Recorded CDD Webinar: Capturing Mixtures — Bringing Informatics to the World of Practical Chemistry
Capturing Mixtures — Bringing Informatics to the World of Practical Chemistry
Recorded live December 19, 2019
Watch our webinar featuring Dr. Chris Jakober (Johns Hopkins), Leah McEwen (Cornell), and Dr. Alex Clark (CDD) to hear about our work toward new data structures for capturing chemical mixtures in a machine-readable format, as well as the potential impact this will have on all industries that intersect with chemistry.
Our industry has been using cheminformatics to support drug discovery for decades, leveraging formats for describing organic molecules, such as Molfile, SMILES, and InChI. These are idealized concepts rather than a description of the laboratory reality: it is rare that a substance can be accurately described with a single molecule.
Almost every sample has an impurity level, or is dissolved in solvent, or exists as an adduct, or is explicitly combined with other substances. Mixtures often combine certainty and uncertainty within the same description: some components can be well-defined molecules with an accurately measured molar concentration, while others are estimated portions, or amorphous adjuncts.
The cheminformatics community has yet to select a standard format for describing mixtures in a machine-readable, standardized, and interoperable way, and most publications fall back to using a text description. Electronic lab notebooks and inventory databases are forced to choose between using text, proprietary formats, or ignoring mixture composition altogether.
We will describe our work toward two new data structures: Mixfile and MInChI, which are intended to fill roles that are analogous to Molfile and InChI, respectively. We will describe the ways in which we expect that mixtures-based informatics tools will affect all industries that intersect with chemistry.
Join our expert panelists as we discuss the future of mixture representation, including:
- Introduction of the new mixtures standards, MInChI and Mixfile
- Impacts on health and chemical safety communities
- New technologies for unambiguous mixture capture
Featuring these leading scientists...
Graduate Instructor, Johns Hopkins University, Whiting School of Engineering
Dr. Jakober is involved in environmental chemistry research within academia, government, and consulting for the past 20 years. His focus is analytical and atmospheric chemistry in combination with air pollution control research. Secondarily, he has a passion for safety in research and chemical management.
He’s held research, teaching, and administrative positions at Johns Hopkins University, the University of California at Davis (UC Davis), Oklahoma State University, the California Air Resources Board, and Air Sciences, Inc. Projects have included regulatory efforts on ozone emissions from indoor air cleaning devices, minimizing the impacts of animal confinement waste on water quality, particulate matter control methods for Owens (dry) Lake, greenhouse gas emissions verification, and community-level public health air quality assessment. He recently served as the Chemical Hygiene Officer for UC Davis.
He holds a Ph.D. in Agricultural and Environmental Chemistry from UC Davis. He’s published in numerous journals on topics of air quality, water quality, and public health protection. A true lover of all things outdoors, he maintains interests in the family cattle ranch and pursues mountaineering adventures when time permits. He’s an active member of the American Chemical Society, with personal interests on chemical safety information management and dissemination.
Chemistry Librarian, Cornell University
Leah R. McEwen is the Chemistry Librarian at Cornell University, where she manages digital library and information services for chemistry and related research and learning communities. She is an active community leader in many professional chemistry and data organizations, including the American Chemical Society (ACS), the International Union of Pure and Applied Chemistry (IUPAC), and the Research Data Alliance (RDA). She is currently chair-elect of the IUPAC Committee on Publications and Cheminformatics Data Standards, and a Trustee of the IUPAC International Chemical Identifier (InChI) project.
For the past several years, she has been building a global network of stakeholders to promote chemical data reporting, including researchers, publishers, librarians, repositories, informaticians, and system developers. She works across sectors and disciplines, connecting with other scientific unions and data initiatives to identify gaps and develop collective workflows to facilitate FAIR data exchange across the chemistry enterprise and beyond.
Research Scientist, Collaborative Drug Discovery
Dr. Clark formed the Research Informatics group at Collaborative Drug Discovery in 2014, which has subsequently grown to a team of veteran scientists working on a number of frontier projects. These cover chemistry, biology, data science, and a large amount of cross-domain expertise. The team is actively prototyping new functionality with a mind to integrating it into CDD Vault, as well as commercializing entirely new products like BioAssay Express.
Before joining CDD, Dr. Clark spent 15 years building software tools for all aspects of computer-aided drug design, including technologies for handling large databases of small molecules, small databases of large molecules, and 3D visualization and modelling tools. His particular focus is on solving the data acquisition problem, which is the often overlooked "step zero" for machine learning.
He has a Ph.D. in synthetic organometallic chemistry from the University of Auckland, New Zealand. These classical benchtop origins provide a personal perspective on the translation point from experimental results to informatics data structures, which is currently the weakest link for the informatics community.