Biology Reference
In-Depth Information
are able to comply with these guidelines. This has highlighted that
in practice some fi ne tuning related to required information should
be addressed before that MIAPE guidelines are fully adopted by
journals as integral part of their rules. For example, the percentage
of publication in which raw data has been made available by submit-
ting it to a public repository is still low, often due to technical prob-
lems (data storage and/or bandwidth of transferring large amount
of data) or a lack of bioinformatics resources to do it. Other explic-
itly required details in MIAPE guidelines were also diffi cult to com-
pile by authors, due to ignorance or to lack of clarity on some
defi nitions in the MIAPE modules.
All that reasons have been resulted in a further review of some
MIAPE modules to facilitate their adoption as much as possible to
the real life. So, the PSI document process actually allows the
review of documents describing standards even if they were already
published previously, provided that changes are well documented
and justifi ed [
3
]. It is the case of MIAPE MS and MSI modules,
that were published on 2008 [
32
,
34
], and they are currently
under the PSI document process, after having changed some of
their content. The reasons for these modifi cations have been the
following:
-Some sections about quantifi cation processes were present in
2008 MIAPE MS and MSI modules. These sections were
deleted when a new MIAPE module (MIAPE-Quant) about
quantifi cation data was decided to be defi ned.
-A number of terms were removed and replaced by more generic
terms to reduce over-specifi cation.
-Some parts of the guidelines were restructured and defi nitions
in the appendix were modifi ed to improve the clarity of the
checklist and make it easier to comply with journals require-
ments and PSI data standards.
So, hopefully, MIAPE MS and MSI documents will again be
released after passing by a new PSI formal document process.
But, MIAPE modules are not the only standards that have been
redefi ned. For example the standards for proteomics data represen-
tation mzML and mzIdentML were also slightly modifi ed (from
v1.0 to 1.1) after the detection of some technical issues by some
developers that were implementing these formats in their tools.
MIAPE guidelines are not suffi cient to describe all kinds of
publishable data and results. They cover a large part of proteomics
related experiments, but do not cover other fi elds such as micro
array experiments, RNAi experiment, a T Cell Assay, a genotyping
experiment. In that respect, MIAPE is registered to the MIBBI
foundry [
38
], where over 30 similar projects covering a wide range
of fi elds and technologies have deposited minimal information
guidelines.
