Cell Browser filters

The Cell Browser utilizes a set of filters to allow people to narrow down the dataset list to only those of interest:

The values in these filters are determined based on tags in a dataset's cellbrowser.conf:

• body_parts
• diseases
• projects
• organisms
• sources
• life_stages
• domains

This page will walk you through the process of curating these tag values for a single dataset. You can combine some of the steps here regarding BLAH with the information on the Managing_cellbrowser.conf_tag_values_for_multiple_datasets page to update the values for filter tags for many datasets.

Tag/value conventions

This sections covers our internal conventions for each set of tag/value pairs.

body_parts

For us at the Cell Browser, this tag is required for every dataset. (As determined by the 'reqTags' in your ~/.cellbrowser.conf

Values in this field are always lower case.

If you have a super high-level value, it's good to have a lower-level one as well. e.g. if you include 'brain' then you should also include a more specific brain region like 'cortex', 'hippocampus', etc.

diseases

If data is only from non-diseased sample, use the value 'Healthy'.

If data covers a disease, then look up disease in ontology (which one?) to ensure that we're using a common label for all datasets of that disease. If this disease dataset also includes healthy samples, then include the value 'Healthy Control'.

The distinction between 'Healthy' and 'Healthy Control' allows people who want to see only healthy datasets to see those and not clutter the list with disease datasets. (Often the healthy control samples are mixed in with the disease samples and separating them out is non-trivial.)

organisms

List all species include in the dataset (or subdatasets).

For vertebrate species use the form: Common name (G. species) e.g. Human (H. sapiens) Mouse (M. musculus)

For non-vertebrates, use the form: G. species e.g. C. robusta

sources

Where you got the data from.