Biology Reference
In-Depth Information
working groups divide the vertical topics: Molecular Interactions
(MI), Proteomics Informatics (PI), Mass Spectrometry (MS),
Protein Separations (PS) and Protein Modifi cations (MOD).
Additionally, a proposal for the creation of a new working group
dedicated to proteomics experimental protocol standardization
was presented in the last PSI meeting in San Diego (USA) on
March 2012. It also has a steering committee that takes care of
horizontal administrative and logistical tasks. Every year, a work-
shop [
6
-
16
] is organized in which the participants report on the
status of the projects and split in different tracks to address specifi c
outstanding issues. Developments and defi nitions are also carried
out by individuals during the year, followed up and coordinated via
regular teleconferences and in some cases, by face-to-face work-
shops on a specifi c topic. Additionally, progresses of HUPO-PSI
standard developments are presented every year in the HUPO
World Congress where a satellite meeting or a specifi c session
[
17
-
20
] is dedicated; this also provides a wider panel to make the
deliverables visible and to allow for additional discussions with the
proteomics community.
HUPO-PSI is producing the following types of standards:
-
Standard formats for proteomics data representation
. These data
formats are primarily XML formats defi ned by XML schemas
(xsd) (Extensible Markup Language). In addition to the schema,
a semantic validator [
21
] is provided in most of the cases to
check the schema but, more importantly, also to ensure the
proper usage of controlled vocabulary terms as well as the com-
pliance with specifi c constraints (
see
Subheading
5.2.3
). These
standard data formats are meant to allow seamless exchange of
data all the way along a proteomics workfl ow. They also, with
the help of converter tools, aim to solve the problem of the dif-
fi culty of handling different proprietary data formats from
various vendors while proposing a common way to represent
data and meta-data. Current released formats are mzML [
22
],
mzIdentML [
23
,
24
], traML [
25
], gelML [
26
], and PSI-MI
XML [
27
].
-
Controlled vocabularies
. A number of controlled vocabularies
are developed to support the implementation of the data for-
mats. They cover all concepts, procedures, materials, equip-
ment, bioinformatics tools, etc. that are necessary to encode
information into the data formats. They are integrated in
The
Open Biological and Biomedical Ontologies (OBO) foundry
[
28
], a collaborative project for the establishment of a set of
principles for ontology development in the biomedical domain.
Proteomics information is coded into the standard data fi les
using these ontology terms, which enormously facilitates the
data interpretation by third-party bioinformatics tools.
