Aims

1. Publication standards for interaction analysis data

Interaction analysis includes experiments which seek to identify and define the recognition of glycan receptors by binding partner proteins. These interactions may be as limited as the interaction of an individual proteins with a single glycan or as broad as the evaluation of whole binding of cells to populations of glycans.

Initial efforts focus on the interactions that can be evaluated on a glycan microarray. Future expansion would include all types of interaction experiments, including, but not limited to: SPR (surface plasmon resonance), flow cytometry, ELISA, STD-NMR and ITC (isothermal calorimetry).

The aims for this task are:

• define and provide for interaction experiments, e.g.,

1. sample reporting guidelines
2. experimental guidelines
3. platform guidelines
4. results guidelines

• provide templates for reporting within the above guidelines
• suggest guidelines for data reporting (normalization standards)
• conventions for glycan nomenclature in order to facilitate cross platform comparisons of different glycan arrays
• interact with the MIRAGE working group “Bioinformatics” to establish basic structure for data reporting
• recruit users/experts in other platforms to review/critique guidelines for use in those experiments

Status

In 2010 a subgroup of the WGGDS (Working Group for Glycomics Data(base) Standards) started a initiative to create a standard exchange format for glycan array data. The initative started with a data collection of information that have to be stored to consistently describe an glycan array experiment.

Reporting Guidelines for Glycan Microarray Data have been developed, approved by both the MIRAGE Commission and the community and published in 2017. These guidelines were drafted to be intentionally minimal and apply only to information required for generating interpretable data from a glycan array experiment. Bearing in mind the authors' hestiance to follow guidelines, here, the Commission provides a number of exemplar publications reporting glycan microarray data and a template completed with a data example.

Reporting Guidelines for Sample Preparations are designed to include all aspects of sample generation, purification and modification from biological and/or synthetic material. These guidelines are considered as a common basis for any further MIRAGE reporting guidelines in order to keep the requirements for data analysis short and consistent. After their approval the guidelines were published in 2016.

Reporting Guidelines for NMR Data on binding of glycans to receptors are proposed to comprehensively describe the NMR experiments and data obtained to characterize glycan recognition by various receptors. These guidelines are approved by the MIRAGE Commission and await their approval of application in dedicated NMR labs. It is then planned to publish the guidelines along with the experimental results reported in compliance with the guidelines.

The Reporting Guidelines for Lectin Microarray Data cover all aspects of a lectin microarray experiment including sample preparation, lectin libraries, description of the immobilization surface (e.g. the microarray slide) and its production, detection and data processing as well as data representation and storage. The manuscript describing these guidelines is currently in preparation.

(July 2024)

2. Publication Standards for structural analysis Data

With the rising interest in global glycoconjugate characterization (glycomics/glycoproteomics) a growing number of labs are implementing a range of technologies to achieve this goal. This increasing interest presents an important step towards glycomic systems biology, especially with concomitant development of suitable data repositories that allow access to the large amount of data acquired at different institutions.

Nevertheless, sample preparation plays a crucial role in glycoconjugate analysis. It can influence the occurrence of artefacts, which, in turn, can result in misinterpretations. In this context it is of utmost importance that critical sample handling and data analysis parameters are reported in an organised fashion to enable critical review of recorded data at a later stage. The lack of adequate and generally applicable software tools as utilised in proteomic research adds an additional challenge for glycoconjugate structural determination.

Thus, the goals of this task are:

• identify and define crucial sample preparation and analysis parameters
• provide templates for reporting
• suggest guidelines for data reporting / data deposition
• interact with the MIRAGE working group “Bioinformatics” to establish basic structure for data reporting
• seek input from the wider glycobiology research community.

3. Development of Data exchange formats

The Comission is collaborating with interested members from the community to cover the informatics aspects of the MIRAGE project.

The aims are:

• definition of data exchange file formats based on the guidelines provided by the other working groups
• definition of a guideline for the development of glycomics databases
• working with the two other working groups to integrate guidelines for data processing into the general guidelines

Status

Definition of the Biological source data collection at the Second GlycoInformatics Workshop in Potsdam, 2011.

A prototype of the software-based decision tree has been developed for the mass spectrometry guidelines and discussed with the members of all the three working groups. This tool provides the user a framework to navigate through the comprehensive mass spectrometry guideline by retrieving the required information about the experiment performed and presenting the user only those parts of the guideline which apply to this match. The work on this tool is still in progress.

First steps have been made towards a data exchange format for mass-spectrometry data on the basis of mzML but this projects has been stopped due to some reasons. With regards to glycopeptide analysis data, members of the MIRAGE Commission are now collaborating with HUPO-PSI on an eventual extension of mzIdentML to include glycan information in this data exchange format. First results are to be expected soon.

The creation of a glycan-relevant ontology has been started and is going to be implemented in GlycoPOST and UniCarbDR along with other relevant ontologies that can be found in the Ontology Lookup Service.

In accordance to the definition of metadata, a sub-group is currently working on metadata that describe Glycan MIcroarray data in more detail and can be used for the development of a database model.

(July 2024)