Describing datasets

A dataset can be described with three HTML files, summary.html, methods.html and downloads.html. You can put these in the same directory where cellbrowser.conf is stored and they will get copied along to the webserver and shown in the File > Open Dataset... dialog.

Howver, when you have many datasets, writing the html files gets repetitive. This is where desc.conf is handy, it’s a key-value file with the description of the dataset in a standardized format.

A sample file can be created with the command cbBuild --init.

The following lists all tags that are currently supported.

These tags contain longer text that can include HTML markup:

  • title: title of the dataset, often the paper title
  • abstract: a big picture summary of the dataset, as a string
  • methods: the methods for the dataset, as a string
  • unitDesc: a description of the values / the unit in the expression matrix (e.g. ‘TPM’ or ‘log’ed counts’)

Instead of long strings with HTML content for abstract and methods, you can also create the files abstract.html and methods.html, they will be used instead. Or use the statements abstractFile and methodsFile to specify other file names. In the HTML, you can use text like <section>some subtitle</section> to split the text into sections.

This tag contains an image file name: - image: usually a 400px-wide thumbnail of the dimensionality reduction

The following tags can contain URLs and optionally, separated with a space, a label for the link. If you do not specify the label, a default label will be used (e.g. ‘Biorxiv Preprint’):

  • biorxiv_url: URL of the pre-print
  • paper_url: URL to any website with the fulltext
  • other_url: URL to a website that describes the dataset

The following tags contain accession IDs and will be translated to links:

  • pmid: Pubmed ID of the publication (CIRM TagsV5)
  • geo_series: NCBI GEO series ID (CIRM TagsV5)
  • sra: NCBI SRA accession
  • sra_study: NCBI SRA SRPxxxx accession
  • doi: DOI of paper fulltext
  • dbgap: NCBI dbGaP accession, starts with phs

The following tags contain just text:

  • submitter: name and/or email of submitter
  • lab: lab and University of submitter
  • submission_date: ideally in format year-month-day
  • version: version of dataset, a simple number (1,2,3,…) that should be increased each time a major change (usually meta data) was received from the lab