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Highlights of 2021 Fall ACS Meeting, Aug. 22-26, 2021 (Atlanta, GA & Virtual) Part 2: CINF 8/23-8/24 Part 2 of Highlights of 2021 Fall ACS Meeting includes selected presentations selected presentation several CINF Symposiums for Aug. 23-26, 2021: Natural products & food informatics (8/23) (5 presentations), Machine and Deep Learning in Drug Discovery (8/24) (1 presentations); Chemical Information Across the Chemical Enterprise (8/24) (2 presentation) See Part 1 of Highlights of 2021 Fall ACS Meeting (CHAL Aug. 22-23, 2021 and CINF
Aug. 22, 2021 in the main body of this PIUG-PF post
[CINF] Division of Chemical Information (Program)
August, 23, 2021
10:30am - 12:30pm ETNatural products & food informatics (Program w/abstracts)
Organizer: Jose Medina-Franco
The symposium presents advances on informatics applications to advance natural products research including but not limited to drug discovery, and food chemistry. Examples of contributions include developments on compound databases… https://acs.digitellinc.com/acs/live/21/page/411/1?eventSearchInput=&eventSearchTrack=83&eventSearchTag=51&eventSearchRoom=70
10:30am - 10:50am ET
CAS: providing access to more than 110 years of natural products research Dr. Elaine N. Cheeseman, Senior Searcher, CAS, Columbus, Ohio
…For over 110 years, CAS has been providing access to research on chemistry and surrounding areas, including natural products, from patents, non-patents, and other document types. CAS’ intellectual indexing includes concepts, exemplified compounds, Markush structures, and reactions to enable the retrieval of information relating to natural products research. The sources can be searched in a variety of ways depending on the type of information which is required. This information is accessible on both STNext and SciFinder-n. A new CAS visualization tool, ChemScape, will be shown using a natural products example. 10:50am - 11:10am Collecting and standardizing natural products: The COCONUT projectMaria Sorokina, Christoph Steinbeck, Friedrich-Schiller-Universitat Jena (Germany)… To facilitate in silico NP studies, we assembled the COllection of Open Natural Products (COCONUT) from more than 55 open resources and it is currently the biggest repository for validated and predicted NP. A multitude of molecular features is precalculated for the NPs in COCONUT, facilitating compound search and selection on physicochemical and structural properties. The COCONUT database web interface allows for diverse simple searches (e.g. by molecule name, InChI, InChI key, SMILES, molecular formula, predicted bioactivity), advanced search by molecular features, but also chemical searches based on structure similarity and substructure. COCONUT: https://coconut.naturalproducts.net.
11:10am - 11:30am ET SistematX, a free web portal for the management of secondary metabolites Chonny Alexander Herrera Acevedo, Renan Paiva; Lucas Lucena; Marcus Scotti, Universidade Federal da Paraiba, Brazil
… Here, a Web Portal of secondary metabolites called SistematX is described (http://sistematx.ufpb.br), which was developed at the Federal University of Paraíba, Brazil, being introduced for the first time in 2018, considering the following aspects: (a) the ability to search by structure, SMILES, compound name and species; (c) compound data results include important characteristics for natural products chemistry… (d) the user can find specific information for taxonomic rank (from family to species) of the plant from which the compound was isolated, the searched-for molecule, the bibliographic reference and Global Positioning System (GPS) coordinates; and (e) The ability to save chemical structures found by searching with the batch download option…
11:30am - 11:50am ET
NP navigator: A new look at the natural product chemical spaceYuliana Zabolotna (University of Strasbourg, France), Dr. Peter Ertl (Novartis Institutes for BioMedical Research, Basel, Switzerland ); Dragos Horvath, Fanny Bonachera, Gilles Marcou & Alexandre Varnek (University of Strasbourg, France) … we present NP Navigator – a free, intuitive online tool for visualization and navigation through the NPs chemical space. It is based on the hierarchical ensemble of more than 200 generative topographic maps (GTM), featuring NPs from the COCONUT [see above], bioactive compounds from ChEMBL and commercially available molecules from ZINC. …. Hierarchical extension of GTM, combined with maximum common substructure (MCS) detection, allows to establish the link between the generalized visualization of the known chemical space of NPs/NP-like molecules and structural features of small compound clusters….NP Navigator allows to efficiently analyze …. commercial availability of NPs… and their close analogs (pseudo-NPs). Users could project several external molecules (“chemical trackers” ) allowing to trace particular chemotypes in the NPs chemical space and detect analogs of the compound of interest. https://infochm.chimie.unistra.fr/npnav/chematlas_userspace
11:50am - 12:10pm ET
Navigating the known natural products chemical space
Stefan Furrer, Ioana Ungureanu & Andrew Daniher (Givaudan Flavors Corp, Cincinnati, OH); Cristian Bologa & Tudor Oprea (University of New Mexico School of Medicine, Albuquerque, NM)
…Here we are describing approaches for the representation and interactive visualization of the natural products chemical space, allowing the rapid identification of areas of relative low interest, as well as high-value sub-spaces. The integration of structural data with data from physico-chemical parameters, to occurrence in nature and biological activities, enable an effective navigation and identification of spaces of interest and structurally closely related members of natural products.
August 24, 2021
04:30pm - 06:25pm ETThe Race and Road Ahead of Machine and Deep Learning in Drug Discovery, Metabolomics, and Toxicology - CINF SymposiumOrganizers: Karina Martinez Mayorga, Jose Medina-Franco
07:05pm - 07:25pm ET Artificial intelligence in chemistry-related discoveries: Current trends and future opportunities Zachary Baum, Dr. Qiongqiong Angela Zhou, Philippe Ayala, Yanan Zhou and Xiang Yu, Chemical Abstracts Service, Columbus, OH
… Here, the CAS content collection, covering chemistry from thousands of journals, 64 patent authorities, and many other sources, is analyzed as a corpus of literature to reveal the current trends and future opportunities of AI in chemistry. We contextualize the current research landscape by classifying and quantifying AI-related chemistry publications from 2000 to 2020. AI applications in various research areas of chemistry, their conditions for successful applications, and the connections among different research areas are discussed together with emerging use cases and challenges. Our work may assist researchers working in AI-amenable chemistry to identify growth opportunities, potential collaborations, and emerging work in underdeveloped areas.
August 24, 2021
07:00pm - 09:00pm ETChemical Information Across the Chemical Enterprise - CINF Symposium 07:00pm - 09:00pm USA / Canada - Eastern - August 24, 2021 | Room: Row 5 Organizer: Judith N Currano, University of Pennsylvania
07:00pm - 09:00pm Community involvement within NFDI4Chem towards digitalisation of all key steps in chemical research
Willis Muganda (Universitat Siegen, Germany); Hans-Georg Weinig (Gesellschaft Deutscher Chemiker eV, Frankfurt am Main, Germany) NFDI4Chem is an initiative to build an open and FAIR infrastructure for research data management in chemistry. Since its launch in 2018 as a grass root movement, there has been enormous support from different partners within the chemistry community. The main fundamental aim of NFDI4Chem is to promote Open Science and Research Data Management (RDM) in accordance with the FAIR data principles. Thus, to create a holistic concept for access to and (re-)usability of research data…
07:00pm - 09:00pm ET Pharos: An open data resource for examining target, disease and ligand interactions Timothy Sheils, Keith Kelleher; Dac-Trung Nguyen, National Center for Advancing Translational Sciences/NIH, Bethesda, MD Pharos is a web resource that originated from the NIH "Illuminating the Druggable Genome" (IDG) program to characterize the understudied regions of the druggable genome. … Pharos is built on top of the Target Central Resource Database (TCRD), and the most recent update for TCRD now incorporates 78 disparate data sources, incorporating target expression, protein-protein interaction, disease ontology and chemical activity databases. …
See Part 1 of Highlights of 2021 Fall ACS Meeting (CHAL Aug. 22-23, 2021 and CINF
Aug. 22, 2021 in the main body of this PIUG-PF post
Part 1 of Highlights of 2021 Fall ACS Meeting includes 7 selected presentations CHAL Symposiums Aug. 22-23, 2021 and selected presentation of the following CINF Symposiums for Aug. 22, 2021: Chemistry Babylon (6 presentations), Reaction Informatics (5) and ML/AI for Organic Chemistry (1)
See Part 2 of Highlights of 2021 Fall ACS Meeting which includes selected presentations of CINF symposia for Aug. 23-24, 2021 and posted in the reply to this PIUG-PF post.
[CHAL] Division of Chemistry & the Law (Program)
Aug. 22, 2021
Strengthening Your Patent Rights in Light of Recent Federal Circuit Court Decisions Symposium [CHAL]
04:30pm - 05:00pm ET
Update on Federal Circuit and PTAB case law affecting chemical scientists
Dr Andrew Berks, Ph.D., J.D. (Gallet Dreyer Berkey LLP, New York, NY)
…This talk will review recent Federal Circuit Court decisions on patents and provide insights to scientists on how to write and review patent applications such that the patents that are granted from these applications would be successful in a court of law.Note: Andy Berks was PIUG Chair in 1992-1994
06:00pm - 06:30pm ET
How Recent Federal Court Decisions and USPTO Proceedings are Impacting Intellectual Property Rights in the Chemical Arts Fields
Katherine Rubino, Caldwell Intellectual Property, Boston, MA
… Discussed in this presentation will be an overview of various recent cases that have been decided in Federal Courts, and the impact of these cases on intellectual property rights…specifically … in the chemical arts space.
Aug. 23, 2021
08:00am - 10:00am ET
Post issuance proceedings: Certificates of Correction, Supplemental Examination, and Reissue Patents [CHAL]
Jonathan Kennedy, McKee, Voorhees & Sease PLC, Des Moines, Iowa, US [Presenter]
…This symposium will cover common types of issues identified by patentees with their issued patents and options available to address them including, Certificates of Correction, Supplemental Examination, and Reissue Patents
Hot Topics in IP Law Symposium [CHAL]02:00pm - 02:30pm ET
Anthony Zucchero, Meunir Carlin & Curfman, Atlanta, GA
… This presentation will outline the legal standard for inventorship using several key Federal Circuit Cases, with a particular focus on cases related to the chemical and pharmaceutical arts.
02:30pm - 03:00pm ET
Is your structure sound? Testing the limits of the structural obviousness framework Dr. Kimberlynn B. Davis, J.D., Ph.D., Kilpatrick Townsend & Stockton LLP
To determine whether structurally “close” compounds are obvious for patentability purposes, the Federal Circuit established a framework that has been consistently applied since its inception, often with favorable results for the patentee in Hatch-Waxman litigations. Patent applicants are also able to utilize this framework to establish the patentability of novel compounds, though examiners continue to refute the applicability of the framework by pointing to older standards. This presentation will provide an overview of the framework and its application in key cases…
03:00pm - 03:30pm
Is the BPCIA the new ANDA?
Shannon Patrick, Finnegan Henderson Farabow Garrett and Dunner LLP, Washington, DC
ANDA litigation has become almost a more specialized subset of patent law that focuses on the filings of new drug applications and the statutorily infringing abbreviated new drug applications. Recently, Congress has enacted the BPCIA which creates a similar scheme to the laws regulating ANDA litigations for biological products. This presentation will discuss this new abbreviated pathway for biosimilars and try to elaborate on the steps to the BPCIA patent dance.
04:30pm - 05:00pm ETThe importance of the priority application
Jonas Jarvholm, Ballard Spahr LLP, Atlanta, GA
…This talk will focus on the disclosure in the priority application compared to the disclosure in a conversion application and how this relates to prior art and intervening inventions.https://acs.digitellinc.com/acs/live/21/page/411/1?eventSearchInput=&eventSearchTrack=63
[CINF] Division of Chemical Information (Program)
August, 22, 2021
Chemistry Babylon: Overcoming Language Barriers to Share Chemical Information Symposium [w/ abstracts]
Organizers: Susan K Cardinal, David Deng
In this symposium we will explore the roots of technical language translation, discuss services that support chemists whose primary language is not English and find out how close we are to a "universal translator."
04:40pm - 05:05pm ET
Semantic and chemistry structure search on 250 million scientific documents
Lutz Weber, OntoChem, Halle (Saale), Sachsen-Anhalt, Germany
… In the current presentation we will demonstrate semantic and chemistry structure search in more than 110 million scientific articles and 130 million patents. Based on our context sensitive named entity recognition, we also extract specific relationships between those indexed entities - such as chemical reactions or biological activities of chemical compounds. These relationships are stored and searched using a novel, patented database technology - xfactDB - that allows to efficiently store complex and structured scientific data.
Examples provided: which natural products from edible plants support the treatment of diabetes ; which non-lactame natural product compound classes are likely to exhibit anti-infective properties; what is the likelihood of a succesful clinical development of a given chemical compound ?05:05pm - 05:30pm ET
IUPAC Apocalypse: How changing standards can make chemical nomenclature knowledge and software obsolete
Roger Sayle, NextMove Software Ltd, Cambridge, Cambridgeshire, UKThe latest 2013 revision of IUPAC's "blue book" includes one obscure recommendation rule (sec. P-220.127.116.11, [which] requires the use of Phane Nomenclature for organic molecules for which it is (sufficiently) applicable, …including names of many drug-like molecules. For example, WHO’ INN for Danuglipron is (now) officially named (12S)-94-cyano-92-fluoro-7-oxa-3(1,2)-benzimidazola-6(2,6)-pyridina-5(1,4)-piperidina-1(2)-oxetana-9(1)-benzenanonaphane-36-carboxylic acid.05:35pm - 06:00pm
Extracting chemicals, reactions and other named entities from non-English documents
Richard Gowers, John Mayfield; Roger Sayle, NextMove Software Ltd, Cambridge, UK
...In this talk we will present the latest advances in NextMove Software’s Leadmine software, and how it can be used to extract chemical data from sources in a variety of languages including Chinese, Japanese and Korean. We will discuss the approaches used to process chemical nomenclature and reaction descriptions, the algorithms used for correcting perceived errors, and how these are affected when considering the interlingual dimension.
06:00pm - 06:25pm
Challenges of chemical name recognition in Japanese documents
Bela Pukanszky, Árpád Figyelmesi, Chemaxon, Budapest, Hungary
…We investigate the bidirectional conversion of chemical and biochemical structures and names in various formats [in Japanese documents which use the combination of katakana, kanji, roman characters and numbers], in addition to IUPAC and traditional name support, also recognizing common names, and CAS registry numbers. We enable indexing documents, facilitating retrieval of the exact location of the chemical data extracted for each document.
07:10pm - 07:35pm ET
Roots of finding chemical translations: Tools that uncover technical reports
Chris Sherratt, MIT, Cambridge, MA
… This presentation will briefly review the resources used to find English translations in the technical report literature [which decades ago expanded access to chemistry's international literature]; the tools' digital availability through the HathiTrust Emergency Access Temporary Service (ETAS); and how one particular resource might be used to uncover an institution’s own historical, chemical research.
07:35pm - 08:00pm
Mitigating challenges in multilingual communication for the scientific community: Using machine translation to search and understand the world of scientific information
Ian Wetherbee (Google Inc, Mountain View, CA); Stephen Boyer (Collabra Inc, San Jose, CA); Jane Frommer (IBM Almaden Research Center, San Jose, CA)
…Google Patents implements Google Translate to bring the world’s patent and scientific literature to the public. This talk presents technical advances in architecture and quality of neural machine translation of international scientific documents, from searching to understanding content.https://acs.digitellinc.com/acs/live/21/page/411/1?eventSearchInput=&eventSearchTrack=83&eventSearchTag=487&eventSearchRoom=190
August 22, 202102:00pm - 04:00pm ET
Reactions: Representation, Planning and Robotics Symposium [CINF] [w/ abstracts]
[w/ abstracts]Organizers: Gerd Blanke, Prof. Jonathan M Goodman, Guenter Grethe, Christina KeilWhat information is necessary to record about a reaction? How can machine learning and AI support the process? … Topics include… RInChI, UDM, AI methods for analysing reaction databases, data exchange formats to run and extract data from synthesis, and robots for synthesis execution.https://acs.digitellinc.com/acs/live/21/page/411/1?eventSearchInput=&eventSearchTrack=83&eventSearchRoom=8511:25am - 11:50am
Extracting chemical reaction information from patent documents
Lutz Weber, Matthias Irmer; Shadrack Barnabas; Claudia Bobach; Christoph Ruttkies, OntoChem (Germany)
… The BQ SciWalker Open Data project  maintains BQ chemistry-related tables of … (>4 million chemical reactions that are updated daily from mentions found in the text or images of patents. In the present talk we present our efforts to extract reaction SMILES, RInChIs, and RInChI-Keys as well as unique public Ontology Concept IDentifiers, OCIDs  for each unique chemical reaction. Extracted reactions are classified into their respective reaction ontology classes using compregensive SMIRKS representations of reaction transforms like SMARTS in case of compounds . A particular challenge of such reaction classification is a correct mapping of the atoms in reacting centers. We have compared the precision of several methods for such atom mappings.  https://console.cloud.google.com/bigquery?project=sciwalker-open-data
 Automated compound classification using a chemical ontology. J. Cheminform. 2012, 4(1), 40. 11:50am - 12:15pm
RInChI: Collecting and integrating more reaction data Prof. Jonathan M Goodman, University of Cambridge (UK); Gerd Blanke, StructurePendium Technoligies GmbH, Germany
… In this talk we will report the results of an investigation into how effectively the RInChI [The Reaction InChI] is able to link different reports of the same reaction and distinguish similar but different reactions. We will also discuss how it is possible to gather more data for databases and what additional information could usefully be associated with the standard RInChI. Finally, we will discuss how developments in the InChI itself (stereochemistry, organometallics and variable structures) might strengthen the RInChI's ability to identify reactions.
02:00pm - 02:25pm ET
Inferring missing molecules in incomplete chemical equations Dr. Alain C. Vaucher, Presenter; Philippe Schwaller; Alessandra Toniato; Teodoro Laino (IBM Research Europe, Rüschlikon, Zürich, Switzerland)…We present a deep-learning model based on the transformer architecture that infers the molecules in partial reaction SMILES strings . This model does not contain any chemical knowledge except the one learned from the data during training. We illustrate its application for data curation, as well as its use for forward and retrosynthesis prediction. Vaucher, A.C., Schwaller, P., Laino, T., 2020. Completion of Partial Reaction Equations . https://doi.org/10.26434/chemrxiv.13273310.v1
02:25pm - 02:50pm
Deep learning prediction of reaction conditions Matthew Clark1, Eric Gilbert1; Frederik van den Broek2 (1)Elsevier Inc Philadelphia, PA; (2) Elsevier BV, Amsterdam, Noord-Holland, Netherlands… The Reaxys database has reactions and conditions reported for over 20 million organic reactions reported over the last 200 years. In many cases the same reaction has been reported using diverse conditions by many different authors. We have used these diverse conditions to train a neural-network that predicts the reagents, catalysts, solvents, time, temperature to carry out any proposed reaction, as well as yield for the products. We will present our results and share our experience from building these models.
03:15pm - 03:40pm ET
The unified data model [UDM]
Gerd Blanke (StructurePendium Technoligies GmbH, Germany); Elena Herzog & Markus Fischer (Elsevier BV, Amsterdam, Netherlands); Jaroslaw Tomczak (Informatics Unlimited Ltd, Cambridge, UK)…The Unified Data Model (UDM) aims at improving data exchange and integration of chemical reaction data for efficient search, visualization, analysis and predictive modeling…. The UDM project has been fully moved to open source under the MIT license this year.
In our presentation, we will discuss the current status of the data exchange and integration needs and how the UDM can facilitate an easy exchange of data in a variety of reaction data workflows and provide an example of how the UDM is used to simplify the data exchangehttps://acs.digitellinc.com/acs/live/21/page/411/1?eventSearchInput=&eventSearchTrack=83&eventSearchRoom=85August 22, 202104:30pm - 06:30pm ET
Machine Learning & AI for Organic Chemistry Symposium [w/ abstracts] Organizer: Connor Coley (MIT)This symposium will focus on the application of machine learning techniques to the understanding and prediction of chemical reactivity. Specific topics might include data-driven catalyst design, reaction product prediction, reaction yield prediction, optimization of reaction conditions, reactive force fields.https://acs.digitellinc.com/acs/live/21/page/411/1?eventSearchInput=&eventSearchTrack=83&eventSearchTag=253&eventSearchRoom=70
04:55pm - 05:15pm ET
NameRxn: More than just a reaction classifier
Ingvar Lagerstedt, Roger Sayle; John Mayfield, NextMove Software Ltd, Cambridge, UKNameRxn was developed to recognise and categorise reactions from their connection tables [from… journal or patent data. ] The recently added reactions together with improvements to existing reaction rules and data extraction increased the classification rate from ~ 66 to ~ 73 % on reactions extracted from patents (Pistachio). …https://acs.digitellinc.com/acs/live/21/page/411/1?eventSearchInput=&eventSearchTrack=83&eventSearchTag=253&eventSearchRoom=70
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