The pathway ontology – updates and applications

Journal of Biomedical Semantics

Howard J Jacob¹  Elizabeth A Worthey¹  Diane H Munzenmaier²  Melinda R Dwinell²  Mary Shimoyama⁴  Shur-Jen Wang³  Rajni Nigam³  Timothy F Lowry³  Stanley JF Laulederkind³  Jeff De Pons³  Jennifer R Smith³  G Thomas Hayman³  Marek Tutaj³  Pushkala Jayaraman³  Victoria Petri³ 

[1] Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA;Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA;Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA;Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA

关键词: Pathway diagrams;    Pathway annotations;    Pipeline;    Ontology;    Biological pathway;   

Others  :  806116
DOI  :  10.1186/2041-1480-5-7

 received in 2013-05-21, accepted in 2013-12-05,  发布年份 2014

【 摘 要 】

Background

The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hierarchical structure of a directed acyclic graph. The ontology allows for the standardized annotation of rat, and of human and mouse genes to pathway terms. It also constitutes a vehicle for easy navigation between gene and ontology report pages, between reports and interactive pathway diagrams, between pathways directly connected within a diagram and between those that are globally related in pathway suites and suite networks. Surveys of the literature and the development of the Pathway and Disease Portals are important sources for the ongoing development of the ontology. User requests and mapping of pathways in other databases to terms in the ontology further contribute to increasing its content. Recently built automated pipelines use the mapped terms to make available the annotations generated by other groups.

Results

The two released pipelines – the Pathway Interaction Database (PID) Annotation Import Pipeline and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Annotation Import Pipeline, make available over 7,400 and 31,000 pathway gene annotations, respectively. Building the PID pipeline lead to the addition of new terms within the signaling node, also augmented by the release of the RGD “Immune and Inflammatory Disease Portal” at that time. Building the KEGG pipeline lead to a substantial increase in the number of disease pathway terms, such as those within the ‘infectious disease pathway’ parent term category. The ‘drug pathway’ node has also seen increases in the number of terms as well as a restructuring of the node. Literature surveys, disease portal deployments and user requests have contributed and continue to contribute additional new terms across the ontology. Since first presented, the content of PW has increased by over 75%.

Conclusions

Ongoing development of the Pathway Ontology and the implementation of pipelines promote an enriched provision of pathway data. The ontology is freely available for download and use from the RGD ftp site at ftp://rgd.mcw.edu/pub/ontology/pathway/ webcite or from the National Center for Biomedical Ontology (NCBO) BioPortal website at http://bioportal.bioontology.org/ontologies/PW webcite.

【 授权许可】

   
2014 Petri et al.; licensee BioMed Central Ltd.

【 图 表 】

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