The construction and maintenance of a high quality and interoperable knowledge commons that covers the area of gene regulation information involves key players in the field of bio-curation, database management and computational biology who collaborated with knowledge commons users under aegis of the GREEKC COST Action. This special issue of BBA-Gene Regulatory Mechanisms reports on progress in the following areas; ontologies and controlled vocabularies, the development of curation guidelines and standards, identify literature content by text mining and storing and sharing of the gene expression regulation knowledge commons.