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PRESENTATION ACS Spring 2018: Curating “Suspect Lists” for International Non-target Screening Efforts

25 Mar

Curating “Suspect Lists” for International Non-target Screening Efforts

Emma L. Schymanski, Reza Aalizadeh, Nikolaos S. Thomaidis, Juliane Hollender, Jaroslav Slobodnik, Antony J. Williams5

1Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Luxembourg.
2National and Kapodistrian University of Athens, Department of Chemistry, Panepistimiopolis Zografou, 157 71 Athens, Greece.
3Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.
4Environmental Institute, Okružná 784/42, 972 41 Koš, Slovak Republic.
5National Center for Computational Toxicology, US EPA, Research Triangle Park, Durham, NC, USA.

PRESENTED by Emma Schymanski

The NORMAN Network (www.norman-network.com) is a unique network of reference laboratories, research centres and related organisations for monitoring of emerging environmental substances, through European and across the world. Key activities of the network include prioritization of emerging substances and non-target screening. A recent collaborative trial revealed that suspect screening (using specific lists of chemicals to find “known unknowns”) was a very common and efficient way to expedite non-target screening (Schymanski et al. 2015, DOI: 10.1007/s00216-015-8681-7). As a result, the NORMAN Suspect Exchange was founded (http://www.norman-network.com/?q=node/236) and members were encouraged to submit their suspect lists. To date 20 lists of highly varying substance numbers (between 52 and 30,418), quality and information content have been uploaded, including valuable information previously unavailable to the public. All preparation and curation was done within the network using open access cheminformatics toolkits. Additionally, members expressed a desire for one merged list (“SusDat”). However, as a small network with very limited resources (member contributions only), the burden of curating and merging these lists into a high quality, curated dataset went beyond the capacity and expertise of the network. In 2017 the NORMAN Suspect Exchange and US EPA CompTox Chemistry Dashboard (https://comptox.epa.gov/) pooled resources in curating and uploading these lists to the Dashboard (https://comptox.epa.gov/dashboard/chemical_lists). This talk will cover the curation and annotation of the lists with unique identifiers (known as DTXSIDs), plus the advantages and drawbacks of these for NORMAN (e.g. creating a registration/resource inter-dependence). It will cover the use of “MS-ready structure forms” with chemical substances provided in the form observed by the mass spectrometer (e.g. desalted, as separate components of mixtures) and how these efforts will support other NORMAN activities. Finally, limitations of existing cheminformatics approaches and future ideas for extending this work will be covered. Note: This abstract does not reflect US EPA policy.

https://doi.org/10.6084/m9.figshare.6025799.v1

 

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on March 25, 2018 in ACS Meetings

 

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