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InChI Symposium, San Diego Aug 2019

Status and Future of the IUPAC InChI
InChI Symposium held at the San Diego Convention Center, 23-24 August 2019

Introduction

Ray Boucher: InChI Trust Report

Ian Bruno: Overview of the Meeting

Community perspectives

Steffen Pauly: Deposit of chemical structure data from publications to public databases

Steve Boyer: Patents

Lutz Weber: Ontologies

Tina Qin:Teaching InChI to chemistry students

Peter Linstrom: NIST WebBook

Bob Belford: Education – InChI OER

Hunter Moseley: Isotopologues

Richard Kidd: Open Source Development

Roger Sayle: SMILES and IUPAC

Yulia Borodina: InChI at the FDA – recent developments, current challenges

Markus Bussen: ChemChain

Project and working group updates

Alex Clark: Mixtures (CDD/NIH projects) MinChI

Leah Rae McEwen, Evan Bolton: Large Molecules – complementarity w/ HELM & Mixtures

David Deng: Use case of HELM

Andrey Yerin: Polymers

Gerd Blanke: Reaction Inchi, RInChI

Marc Niklaus: Tautomers

Ian Bruno: Organometallics

Richard Hartshorn: QR Codes

Vin Scalfani: SMILES+ 

Future discussions

Mark Niklaus: InChI 2.0

Andrey Yerin: Stereochemical configuration

Jonathan Goodman: Variability

Summary

Richard Kidd, Ray Boucher: Keeping up the momentum: Brief report from the InChI San Diego workshop

IUPAC/InChI mini-workshop

There will be an IUPAC/InChI mini-workshop at the upcoming Boston ACS meeting. It will be held on the Friday Aug 17 and Saturday Aug 18 prior to the ACS meeting in the Westin Waterfront next to the convention center. There are several break-out sessions planned on current topics relevant to InChI and IUPAC data standards, and some meetings of the InChI Trust. We envision this to be a working meeting focused on advancing various projects and proposals at various stages of completion.

Topics and discussion leads expected:
[1] Large molecules (Evan Bolton)
[2] Organometallics (Ian Bruno)
[3] Mixtures (Leah McEwen, Gerd Blanke, Alex Clark)
[4] Education portal (Bob Belford, Vin Scalfani)
[5] IUPAC file formats – SMILES, CTAB (Evan Bolton, Vin Scalfani)
[6] Variability in InChI general discussion (Leah McEwen, Evan Bolton)
[7] Open discussion on other topics of community interest

Working agenda for the meeting is here.

 

For further details please contact Evan Bolton or Leah McEwen

Call for papers – Pure & Applied Chemistry – Research Data, Big Data and Chemistry

The International Union of Pure and Applied Chemistry (IUPAC) held a symposium on Research Data, Big Data, and Chemistry at the 2017 World Chemistry Congress in São Paulo. The Union published a special issue of Chemistry International (CI) to accompany the symposium (https://doi.org/10.1515/ci-2017-0300). We have been asked to develop a special issue on a similar topic for Pure and Applied Chemistry (PAC), the scientific and technical journal of the Union. The CI issue focused on the historical context around research data in chemistry, and also looked at current issues and advocacy around research data. In the PAC issue, we also seek to include more specific examples of research data sharing, successes of big data analyses in chemistry and related areas, ethical considerations in applications of big data technologies in the sciences, as well as education and outreach. The target article length is 8-15 published pages, approximately 4000-7500 words. We aim to receive manuscripts before the end of the year, for publication in the first half to 2018. PAC offers ahead-of-print publication, so articles will be posted as accepted. In addition, PAC offers hybrid Open Access options for authors who desire immediate OA. Authors are also allowed to self-archive the final published manuscript 12 months after publication.

We would welcome your submission to this special issue. If you have any questions, please let us know. We can provide additional details, including instructions on submission. All manuscripts will be subject to the usual PAC peer review process. Also, if you have any colleagues who might be interested in submitting a publication in this area, please let us know.

Thanks for your interest,

Leah McEwen, Cornell University
David Martinsen, David Martinsen Consulting

Update – March 2012

An all-day symposium dedicated to the International Chemical Identifier (InChI) will be held at the 243rd ACS National Meeting in San Diego, CA. In sixteen presentations (including several talks by InChI Trust members and supporters) the current status and future of the InChI will be discussed and the use and usefulness of InChIs in databases, publications, software and other resources will be presented. The InChI Symposium Speakers Dinner is sponsored by the InChI Trust.

The InChI Symposium takes place in Room 27A of the San Diego Convention Center on Wednesday, 28th March 2012, and starts at 8:30 am.

Update – October 2011

The InChI Trust and the International Union of Pure and Applied Chemistry (IUPAC) are pleased to announce the release of a new version of the IUPAC International Chemical Identifier (InChI) software. Version 1.04 of the open source software is now available on the InChI Trust Download page. This version now supports the chemical elements up to 112, copernicium (the last one which is currently recognized by IUPAC; support for elements 105-112 is newly added). The inchi-1 executable (both Windows and Linux versions) now allows the processing of multiple input files in a single run (common file name wildcards are recognized).

The InChI Certification Suite is now available from the InChI Trust. This software was developed to check that an installation of the InChI program has been performed correctly. More information on the InChI Certification Suite and the contact information can be found here.

New InChI working groups on “Inorganics” and “Biopolymers & Proteins” are planned for 2012.

Update – July 2010

The InChI Trust has initiated a contract with GGA Software Services LLC for its subsidiary SciTouch LLC to develop software programs to test and certify that InChIs and InChIKeys produced by whatever means are correct and valid. This work will expand on and make even more robust the original programs developed by NIST as part of the original InChI project. Trust members and others are contributing both large and diverse databases for testing to assure that current and future versions of the InChI software are of the highest possible quality and meet all needs of the community using the InChI algorithms. We expect the testing software to be available in autumn 2010.

InChI Trust release new version of software – June 2010

28 June 2010

The InChI Trust (InChI Trust) and the International Union of Pure and Applied Chemistry (IUPAC) are pleased to announce the release of a new version of the IUPAC International Chemical Identifier (InChI) software. Version 1.03 of the open source software is now available.

The InChI algorithm turns chemical structures into machine-readable strings of information. Among other enhancements, version 1.03 integrates the generation of the standard InChI string and non-standard, customized strings. The standard InChI/InChIKey should be used as a public identifier to allow linking and interoperability. Options to generate the non-standard InChI within the same package make it easier for organisations to use these additional options within their internal systems, conforming to their business rules. Developers and users can download the new software from here or here.

Version 1.03 also fixes a number of minor bugs, with respect to stereochemistry. It clarifies how undefined/unknown stereochemistry is handled, and clarifies some structure perception and stereo interpretation option issues.

“We are delighted to release InChI version 1.03 to the chemical community. This unification of the previous versions of the InChI algorithm means, for the first time, users can generate both the standard and non-standard versions of InChI from the same software.” says Dr Jason Wilde, Chairman of the InChI Trust. “This release also marks the first of many public outputs from the newly formed InChI Trust.”

IUPAC and the InChI Trust recommend the use of the standard InChI, an interoperable standard, as it enables linking between journals, databases and other sources of chemical information. This interlinking is one of the major advantages of the InChI standard.

Originally developed by IUPAC, InChIs are unique to the compound they describe and can encode absolute stereochemistry. The InChI was developed as a new, non-proprietary, international standard to represent chemical structures. The software is open source, with ongoing development done by the community.

Formed in 2009, The InChI Trust is a not-for-profit organization, established to expand and develop the InChI chemical structure representation algorithm. InChI Trust Members and Associates help support, shape, and direct the Trust’s ongoing development: ACD/Labs, ChemAxon, Elsevier, FIZ CHEMIE, Informa/Taylor & Francis, IUPAC, Microsoft, Nature Publishing Group, OpenEye, The Royal Society of Chemistry, Symyx Technologies, Thomson Reuters, and Wiley.

For further information, please contact: Project Director, Dr. Stephen Heller at Steve@InChI-Trust.org

Links:

About The InChI Trust

The InChI Trust is a not-for-profit organization to expand and develop the InChI chemical structure representation algorithm. The InChI project was initially undertaken by the International Union of Pure and Applied Chemistry (IUPAC) with the cooperation of National Institute for Standards and Technology (NIST). The IUPAC International Chemical Identifier (InChI) is an alphanumeric character string generated by an algorithm. The InChI was developed as a new, non-proprietary, international standard to represent chemical structures. In 2009, a standard version of InChI and the InChIKey were released and the InChI Trust was established to support the continued development of InChI, and maintenance of the InChI algorithm.

Update – March 2010

A contract to investigate the feasibility of QC/validation tools, documentation and InChI extensions has been awarded to Digital Chemistry and the results will be available in mid 2010.

Support for the main InChI developer has been secured.

To expedite progress by the IUPAC InChI Subcommittee working groups, the InChI Trust has provided funds to hold the initial Task Group meetings for the working groups examining Markush structures and polymers, splitting the funding of these two groups with IUPAC.

Elsevier Joins InChI Trust as a Charter Member – September 2009

10 September 2009

Originally distributed by Elsevier

Neuchâtel, Switzerland, 10 September 2009 – Elsevier, a leading publisher of scientific, technical and medical information products and services, today announced it has become one of the Charter Members of the InChI Trust and will have a seat on the board at the first InChI Trust Board meeting on September 11th.

Originally developed by the International Union of Pure and Applied Chemistry (IUPAC), the IUPAC International Chemical Identifier (InChI) is a non-proprietary, international standard to represent chemical structures as an alpha-numeric character string generated by an algorithm. InChIs are machine readable and therefore allow chemistry and chemical structures to be much more navigable and discoverable. The InChI Trust is a not-for-profit organization established to develop and improve on the current InChI standard and thereby further enable the interlinking of chemistry and chemical structures on the web.

Recognizing that scientists need to navigate through a range of information sources, Elsevier has already implemented InChI Keys within Reaxys®, the leading workflow solution for synthetic chemists. The use of InChIs also ties into the broader Elsevier strategy of Content Innovation in which research articles are enriched to provide more depth, value, and context to our users. For the chemistry journals available on ScienceDirect, the incorporation of InChI keys will accordingly improve the discoverability and organisation of compounds within the chemistry scientific literature, facilitating and accelerating connectivity to other research tools and content sources.

“Elsevier understands that chemists use a variety of tools and information sources in their research work,” said Dr. David Evans, Director Scientific Affairs at Elsevier Properties SA, and representing Elsevier at the Trust Board meeting. “The aim is to help them to navigate seamlessly through the relevant data and ultimately help them to increase their research productivity. We believe that InChIs will make an increasing contribution to this ambition and we are therefore delighted to be involved in the InChI Trust from the start.”

“Elsevier is without doubt one of the world’s most important providers of chemistry information.” said InChI Trust Project Director, Dr. Stephen Heller. “They have used InChIs since the outset and we are all delighted to have them as charter members of the InChI Trust as it further reinforces the message that InChIs are set to become a major standard in the communication of chemistry information.”

For more information about Elsevier joining the InChI Trust please contact David Evans, Director Scientific Affairs, Elsevier Properties SA, at David.Evans@reedelsevier.ch

About Elsevier

Elsevier is a world-leading publisher of scientific, technical and medical information products and services. The company works in partnership with the global science and health communities to publish more than 2,000 journals, including The Lancet and Cell, and close to 20,000 book titles, including major reference works from Mosby and Saunders. Elsevier’s online solutions include ScienceDirect, Scopus, Reaxys, MD Consult and Nursing Consult, which enhance the productivity of science and health professionals, and the SciVal suite and MEDai’s Pinpoint Review, which help research and health care institutions deliver better outcomes more cost-effectively.

A global business headquartered in Amsterdam, Elsevier employs 7,000 people worldwide. The company is part of Reed Elsevier Group PLC, a world-leading publisher and information provider. The ticker symbols are REN (Euronext Amsterdam), REL (London Stock Exchange), RUK and ENL (New York Stock Exchange).

About Elsevier Properties SA

Elsevier Properties SA since 2007 has been the owner of the Beilstein Database and the Reaxys trademark. Elsevier Properties SA is a part of Reed Elsevier.

About The InChI Trust

The InChI Trust is a not-for-profit organization to expand and develop the InChI chemical structure representation algorithm. The InChI project was initially undertaken by the International Union of Pure and Applied Chemistry (IUPAC) with the cooperation of National Institute for Standards and Technology (NIST). The IUPAC International Chemical Identifier (InChI) is an alpha-numeric character string generated by an algorithm. The InChI was developed as a new, non-proprietary, international standard to represent chemical structures. In 2009, a standard version of InChI and the InChIKey were released and the InChI Trust was established to support the continued development of InChI, and maintenance of the InChI algorithm.

Media Contact:

David Evans
Elsevier Properties SA
David.Evans@reedelsevier.ch

Launch of the InChI Trust – July 2009

21 July 2009

Originally distributed by Nature Publishing Group

The InChI Trust, a not-for-profit organisation to expand and develop the InChI Open Source chemical structure representation algorithm, is formally launched this week. Originally developed by the International Union of Pure and Applied Chemistry (IUPAC), the IUPAC International Chemical Identifier (InChI) is an alpha-numeric character string generated by an algorithm. The InChI was developed as a new, non-proprietary, international standard to represent chemical structures. The Trust aims to develop and improve on the current InChI standard, further enabling the interlinking of chemistry and chemical structures on the web. The connection with IUPAC is maintained through IUPAC’s InChI Subcommittee.

The InChI algorithm turns chemical structures into machine-readable strings of information. InChIs are unique to the compound they describe and can encode absolute stereochemistry Machine-readable, the InChI allows chemistry and chemical structures to be navigable and discoverable. A simple analogy is that InChI is the bar-code for chemistry and chemical structures. The InChI format and algorithm are non-proprietary and the software is open source, with ongoing development done by the community.

“The goal of the InChI Trust”, says Project Director Stephen Heller “is to continue to develop the InChI and InChIKey, the condensed machine-searchable version, as a tool to enable widescale linking of chemical information.”

The InChI Trust was formally incorporated in the UK in May 2009, and now has 6 charter members: The Royal Society of Chemistry, Nature Publishing Group, FIZ CHEMIE Berlin, Symyx Technologies, Taylor & Francis and OpenEye. Further organizations and publishers are in the process of joining the InChI Trust.

“Nature Publishing Group is delighted to be a charter member of the InChI Trust”, says Jason Wilde, Publisher for the Physical Sciences, Nature Publishing Group. “We view the ongoing maintenance of the InChI algorithm, and the resulting adoption of InChI, as important for the development of chemistry communication. The interlinking that the InChI offers between journal content and databases ensures that chemistry is the first truly web-enabled scientific discipline.”

“The InChI has already gained a wide user base,” says Richard Kidd, Informatics Manager at the Royal Society of Chemistry, “and the Trust will ensure continuing development and support for this key standard, helping to link together chemical resources across the internet. The RSC is proud to support the InChI Trust.”

Since the introduction of the InChI in 2005, there has been widespread take-up of InChI standards by public databases and journals. Today, there are more than 100 million InChIs in scientific literature and products.

To date, numerous databases, journals, and chemical structure drawing programs have incorporated the InChI algorithm. These include the NIST WebBook and mass spectral databases, the NIH/NCBI PubChem database, the NIH/NCI database, the EBI chemistry database, ChemSpider, Symyx Draw and many others.

The initiative serves chemists, publishers, chemical software companies, chemical structure drawing vendors, librarians, and intermediaries by creating an international standard to represent defined chemical structures. This provides a consistent, credible and compatible way for databases of chemical structures to be linked together for the benefit of users of chemical information around the world.

For further information, please contact:

Project Director, Dr. Stephen Heller at Steve@InChI-Trust.org

Background notes

The InChI project was initially undertaken by IUPAC with the cooperation of National Institute for Standards and Technology (NIST). In 2009, a standard version of InChI and the InChIKey were released. Members of the InChI Trust will pay annual dues to support the continued development of InChI, and maintainance of the InChI algorithm. This income will be used exclusively for InChI algorithm development, maintenance, outreach, and educational activities associated with the project.

Details of the up-take by many chemical database providers, software developers, and journal publishers are available at here.