ICCE 2014: The Green Lab Notebook
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Green chemistry is an important subject that needs to be a part of every chemist's education, as well as a part of the daily routine of the professional synthetic chemist. This talk describes how a new app can be used to bring green chemistry metrics to reaction descriptions, once they are captured in a proper cheminformatics format. It also describes some of the additional data resources that can be incorporated into the user experience, and how this helps both students and professionals.
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This document discusses representing and modeling chemical mixtures. It proposes a new data format called Mixfile or MInChI to hierarchically define mixtures and their components, including concentrations. This format aims to support cheminformatics applications like property prediction. Examples are given modeling theophylline solubility and gas absorption using mixture data. The document also describes applying similar methods to model polymer entropy of mixing using a spreadsheet dataset converted to the mixtures format. It concludes that defining mixtures in digital formats will enable greater analysis, modeling and use of mixture data.
Mixtures InChI: a story of how standards drive upstream products
This document discusses the development of Mixtures InChI (MInChI), a standard for representing chemical mixtures in a machine-readable format. MInChI was developed to address the lack of standards for mixture informatics and interoperability. The document outlines the development of open source tools to generate and edit MInChI notation, as well as efforts to build a community and integrate MInChI into commercial products and databases to enable widespread use and generation of mixture data. Future work discussed includes finalizing the MInChI specification, extending it to additional chemical entities, developing associated properties and metadata, and implementing MInChI at large scale.
Mixtures as first class citizens in the realm of informatics
Presented at Cambridge (UK) cheminformatics meeting, February 2021. Mixtures of chemicals are underutilised from an informatics point of view, and this presentation shows some of the work done by Collaborative Drug Discovery, IUPAC and InChI Trust to remedy this.
See recording: https://www.youtube.com/watch?v=0ILc0owuEzQ&list=PLfj_gc4RCduuwv9p8lh2xS1EhQ3p_Nd9S&index=1 ... my part starts at 1:05:00
Mixtures: informatics for formulations and consumer products
The document proposes standards for representing mixtures in a machine-readable format. It introduces Mixfile and MInChI (Mixtures InChI) as hierarchical and concise formats for describing mixtures. Examples of formulations are provided to demonstrate how components, concentrations, and metadata can be encoded. Potential applications of the standards are discussed, such as enabling sophisticated searches of mixture data from publications and vendors to facilitate properties prediction and hazards assessment. Adoption of the standards could help ensure the longevity and sharing of mixture data.
Coordination InChI (2019)
Preliminary survey of inorganic compounds
For extensive details and updates, see https://github.com/aclarkxyz/data_coordinchi
Chemical mixtures: File format, open source tools, example data, and mixtures...
This document discusses representing chemical mixtures using an open format called Mixfile. It proposes Mixfile as a standard format for mixtures, analogous to Molfile for individual molecules. Tools were created to edit and manipulate Mixfiles. Over 5,600 real-world mixture examples were extracted from text and represented in the Mixfile format. A MInChI notation was also defined as a condensed representation of mixtures. Future work is proposed to integrate mixture definitions and lookups into electronic lab notebooks and improve automated extraction of mixture information from text.
Bringing bioassay protocols to the world of informatics, using semantic annot...
This document discusses bringing bioassay protocols into the world of informatics by using semantic annotations. It describes how measurements from bioassays contain many details that are usually only available as text, and outlines an approach using ontologies, natural language processing, and machine learning to extract this information and make it accessible for searching, comparing datasets, and identifying trends. The goal is to make all bioassay protocol data machine readable by developing common templates and annotation standards that can be applied to existing and new assay data sources.
ACS CINF Luncheon talk (Boston 2018)
Leveling up chemical information for the era of big data: an appeal to make data a top priority in the peer review process...
Autonomous model building with a preponderance of well annotated assay protocols
Combining large amounts of publicly available structure-activity data with assays that have carefully curated annotations opens the door to a number of ways to analyze the data behind the scenes. Combining fully machine readable input for a diverse variety of projects with modelling techniques that can be used without fussy parametrization allows models to be created and updated whenever new data arrives. Predictions from these models can be integrated into normal searching and visualization workflows, without any need for the user to opt-in or make extra decisions. This approach is novel and different from the way structure-activity models are normally deployed: useful predictions can be presented ubiquitously with literally zero additional work on behalf of the user. We will present our efforts to date regarding ways to both passively and actively draw attention to important drug discovery trends while exploring compounds and assays.
Representing molecules with minimalism: A solution to the entropy of informatics
Cheminformatics as we know it is possible because so many molecular structures can be represented with datastructures and rules that are at first glance quite trivial. This first impression is highly misleading, since even within supposedly well behaved domains, edge cases arising from issues such as resonance, tautomerization, symmetry and stereochemistry - to name but a few - quickly add up. To supplement these genuine challenges, there is a whole additional class of problems caused by the mismatch between chemists' understanding of molecules and the datatypes that are necessary to capture a structure for informatics purposes. This line is blurred by the convenience of representing structures in a form that is very closely related to the diagram styles that have been in use since the dawn of chemistry. There are currently four major approaches to structure representation: connection tables (e.g. MDL Molfile), sketches (e.g. ChemDraw), canonical strings (e.g. SMILES and InChI) and atomic models (numerous 3D formats). Not only do all of these approaches have valid use cases, but they are deceptively incompatible with each other, even when addressing identical needs. Almost without exception, format conversions are not commutative, and every translation involves losing some amount of data. Given that recording chemical structures in machine readable form has become such a critical part of scientific research, it is essential to define a fundamental representation that captures the key structural definition asserted by the experimental chemist, for a broad and useful range of molecules, and ideally in a way that is closely related to visual drawing mnemonics. The number of data concepts needed to satisfy these conditions is quite small, and is mostly satisfied by the most commonly used subset of the venerable MDL Molfile format. This presentation will discuss how this subset, with a few minor corrections and clarifications, can and should be used as the reference standard for molecules, and how the informatics community can benefit from having well defined standards.
CDD BioAssay Express: Expanding the target dimension: How to visualize a lot ...
Presented to the American Chemical Society: Chemical Information symposium, April 2017 (San Francisco)
BioAssay Express
Presentation to the EPA (August 2016) about the BioAssay Express project, from Collaborative Drug Discovery. Describes the history and potential of the project, with the intention of opening a dialog about incorporating EPA toxicity data.
SLAS2016: Why have one model when you could have thousands?
Society for Laboratory Automation & Screening, San Diego, January 2016. Presented by Dr. Alex M. Clark. Describes the use of open data resources (ChEMBL) to build target-activity models for drug discovery and toxicity prediction, on a massive scale, using a fully automated process. Concludes with a demo of the PolyPharma app, which shows how these models can be used for prospective drug discovery.
Compact models for compact devices: Visualisation of SAR using mobile apps
Presented at American Chemical Society meeting, Boston, 2015. Describes how cheminformatics algorithms and visualisation interfaces have advanced on mobile apps to cover a diverse variety of functionality, increasingly calculated on the device itself rather than deferring to a web service. Culminates in a demo of the PolyPharma app prototype (see http://cheminf20.org/2015/08/06/the-polypharma-app-a-mash-up-of-ideas-and-technology)
Cloud hosted APIs for cheminformatics on mobile devices (ACS Dallas 2014)
Mobile apps for cheminformatics are quite powerful on their own, but can be significantly boosted by connecting them with cloud-hosted functionality. This talk explores the range of functionality that can be covered simply by making use of apps with stateless webservices, i.e. anonymous access without persistent data.
Reaction Lab Notebooks for Mobile Devices - Alex M. Clark - GDCh 2013
Presented at 2013 the German Chem[o]informatics Conference in Fulda, 2013: entitled "Putting together the pieces: building a reaction-centric electronic lab notebook for mobile devices".
Alex Clark : NETTAB 2013
Cheminformatics
workflows using the
mobile + cloud platform. Presentation by Dr. Alex M. Clark of Molecular Materials Informatics at the NETTAB 2013 meeting in Venice, Italy. The presentation introduces the significance of mobile apps in science, and the scope of their capabilities in chemical structure informatics. The bulk of the talk describes an account of a preliminary workflow using open science data to search for viable leads for a cure for tuberculosis. The workflow described makes use of a combination of mobile, cloud and conventional desktop-based technology, all stitched together by facile communication, sharing and collaboration features.
Open Drug Discovery Teams @ Hacking Health Montreal
Alex Clark of Molecular Materials Informatics (http://molmatinf.com) presents the Open Drug Discovery Teams project to the Hacking Health Montreal audience, April 2013.
Pistoia Alliance App Strategy
Presentation to the American Chemical Society (New Orleans, April 2013) describing the app strategy of the Pistoia Alliance.
Mobile+Cloud: a viable replacement for desktop cheminformatics?
Introduces the prospect of performing cheminformatics workflows using mobile devices for the UI and cloud resources for heavy duty computation. Describes a sample workflow using the SAR Table app to propose potential new drugs for eliminating malaria.
More from Alex Clark (20)
Mixtures InChI: a story of how standards drive upstream products
Mixtures InChI: a story of how standards drive upstream products
Mixtures as first class citizens in the realm of informatics
Mixtures as first class citizens in the realm of informatics
Mixtures: informatics for formulations and consumer products
Mixtures: informatics for formulations and consumer products
Chemical mixtures: File format, open source tools, example data, and mixtures...
Chemical mixtures: File format, open source tools, example data, and mixtures...
Bringing bioassay protocols to the world of informatics, using semantic annot...
Bringing bioassay protocols to the world of informatics, using semantic annot...
Autonomous model building with a preponderance of well annotated assay protocols
Autonomous model building with a preponderance of well annotated assay protocols
Representing molecules with minimalism: A solution to the entropy of informatics
Representing molecules with minimalism: A solution to the entropy of informatics
CDD BioAssay Express: Expanding the target dimension: How to visualize a lot ...
CDD BioAssay Express: Expanding the target dimension: How to visualize a lot ...
SLAS2016: Why have one model when you could have thousands?
SLAS2016: Why have one model when you could have thousands?
Compact models for compact devices: Visualisation of SAR using mobile apps
Compact models for compact devices: Visualisation of SAR using mobile apps
Cloud hosted APIs for cheminformatics on mobile devices (ACS Dallas 2014)
Cloud hosted APIs for cheminformatics on mobile devices (ACS Dallas 2014)
Reaction Lab Notebooks for Mobile Devices - Alex M. Clark - GDCh 2013
Reaction Lab Notebooks for Mobile Devices - Alex M. Clark - GDCh 2013
Open Drug Discovery Teams @ Hacking Health Montreal
Open Drug Discovery Teams @ Hacking Health Montreal
Mobile+Cloud: a viable replacement for desktop cheminformatics?
Mobile+Cloud: a viable replacement for desktop cheminformatics?
ICCE 2014: The Green Lab Notebook
- 1. The Green Lab Notebook:! ! Chemical intelligence and green informatics in a mobile app Holly K.M. Hampson! Alex M. Clark July 2014 © 2014 Molecular Materials Informatics, Inc.! http://molmatinf.com
- 2. MOLECULAR MATERIALS INFORMATICS • Green chemistry is like a distinct profession: - its own journals, grants, conferences… • Students need to develop habits early • Professionals need information access 2 Green! Chemistry Chemistry! Students Professional! Chemists
- 3. MOLECULAR MATERIALS INFORMATICS Software Can Help • percentage yield • atom efficiency • process mass intensity • E-factor 3 Calculations Information • greener solvents • sustainable feedstocks • hazardous byproducts • benign reactions
- 4. MOLECULAR MATERIALS INFORMATICS Mobile App • Mobile: the platform of the future • Where the action is: UX/UI innovation • Where the students are now: iPhones, iPads, etc. • Needs to be accessible, affordable, simple, effective… 4
- 5. MOLECULAR MATERIALS INFORMATICS Making Aspirin • The quintessential undergraduate reaction… 5 Reactants Reagents Products
- 6. MOLECULAR MATERIALS INFORMATICS Entering Quantities • Use the app to enter quantities for each reaction component 6 • Automagic calculation of molecular weight, moles, volume ↔ mass (density, concentration), yield
- 7. MOLECULAR MATERIALS INFORMATICS Calculations 7 Yield E-factorProcess Mass Intensity Atom Economy actual product amount theoretical product amount product molecular weight reactant molecular weight Σ Σ reactant mass product mass Σ Σ waste mass product mass Σ Σ ☞ 100% ☞ 100% ☞ 1 ☞ 0
- 8. MOLECULAR MATERIALS INFORMATICS Automatic Green Metrics • Green metrics are always calculated… 8 • … always shown, always stored • These metrics become as accessible as yield • Easier to compare & optimise for greenness
- 9. MOLECULAR MATERIALS INFORMATICS Solvents • Choice of solvent has a huge impact on green profile • Curated data regarding: Safety! Health! Flammability! Environmental impact! Waste disposal! Reactivity! Lifecycle 9
- 10. MOLECULAR MATERIALS INFORMATICS Using Solvents 10
- 11. MOLECULAR MATERIALS INFORMATICS Feedstocks • Not all starting materials are created equal • Some can be made from renewable sources • Lab notebook is a chance to guide & educate • Curation is a work in progress… 11
- 12. MOLECULAR MATERIALS INFORMATICS Transforms • Chemical reactions can be curated as transforms • Can be used to search for ways to design a reaction • Curation of green transforms is a way to encourage preferred reaction pathways 12 1 2 3 4 5 6 1 2 3 4 5 6
- 13. MOLECULAR MATERIALS INFORMATICS Availability • The Green Lab Notebook (GLN) app should be in the iTunes AppStore by autumn • For iPhones, iPods & iPads • In the meanwhile, check out: 13 Green Solvents Lab Solvents Reaction101 Yield101
- 14. Acknowledgments http://molmatinf.com http://molsync.com http://cheminf20.org ! @aclarkxyz • Sean Ekins (Green Solvents) • Inquiries to info@molmatinf.com