Glycan array data repository/Data submission

Glycan array data submission to the repository is possible to any registered user account. Since a glycan array data set with all its information, including MIRAGE metadata, can be very complex, the submission is decided into individual steps. One group of steps is done before an experiment is submitted and serve the preparation of the submission. This includes the creation of the metadata, upload of glycans and other molecules, and creation of the slide. The second group of submission steps is related to the upload of the actual data and include the image file submission, raw data submission and processed data submission. There are also optional submission steps that can be used to attach additional information, such as collaborators or papers, to the experiment.

Submission prerequisites

Before the data files can be submitted to the repository several information packages need to be submitted to the repository to prepare the submission. These are mostly information that can be reused for several experiments. For example the same experimental procedure (assay) with the same conditions may be used in dozens or even hundreds of experiments. Having to upload these information for each experiment over and over again is very time consuming and not user friendly. Therefore these information are packaged together in metadata packages and submitted once to the repository. During this submission a unique name is assigned to each information package. When a data set is uploaded to the repository user can select the assay metadata from a list of prepared metadata packages without having to enter the information again. The information that needs to be submitted before the datasets include:

• Sample
• Spot metadata
• Slide metadata
• Printer metadata
• Print run metadata
• Assay metadata
• Scanner metadata
• Image analysis metadata
• Data processing metadata

In addition all molecules and their metadata that have been used on the slide associated with an experiment have to be uploaded as well. This includes:

• Glycan information
• Linker information
• Lipid information
• Peptide information
• Protein information
• Other molecule information

The molecules are subsequently used to create the Features. Features are the glycoconjugates that have been printed on a slide. These include:

• Linked Glycan consisting of the predefined glycans and linkers
• GlycoLipid consisting of the predefined glycans and lipids
• GlycoPeptide consisting of the predefined glycans and peptides
• GlycoProtein consisting of the predefined glycans and proteins
• GlycoProtein linked GlycoPeptide consisting of the predefined glycans, peptides and proteins

In a last preparation step the slide used in the experiment needs to be in the system by using the predefined features. This is done in 3 steps:

• Define Block layout by using the predefined features and associating them with spot metadata
• Define Slide layout by using the block layouts defined above
• Define Slide using the slide layout defined above and associating it with predefined slide metadata, printer metadata and print run metadata

Submission of an experiment

The experiment submission consists of multiple steps that do not have to be done at the same time. Each submitted experiment is by default private and not visible to external users. Once an experiment submission is complete the submitter can choose to make it publicly available.

1. Create an Experiment by providing its name, description and selecting the predefined sample
2. Adding one or multiple Image to the experiment by providing the associated predefined slide, the image file, predefined image metadata, predefined assay metadata and predefined scanner metadata
3. Adding one or multiple Raw data files to an image by providing the GPR file and the predefined image processing metadata
4. Adding one or multiple Processed data files to a raw data file by providing the processed data file and the predefined data processing metadata

Optional submission steps

In addition to the preparation steps and the experiment submission the user can also associate additional information with an experiment:

• Collaborator: Other users that contributed to the experiment and should be named on the experiment webpage.
• Co-Owner: Other users that can make modifications to the experiment. These users will not be named as collaborator. An example could be a lab manager.
• Publication: A list of papers and publications can be associated with an experiment
• Keyword: A list of keywords can be associated with an experiment to help in discovering this experiment.
• Supplemental Files: A list of files to supplement the experimental data. E.g., reports, presentations, posters