Chemists unite! InChI is now built for collaboration — and scale

The InChI story is something like a Hollywood movie. It’s about the quest to encode the essential structural information of a chemical into a character string so it can be used, shared and found by any interested party. It features an unsung cast of quirky characters. And now, there’s even a happy ending that offers a new beginning for any organization seeking to pursue its chemical interests without sacrificing IP.

The International Chemical Identifier (InChI) opens in new tab/window — (pronounced IN-chee) — is widely used to identify the presence of a particular small molecule across the web or in a specific set of data. It has now been reinvented to take on other market-viable compounds such as organometallics, polymers and nanomaterials. In addition, once purely driven by memberships, InChI is now backed by a hybrid business model that allows customers to participate in a way that best suits their needs.

Sharing the love for open innovation

A future-resistant vision

Rapidly boosting its capacity in terms of both quality and quantity, InChI can now welcome new partners who want to go beyond the system’s roots in identifying small molecules and towards other market-oriented compounds.

With InChI’s source code and documentation now on the developer platform GitHub, anyone can contribute to making chemical compounds more identifiable across data stores. In the process, a community of chemists and companies, including fierce competitors, is being formed that sees the benefits of making chemistry data more sustainable and FAIR opens in new tab/window (Findable, Accessible, Interoperable, and Reusable) to drive innovation.

Birth of the InChI

In 1999, the InChI project was undertaken to solve a problem that had existed since the dawn of chemistry: How can a chemist be sure of what another chemist is talking about? Yes, you can draw a compound and share a picture. But how would you then search for it, particularly on the web?

Spurred by the rise of the internet, a group of cheminformatics researchers — initially including Drs Stephen Heller opens in new tab/window and Stephen Stein opens in new tab/window at the National Institute of Standards and Technology (NIST) opens in new tab/window — started to develop a standardized chemical identifier using an easily searchable string of text. Later, the work shifted to the International Union of Pure and Applied Chemistry (IUPAC) opens in new tab/window.

In the delightful video Birth of the InChI opens in new tab/window, we see the two Steves happily bickering about who came up with the original idea. Regardless, the end product had clear and universal advantages:

• It was non-proprietary (and hence free to use by any party)

• It could be computed from structural information (so it didn’t require a bothersome bureaucracy to OK each summation).

Soon, the value of having a standardized system became apparent as it was implemented in chemistry databases and toolkits worldwide — including the world’s largest chemical database, Elsevier’s Reaxys opens in new tab/window.

The InChIKey: Size matters

Still, a problem remained: the InChI needed to be shorter for easy searching. So a new version, the InChIKey, was released in 2007. While directly derived from the original InChI, it’s always only 27 characters long.

Soon after, in 2009, the InChI Trust took over the responsibility of its development, implementation and promotion.

“The Trust followed a very traditional model, with members making contributions for the further development of the InChI,” Gerd explains. “With only a limited membership, the Trust could only afford one developer to take on the full responsibility. And as a result, it sometimes took years between releases.”

The rise of GitHub and open-source

Despite the limitations, the developer, Igor Pletnov opens in new tab/window, a Moscow professor of inorganic analytics, became a beloved figure in the InChI development community opens in new tab/window as he slowly but surely proved the value of a shared and standardized chemical identifier.

However, with Prof Pletnov’s death in 2021, just as he had almost finished a critical bug fix release, InChI reached a crossroads. “He had all the code on one machine at the most important university in Russia, and unfortunately, it was unavailable,” says Gerd, who was then brought in to take over.

“His son helped us retrieve some backups of the code from the new release. But the entire test environment was lost. And the code was also very black box, and nobody really understood it. So, basically, we had to start from scratch.”

“The world had already changed anyway,” Gerd adds. “The world is now about open-source and the role GitHub can play. And this involved a completely new development and testing pipeline, so it’s easier to maintain and extend the standard.”

Laying a new foundation

The latest version opens in new tab/window (1.07) has been released on GitHub for anyone to build on, with IUPAC as an active partner. “It’s essential IUPAC is involved,” says Gerd. “After all, they are the ones who set the actual standards. So it’s a clear message that we’re not just working in the wilderness.”

Another essential part of developing the InChI to be more open and sustainable is to provide a test suite, including test code, data and documentation. “The test suite allows computing of in-house data behind an organization’s firewalls,” Gerd explains. “This way, we set objective and transparent quality criteria and enable convenient and replicable testing. Such a test environment is indispensable for collaborative development, especially with external contributors.”

Looping in a larger community

One early working relationship proved catalytic. “I was lucky to get in contact with Prof Sonja Herres-Pawlis opens in new tab/window of the Institute of Inorganic Chemistry at RWTH Aachen opens in new tab/window, who needed some extensions in InChI for her area of expertise,” Gerd recalls. “She found funding to sponsor two developers. And thanks to that and the involvement of other partners and sponsors, such as German FAIR data champions NFDI4Chem opens in new tab/window, the Data Literacy Alliance-DALIA opens in new tab/window and the Volkswagen Foundation opens in new tab/window, we could move forward.

“In addition, the Beilstein Institute opens in new tab/window provides additional chemoinformatic resources — and thereby acts as a great example of how organizations can support InChI with program development capacity and domain knowledge. This integrated approach allowed us to make the modernized software publicly available via GitHub as open source under MIT License.”

Various working groups opens in new tab/window also exist, including ones for polymers and mixtures, Markush structures, reactions and organometallics. “It’s snowballing now thanks to everyone being able to bring in their in-kind contributions,” says Gerd.

From membership drive to a community-driven hybrid business model

“This is the magic of having an open, collaborative and scalable model that allows people to participate if they want to support the initiative,” says Pieder. “And Gerd, as dedicated project lead, is here to ensure that all these contributions fit together by following the same rules — which also ensures more frequent and reliable updates.”

“Part of my role is convincing others to support us,” adds Gerd. “And this part of the job only gets easier as we get more channels and working groups. People can more easily find a way that suits their needs. After all, we still need continuous income from our members to further the scientific activities and push the standard forward. “And these are early days. So we are still very open to new ways of working together.”

The roadmap to innovation

Indeed, as older companies begin to regard their legacy data as a potential gold mine — especially if this data aligns with publicly available data — the demand for InChI seems set to grow.

“InChI is a neutral way to involve all these different information providers,” Pieder says. “And that’s why it’s an excellent idea to have this common ground of a trust tied to the standards body. It becomes a place where everyone can work together, share the costs and later reap the benefits. The roadmap is now there for all of us to drive innovation.”

In other words, any interested party can now join the trust and co-star in their own InChI sequel.