Oops and Downs of Resolving InChIs For the Chemistry Community

Oops and downs of resolving InChIs for the chemistry community

The InChI Has Arrived
My opinions :
The InChI is a crucial part of the future of structure-based relationships on the web
The semantic web of chemistry will sit on the shoulders of InChI until there is something better
InChIs and publishers are already in relationship – publishers who have not adopted will follow

PPP – Perfection vs Productive vs Prolific
The InChI is not perfect
There are limitations but they are acknowledged and in discussion
The InChI is very “productive”
InChIs are showing up in databases, manuscripts, spreadsheets, on publications, in software

A Lot of Variability in InChIs
Source: Unofficial InChI FAQ page

InChIStrings Hash to InChIKeys

HVYWMOMLDIMFJA-DPAQBDIFSA-N

The InChI Resolver

Inchis.chemspider.com

Resolve an InChI or InChIKey

Resolved

Connection Only Resolving

InChIs and Big Databases
There appears to be a bigger is better mentality with online databases
InChI has shown a lot of “overlap” in the ChemSpider database
Distinction : a unique chemical entity versus what it’s meant to be
Some simple examples …

Spot The Difference

Standard InChIKeys

Spot The Difference

55 Hits in 0.08 Seconds

Large Databases Contain Junk
InChI Resolvers will get us back to results but it’s a look up..
There is an enormous need for curation and linking resolved structures to “correct” structures – a manual task

Generate-It

Draw and generate

Generate

All Flavors

Historical and Future InChIs
The Standard InChI removed variability
There will be new variants in the future
There are already millions of historical InChIs “out there”
Resolvers should accommodate historical and future InChIs

In Our Resolver…

On to ChemSpider…

NEW Patents and Pubmed on ChemSpider

InChIs to Patents and Pubmed Articles

But there will be multiple resolvers…
Each publisher, database, scientist can choose not to publish their structures into a centralized database
There are many large online databases. There is no need to merge/mirror them – each can be a resolver
They need to be federated

Many ways to address resolving
Our approach is simple – lookup. We look up the structure. SIMPLE.

NCI/CADD resolver: 69 million structures

Differences
The NCI and ChemSpider Resolvers are “different”
Different databases behind the resolver – Feedback from NCI: “Preliminary results indicate that inchis.chemspider.com can resolve approx. 28% of our structures.”
Our approaches for resolving differ
Some features are different

The InChI Resolver Protocol
There will not be only one InChI Resolver – there will be many
Publishers
Commercial Databases
Free services and resources : PubChem, ChemSpider, NCI Database, ChEBI
Resolvers will not be mirrors of each other
There is no need to mirror when a protocol is in place

InChI Resolver Protocol
InChI resolving needs to be federated
A common protocol can connect resolvers so that a user gets a complete results set
Individual resolvers can have different capabilities but an agreed common protocol for resolving InChIs

Discuss with us on Google Groups
Draft protocol for ACS Spring 2010 from
RSC ChemSpider
NCI/CADD
PubChem
Symyx
Proof of concept hopefully by end of this year for initial feedback (NCI and ChemSpider
Join us at http://tinyurl.com/r7q9zc http://groups.google.com/group/inchiresolverprotocol

InChI trust
The founder members of the Trust: Elsevier, Thompson Reuters, Wiley, Nature Publishing Group, Royal Society of Chemistry, Symyx, FIZ-Chemie, Taylor & Francis and OpenEye

In InChIs We Trust
It was said….
“ There is a finite, but very small probability of finding two structures with the same InChIKey.”
The first collision was announced on Sunday by Jonathan Goodman

Spongistatin

Probabilities are what they are…
“ The molecule for which a collision has been reported … gives rise to 2 26 = 67,108,864 possible stereoisomers”
The probability of a clash is low but finite…and it happened.
OR…there may be a bug…work underway

The Future
InChI is here
InChIKeys are proliferating
The need for lookup is inevitable – the need for federated resolvers is obvious
Intention to provide draft resolver protocol by end of year
ACS Spring – unveil proof of concept

Acknowledgments
The InChI “Team” – leadership team, developers, advisors, funders and the community providing feedback
Royal Society of Chemistry

Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog

Oops and Downs of Resolving InChIs For the Chemistry Community

by Antony Williams, ChemConnector on Aug 20, 2009

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