bioformats.org, microformats for biology
bioformats.org - microformats for biology
Microformats add value to the data you explore and publish on the web. On this site you can find advice, markup and a blog to start using microformats in biology.

hGene

A working draft for a microformat to represent genes

The hGene microformat allows you to add additional semantic information to web pages containing gene data. This allows visitors to use that data in a more flexible way.

Specification

This microformat aims to map the following common attributes of a gene.
  • Species
  • Chromosome
  • HGNC symbol (if available)
  • Start
  • Genomic location
  • End
  • Length

Schema

The hGene schema consists of the following:
  • hgene
    • symbol (optional)
    • chromosome (optional)
    • species (optional)
    • location (optional)
    • start (optional)
    • end (optional)
    • length (optional)

Example

The BRCA2 gene could be represented on a web page as:
BRCA2 (Homo Sapiens)

Breast cancer type 2 susceptibility protein.

  • Chromosome 13
  • 13:31787611-31871347
With associated HTML:
<div class='hgene'>
  <span class='symbol'><b>BRCA2</b> (<span class='species'>Homo Sapiens</span>)</span>
  <p class='description'>
    Breast cancer type 2 susceptibility protein.
  </p>
  <ul>
  	<li><a href='http://www.ensembl.org/Homo_sapiens/mapview?chr=13' class='chromosome'>Chromosome 13</a></li>
	<li><a href='http://www.ensembl.org/Homo_sapiens/contigview?l=13:31787611-31871347' class='location'><span class='chromosome'>13</span>:<span class='start'>31787611</span>-<span class='end'>31871347</span></a>
  </ul>
</div>

Bioformats.org definitions

  • hGene for genes
  • hAction for workflows

Editor

  • Matt Wood, Wellcome Trust Sanger Institute

Authors

  • Arfon Smith, Wellcome Trust Sanger Institute

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