OpenBIS offers a way to construct a publication portal for HCS data which:
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:
All the presented data is faked.
Note that the openBIS term for an 'assay' is 'experiment', these words are used interchangeably.
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.
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.
This view presents the most detailed data for one gene in one assay:
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.
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:
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:
Material Summary View for a chosen assay - for the gene with code 5347 and experiment with identifier
/PUBLIC/KINASES/BRUCELLAthe link would be:
Material Summary View for all assays - for the gene with code 5347 and all experiments in project
/PUBLIC/KINASESthe link would be:
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.
Here are two examples of HTML code for portal pages which use the links described above:
Note that both pages have experiment identifiers and permanent ids hard-coded.
One can configure material property code which will be rendered as a link in the Material Summary View.
servers/openBIS-server/jetty/etc/web-client.propertiesfile one has to add e.g.:
screening.material-details-property-type = GENE_SYMBOLS