Acknowledgements

        We are grateful to the researchers who have developed and are maintaining the following resources for making their data freely available:

• The sequence ontology (SO).
• The protein modification ontology (MOD), licensed under the GNU LGPL v2.0.
• InterPro (IPR), Copyright (C) 2001 The InterPro Consortium.
• The gene ontology (GO), licensed under the CC-BY license.
• The interproscan software, distributed under the open source Apache license.
• The TMHMM software, data courtesy of the CBS center.
• The UniProt database, licensed under the CC-BY-ND license.
• The dbOGAP database.
• The hUbiquitome database, courtesy of the hUbiquitome team.
• The PhosphoSitePlus database, licensed under the CC-BY-NC-SA license.
• The PhosphoELM database, courtesy of the PhosphoELM team.
• The ProteomeScout database, licensed under the CC-BY-SA license.
• The D2P2 database.
• The IntAct database, licensed under the Apache license, version 2.0.

Exon Ontology: ontology

The Exon Ontology has been built by selecting and organizing terms from existing ontologies such as SO, MOD, IPR and GO. It is available for download as OBO and OWL files, and is licensed under the CC-BY-NC-SA license.

• v1.5.0: OBO file and OWL file (version used in Tranchevent et al).

Exon Ontology: annotations

The human exons have been annotated to Exon Ontology terms using various tools and databases (see the 'Acknowledgements' section above). These data are also licensed under the CC-BY-NC-SA license. Notice that the dbPTM data is not included (licensing issues).

• v1.5.0: TSV file (version used in Tranchevent et al).

Exon Ontology: scripts

Our GitHub repository contains the scripts that are necessary to perform command-line analyses. They are also licensed under the CC-BY-NC-SA license.