V32: shared metadata

Friday, January 31, 2014

From version 32, you are now able to create a custom metadata vocabulary and share/reuse it among your data hubs (instead of having to keep multiple copies over many hubs).

As an example, we put following JSON contents into a text file to define a metadata vocabulary:

{

vocabulary:{

    "epigenetic mark":{

        "dna methylation":["aa","bb","cc"],

        "histone mark":["dd","ee"],

        },

    "rna-seq":{

        "mRNA":["aa","ee"],

        "small RNA":["dd","bb"],

        },

},

tag:"My shared metadata",

}

To make it a shared metadata, put the file on a web server. Now the file is addressable by its URL:

http://vizhub.wustl.edu/hubSample/hg19/t/metadata

To share this metadata with a JSON data hub, add following JSON content into the hub:

{

type:"metadata",

vocabulary_file_url:'[http://vizhub.wustl.edu/hubSample/hg19/t/metadata http://vizhub.wustl.edu/hubSample/hg19/t/metadata]',

show:["epigenetic mark","rna-seq"],

},

The hub file can be found at this URL: http://vizhub.wustl.edu/hubSample/hg19/t/hub1withsharedMD

Load this hub to the browser (you can do this by clicking this link: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://vizhub.wustl.edu/hubSample/hg19/t/hub1withsharedMD)

The shared metadata vocabulary will be in use.

Another hub which also shares this metadata vocabulary is here: http://vizhub.wustl.edu/hubSample/hg19/t/hub2withsharedMD

You can see how the shared metadata works by load this hub following the first one.

When a shared metadata is loaded, you can see the vocabulary by right-clicking term names on top of metadata color map, and choose "Add metadata terms" option:

The custom metadata is indicated by a tag name and orange background color:

Click the tag to get more information about this vocabulary: