everyone. As promised at the last GO meeting, I've come up with a
> proposal for the new GO Flat File format (based largely on the format of
the
> GO.defs file), tentatively titled GO-EFF (Gene Ontology Extensible Flat
File).
> The proposal is attached to this email as a text file.
>
> Please consider this proposal carefully, and email the list with any
concerns
> you have. I have tried to come up with a design that is familiar, yet
usable,
> extensible, and compact.
>
> A warning: This proposal suggests discarding the current method of using
> indentation to indicate parentage, and adopting a more record-based
approach.
> If this is intolerable to our community, I have developed an alternate
> proposal that preserves the current document structure. However, I feel
that
> as the GO grows more expressive, the indentation-based method will grow
> harder and harder to parse, and harder and harder for humans to read. I
hope
> this proposal will address that problem, and remain palatable to users who
> have grown accustomed to the format that has served us well for so long.
>
> 	-John

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Sue Rhee                         	rhee at acoma.stanford.edu
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Tue, May 27 2003 10:05:22: Request 15018423 was acted upon(15046456)
 Transaction: Request created by maglott
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