The name of AnalysisXML

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Eric posted the following comment on the list:

At the risk of reopening old wounds and causing screams of rage, this may
be the last good opportunity to settle on a better name. When I mention
AnalysisXML, it still invokes smirks and muttered comparisons with StuffXML
and OpenXML and DataXML, all fairly meaningless terms.

It seems like the new scheme for PSI seems to be just ML instead of XML
(e.g. sepML, gelML, mzML, etc.)

Can I interest anyone in piaML (proteomics informatic analysis ML) or just
paML or even piML?

Original issue reported on code.google.com by andrewro...@googlemail.com on 17 Dec 2008 at 1:58

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(and Pierre-Alain replied 05/12/2008 08:59)
Hi Eric,
in principle, and for the sake of homogeneity, it would be nice. mzML has got a 
new
name due to a merge, and this is a good justification for it. However, there 
might be
some difficulties to do so. Here are some thoughts:

Pros:
- To homogenize / standardize namings, nnnnnnML could be nice
- We could say that AnalysisXML it is a draft name and would get a stable name
together with version 1.0.

Contra:
- AnalysisXML is already well known under this name and is being mentioned as 
is in a
number of publications.
- It is not sufficient to change to nnnnML to homogenize within PSI: MIF25 (for 
the
molecular interaction group) is not a nnnnnML formated name. (Also MIAPE for MI 
is
named MIMIx and not MIAPE-MI).
- AnalysisXML.com exists and is linked to PSI (although only the domain name is
reserved, no info is there)

Names:
- piML, paML exist already as Markup Language acronyms
- piaML does not exist
- AnalysisML does not exist as markup language
- analysis(X)ML vs analysis(X)ML

Original comment by dcre...@gmail.com on 17 Dec 2008 at 2:11

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I have been talking to several different groups, and I'm not sure 'analysisXML' 
is so
widely recognized as to present a problem with a formal release name change.

My only suggestion would be to keep the name general enough so that anyone who 
could
use the format to hold results from MS experiment analysis would think the name 
makes
sense.

Original comment by rkjul...@gmail.com on 17 Dec 2008 at 2:59

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minor comment from SG during DocProc:
"File extension.  It seems more appropriate to use '.xml'."

ACTION: For discussion, pros / cons of having a specific file extension? Since 
this
was agreed by the PSI-PI working group I think it is our decision to take.

Original comment by eisena...@googlemail.com on 18 Feb 2009 at 3:00

• Added labels: Milestone-Release2.0

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Agreed in Turku and in email that the analysisXML be split into two file 
formats, one for identification 
(mzIdentML), one for quantification (mzQuantML).

Proposed file extensions  for mzIdentML and mzQuantML are ".mzid" and ".mzqt", 
respectively.

Original email from Andy Jones: 
Hi all,

I have uploaded a new version of the schema updated with the changes agreed in 
Turku. For those of you not 
present in Turku, only very minor changes have been made to the core schema in 
response to reviewers 
comments. One major change has been made in that the name has changed from 
analysisXML to mzIdentML. 
We realise that this is a pretty major decision that we discussed at great 
length. Working through use cases 
for quantification demonstrated that quantification support would be far easier 
to develop in a separate file 
format to reduce interdependencies – most software packages separate the 
process of identification from that 
of quantification. With this being the case AnalysisXML will now become two 
formats: mzIdentML and 
mzQuantML.

We will re-submit the final changes to the PSI process shortly and mzIdentML is 
very close to release as a 
version 1. I anticipate that the name change should not cause a problem with 
the PSI process since looking 
over the issues list, this was requested by both Eric and Randy during the 
process.

I’ve uploaded a new schema file to reflect the name change 
(mzIdentML_working.xsd). The following changes 
have been made:

1. Changed name of schema, root element and all references from AnalysisXML to 
mzIdentML

2. Changed SpecificityRule (0 to many) which extended cvParamType:

<SpecificityRule accession="PI:00189" cvRef="PSI-PI" name="modification 
specificity N-term"/>

To:

 SpecificityRules (0 to 1) with a sub-element of cvParam (1 to many)

<SpecificityRules>

< cvParam accession="PI:00189" cvRef="PSI-PI" name="modification specificity 
N-term"/>

</SpecificityRules>

3. Changed IonType from extending cvParam to having a 1:1 sub-element of cvParam

4. Changed ModParam to have a sub-element cvParam

 <ModParam massDelta="15.994919" residues="M">
            <pf:cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD" unitCvRef="UO" 
unitAccession="UO:0000221"/>
 </ModParam>     

5. Moved peptideSequence above other sub-elements of Peptide – I don’t see 
this in the minutes but recall 
this was agreed – correct?

If I missed any agreed changes, please let me know ASAP. 

Original comment by delag...@gmail.com on 5 May 2009 at 1:42

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Original comment by andrewro...@googlemail.com on 7 May 2009 at 3:54

• Changed state: Fixed