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Introduction

OpenBIS offers a way to construct a publication portal for HCS data which:

  • presents the data on the level of assays and genes without talking about plates and wells
  • calculates aggregated statistics and rankings for each gene or assay automatically
  • uses data from the regular "openBIS for HCS" instance

This document describes the offered functionality and a way to construct the portal.

Note that all the publication views make sense not only for gene, but also for siRNAs or chemical compounds.
In general any type of materials inside wells is supported but in this document siRNA screen is considered where genes are the most important objects.

Any table presented below:

  • can be filtered or sorted by any column
  • can be exported to an Excel-friendly format
    directly from the web browser.

All the presented data is faked.
Note that the openBIS term for an 'assay' is 'experiment', these words are used interchangeably.

Available views

Assay Analysis Summary

This view shows aggregated analysis results for all the genes screened in one assay.
It takes into account that one gene can be screened in many wells of different plates of an assay. For each gene and analyzed feature a median value from all the replicas will be displayed together with the rank for that feature.

Material Summary View for all assays

This view allows to do quick cross-assay comparisons of the analysis results for one gene.
It presents the aggregated analysis results for the selected gene and each assay in which that gene has been screened. Clicking on the assay allows to see the fine-grained results and images.

Material Summary View for a chosen assay

This view presents the most detailed data for one gene in one assay:

  • well-level aggregated and detailed analysis results with sub-summaries for different siRNAs
  • all images acquired for the gene in the assay, grouped by siRNAs

    Of course clicking on the image allows to see its magnification and the user can choose which channels should be presented.

At the top of the page there are convenience links to the view with cross-assay comparison of the analysis results for a gene and to the view with the whole assay summary.

Building the portal

All the above mentioned views are accessible by default in each standard "openBIS for HCS" installation.
They are useful for people in the lab who are familiar with openBIS. But for external users or reviewers something much simpler would be suitable.
In this chapter it is described how to construct a portal which hides all the unnecessary details from people who just want to see the final results of the screens.

The basic idea is to build a portal on which some pages are embedded views from openBIS and some are custom and contain any publication-specific content, e.g. project descriptions or information about a group. We suggest to use some of the existing Content Management Systems (CMS) like Weebly to build and manage such a portal. Weebly is very intuitive and can be learned in 5 minutes. Here is an example of how the portal could look like in the end:

Embedding openBIS Views

Each view of openBIS described above can be referenced with a parametrized URL. Thanks to that each view can be embedded in the portal using an HTML iframe.

The most important views are:

  • Assay Analysis Summary - for the experiment with a permanent id '20100702163349260-131166' the link would be:

    https://openbis.mydomain.ch/openbis/index.html?viewMode=embedded#action=FEATURE_VECTOR_SUMMARY&restrictGlobalSearchToProject=true&experimentPermId=20100702163349260-131166
    
  • Material Summary View for a chosen assay - for the gene with code 5347 and experiment with identifier /PUBLIC/KINASES/BRUCELLAthe link would be:

    https://openbis.mydomain.ch/openbis/index.html?viewMode=embedded#entity=MATERIAL&code=5347&type=GENE&experiment=/PUBLIC/KINASES/BRUCELLA&restrictGlobalSearchToProject=true
    
  • Material Summary View for all assays - for the gene with code 5347 and all experiments in project /PUBLIC/KINASESthe link would be:

    https://openbis.mydomain.ch/openbis/index.html?viewMode=embedded#entity=MATERIAL&code= 5347&type=GENE&spaceCode=PUBLIC&projectCode=KINASES
    

Links to all the other available views are described here

All the links should have the "viewMode=embedded" parameter to hide unnecessary details from the user, like the openBIS menu or the footer.

Examples

Here are two examples of HTML code for portal pages which use the links described above:

  • HTML source of a page to find a gene in a particular assay or in all assays
  • HTML source of a page to show the details of the chosen assay

Note that both pages have experiment identifiers and permanent ids hard-coded.
It would be possible to use openBIS JavaScript API to fetch the experiments dynamically. Please contact the helpdesk or openBIS team if you need that.

Configuration

  • One can configure material property code which will be rendered as a link in the Material Summary View.
    In servers/openBIS-server/jetty/etc/web-client.propertiesfile one has to add e.g.:

    screening.material-details-property-type = GENE_SYMBOLS
    
  • Currently all the aggregations are calculated for well materials only if the material's type is GENE, CONTROL or COMPOUND. Switching on support for other material types is not yet possible for openBIS admins. The development team has to be contacted for that.
  • Material Summary View is able to create subgroups of the analysis data and images using one well property.
    For now two well properties are supported:
    • SIRNA which points to a material in siRNA screens or
    • CONCENTRATION which describes a numerical compound concentration in compound screens.
      All the wells which contain the same siRNA or concentration are considered to be replicas.
      Switching on support for grouping by other property type is not yet possible for openBIS admins and the development team has to be contacted for that.
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