Category Archives: Biocuration Highlight

Postgraduate Certificate in Biocuration – University of Cambridge, UK

Launching in October 2018, the Post Graduate Certificate in Biocuration at the University of Cambridge is the first formal educational qualification in the field of Biocuration.
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Developed collaboratively between the University of Cambridge’s Institute of Continuing Education (ICE) and EMBL-EBI, this programme has been designed to provide biocurators with a set of practical skills that are applicable across the biological sciences.  Whether you are new to biocuration and looking to develop your skills, or an established curator looking to gain a recognised qualification, this course will provide a strong foundation in the principles of biocuration with additional focus on computational skills, data management and user-experience.
The course is divided into three modules, each including a 3 day workshop followed by a period of self-study through online activities. You do not need to be based in Cambridge to study for this course, but you must be able to attend all workshops.
For more details on the course and to apply, please visit: http://www.ice.cam.ac.uk/course/postgraduate-certificate-biocuration
Applications close 30th June 2018.

CTD turned 10!

The Comparative Toxicogenomics Database (CTD) recently celebrated its 10-year anniversary on the web. Since its beginnings, CTD has been devoted to centralizing and harmonizing information about genes responding to environmental toxic agents across diverse species. The database has now evolved into a premier toxicology resource, allowing scientists to discover information and develop testable hypotheses about the biological consequences of chemical exposure (both environmental and drug). Today, CTD includes over 24 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, Gene Ontology annotations, and pathways.

This celebratory milestone was recently published in the journal Nucleic Acids Research, which summarized the history and evolution of CTD, including descriptions of curation processes, new content, and enhanced visualization and analysis tools. The article also detailed a new “Pathway View” tool that leverages gene interaction data from BioGRID to allow users to build unique toxicogenomic interaction modules connecting chemical exposure to disease events.

As it was ten years ago, CTD today is still managed by a small team of biologists and software engineers who work with both the toxicology and biocuration communities to advance understanding of chemical-gene-disease data and how best to extract and code this information from the published literature. All CTD data are freely available to the public. As well, CTD content has been disseminated further into the scientific community via more than 55 other databases that routinely incorporate CTD’s annotations. If interested in establishing links to CTD data, please notify us and follow these instructions.

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CTD curates 88K articles for drug-induced events

Understanding chemical toxicity is a common goal shared between environmental health scientists and pharmaceutical drug makers. Now, the Comparative Toxicogenomics Database (CTD, http://ctdbase.org/), which has historically focused on environmental chemicals, has completed a unique curation project coding therapeutic drug-induced disease and phenotype events from more than 88,000 articles published over the last seven decades. The results were recently reported in the journal Database (http://database.oxfordjournals.org/content/2013/bat080.full).

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In the study, five CTD biocurators reviewed and manually curated 88,629 articles in just one year, coding information via controlled vocabularies for pharmaceutical compounds and their potential toxicity in cardiovascular, neurological, renal, and hepatic systems. Over 250,000 interactions were ultimately curated, linking 5,500 chemicals, 9,100 genes, 2,700 diseases, and 120 phenotypes. In the paper, CTD provided details about their curation strategy, performance metrics, and enhanced data content. As well, a new module for capturing chemical-phenotype data was introduced to curate drug-induced events at the molecular and cellular level before a disease developed.

One key finding was the discovery of 360 pharmaceutical drugs with overlapping adverse effects for four physiological systems-of-interest to drug makers resulting in cardiotoxicity, neurotoxicity, renal toxicity, and hepatotoxicity. Integrated into the CTD framework, these results are now combined with other datasets to make novel predictions and help generate testable hypotheses about drug-induced events.

The data are freely available from CTD. As well, the curation has been disseminated further into the scientific community via more than 55 other databases that routinely incorporate CTD’s annotations. If interested in establishing links to CTD data, please notify us (http://ctdbase.org/help/contact.go) and follow these instructions (http://ctdbase.org/help/linking.jsp).

Submitted by Allan Peter Davis.