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

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

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

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 …

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

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

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

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.

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 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

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

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

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

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

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 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

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

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