Re: [Psidev-ms-dev] X-IMail-SPAM-URL-DBL Comments on dataXML0.9

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Hi Alexandre,

I can quickly answer question 1.  You're preferred form of fileName has
been requested by multiople parties, and the unofficial consensus is
that it should be of the form.

<fileName><![CDATA[....]]></fileName>

The issue of the the value of a controlled vocabulary term be in the
element content as opposed to an attribute has also been discussed, but
without apparent consensus.

We should build a concise list that we can work from at the conference.

Regards,

Kent
=20

> -----Original Message-----
> From: psi...@li...=20
> [mailto:psi...@li...] On=20
> Behalf Of Alexandre Masselot
> Sent: Wednesday, February 07, 2007 5:11 AM
> To: psi...@li...
> Subject: Re: [Psidev-ms-dev] X-IMail-SPAM-URL-DBL Comments on=20
> dataXML0.9
>=20
>=20
> Hi a few comments after a quick glance:
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> 1) Attribute limit (this was already a comment a few months ago)?
>=20
> <sourceFile id=3D"1" fileName=3D"ICAT_test4.RAW"=20
> filePath=3D"file://F:/for Jim" fileType=3D"RAW 2.0"
>=20
> we shall not put file name or whatever "rich" info into=20
> attribute, or will have to encode/decode it everytime. Think=20
> of all the strange character that can come here (every one,=20
> by far do not use [\w+] into ther file names...=20
> unfortunaltely Tag value (so possibly with CDATA) would be=20
> more than welcome.
>=20
> <fileName><![CDATA[....]]></fileName>
>=20
>=20
> The sam eproblem may occur with things like
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> <cvParam cvLabel=3D"TMO" accession=3D"TMO:1000001" name=3D"Filter"=20
> value=3D"+ c d Full ms2  445.35@cid35.00 [ 110.00-905.00]"/>
>=20
> no?
>=20
>=20
> 2)
> multiple charge
> I don't see any example of that in the example, but how will=20
> we handle multiple charges for
> * parent peak?
> * more difficult (as info is stored into an array):=20
> fragmentation peaks?
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> And I'm sure there is something for multiple moz for the precursor
>=20
> best regards
> Alex
>=20
>=20
> Fredrik Levander wrote:
> > Hello,
> >
> > After a quick inspection of dataXML0.9, the first=20
> impression is that=20
> > it looks very promising and that all people working with it=20
> have done=20
> > some great work in the fusing of the mz's.
> >
> > I've got some small specific comments which I guess you've already=20
> > discussed, but anyway:
> >
> > 1) The attribute "count" which can be found at some places=20
> > (softwareList, spectrumList etc) could be more of an=20
> obstacle than of=20
> > help. There is no easy way to validate that this number corresponds=20
> > with the actual number of list elements in the XML world. Such a=20
> > validation would require specific validators for each programming=20
> > language. In cases where the count attribute is not equal to the=20
> > number of elements in the list, there could be different parsing=20
> > results depending on if the implementation is using the 'count' or=20
> > standard parsing, the later ignoring the count attribute.=20
> Actually, the example file:
> >=20
> http://db.systemsbiology.net/projects/PSI/dataXML/tiny1.dataXML0.9.xml
> > is an example where the softwareList count=3D"2", but the=20
> actual number=20
> > of elements is 3.
> > I would suggest that either the 'count's are omitted, or=20
> PSIDEV should=20
> > at some time provide validators which verify that list=20
> lengths equals=20
> > to the count attribute. Another option is that the attribute is=20
> > documented only to be used for visual inspection of files, and that=20
> > the actual number of list elements can differ. Are any of=20
> the current=20
> > mzData-parsers using the 'count's anyway?
> >
> > 2) The indexing extension of dataXML.  It is evident that such an=20
> > indexing is useful for fast file access, and it should=20
> definitely be=20
> > part of the standard. However, if I understand the schema correctly=20
> > (no sample file yet), an indexed file would mean that the=20
> dataXML is=20
> > encapsuled within the <indexedDataXML>, with the indexing=20
> information=20
> > at the end of the file. Why not use a separate file for the=20
> indexing,=20
> > which references the dataXML file as an URI?  I think that=20
> would make=20
> > up for faster data access with the indexes in the beginning of the=20
> > file, even if the 'indexOffset' should allow for quick=20
> access to the=20
> > index. A small consideration is that the offset / indexes=20
> would differ=20
> > depending on if the file is opened in binary or text mode, at least=20
> > for large files on a Windows system. I know that it is=20
> working for RAP=20
> > and mzXML, but for new implementations which use other=20
> libraries and=20
> > file readers there may be problems. Anyway,  it should be=20
> made clear=20
> > that indexes (offsets) are for binary file reading (or text=20
> if that is=20
> > the case) The fileCheckSum would also become clearer with=20
> two separate=20
> > files. It is quite complex to have the fileCheckSum of the file=20
> > contained within the file itself, since the checksum is affected by=20
> > the writing of the actual checksum ... If the file checksum is=20
> > contained  in a separate file it is clear that the checksum is the=20
> > checksum of the actual dataXML, excluding the index file.
> > On the other hand it could be more handy to have just one=20
> file to work=20
> > with, but is it really such an advantage? In cases where the index=20
> > file is lost it would be easy to generate a new index file with a=20
> > specific application for generation of dataXML index files anyway.
> >
> > Regards
> >
> > Fredrik Levander
> >
> >
> >=20
> ----------------------------------------------------------------------
> > --- Using Tomcat but need to do more? Need to support web services,=20
> > security?
> > Get stuff done quickly with pre-integrated technology to=20
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> > Download IBM WebSphere Application Server v.1.0.1 based on Apache=20
> > Geronimo
> >=20
> =
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> > 42 _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >  =20
>=20
> --
> Alexandre Masselot, phD
> Senior bioinformatician
> www.genebio.com
> voice: +41 22 702 99 00
>=20
>=20
>=20
> --------------------------------------------------------------
> -----------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
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> Download IBM WebSphere Application Server v.1.0.1 based on=20
> Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
> dat=3D121642
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>=20