Re: [Obo-format] OBO spec 1.2 question

[Wacek K. <wa...@id...>]

  On 7/30/10 9:26 AM, Erick Antezana wrote:
> Hi,
>
> I was wondering whether the OBO spec 1.2 allows to have more that one
> 'remark' tag in a OBO file header? I thought only one was allowed...
> Anyway, the ChEBI ontology header, for instance, has various entries:
>
> format-version: 1.2
> date: 03:07:2010 16:31
> saved-by: pmatos
> default-namespace: chebi_ontology
> remark: ChEBI subsumes and replaces the Chemical Ontology first
> remark: developed by Michael Ashburner&  Pankaj Jaiswal.
> remark: Author: ChEBI curation team
> remark: ChEBI Release version 70
> remark: For any queries contact che...@eb...
> synonymtypedef: IUPAC_NAME "IUPAC NAME"
> synonymtypedef: FORMULA "FORMULA"
> synonymtypedef: SMILES "SMILES"
> synonymtypedef: InChI "InChI"
> synonymtypedef: InChIKey "InChIKey"
> synonymtypedef: BRAND_NAME "BRAND NAME"
> synonymtypedef: INN "INN"
>
> Could that be clarified in the next OBO spec (1.3)? I would prefer to
> have only one; otherwise, parsers would need to be a bit more
> "intelligent" and take into account the order in which the 'remark's
> appear...

In the OBO flat format specification 1.2 (quoted below), there is no 
remark to the effect that the header of an OBO file may include *at 
most* one tag-value pair with a specific tag, including the 'remark' 
tag.  The 'remark' tag is an optional tag, and just like with any other 
optional tag in the header section it seems to be perfectly legal to 
have more than one remark line.  (This is somewhat less reasonable for 
tags such as 'date-version' or 'date', which also seem, in the specs, to 
be allowed to have multiple occurrences in the header.)

The specification says,

"
In general, each stanza type expects a particular set of pre-defined 
tags. However, a stanza may contain any tag. If a parser does not 
recognize a tag name for a particular stanza, no error will be generated.
"

This might desirably be extended to say that any tag that is legal in a 
header or a stanza, may, unless explicitly stated otherwise, appear 
multiple times in the same section (perhaps with the exception of 
redundant identical tag-value pairs in the same section).  The 
'date-version' and 'date' tags might be subject to exceptions.

> @ChEBI, the 'remark' tag line should actually be the last one in the
> header (as specified in
> http://www.geneontology.org/GO.format.obo-1_2.shtml#S.3.5 )
>

The specification says,

"
Header tags should appear in the following order (...)
"

but it doesn't say they *must* in order for the file to be parsed 
successfully.  In general, the specification seems to use the term 
'should' with the rough meaning 'this is a wish, not conforming to it is 
not necessarily a crime'.

vQ

> cheers,
> Erick
>
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