Oops and Downs of Resolving InChIs For the Chemistry Community (Link to Slideshare)

The InChI resolver was rolled out to the community in March 2009 with the purpose of providing a centralized resource for chemists to resolve InChIs (International Chemical Identifiers). This presentation will provide an overview of the development of the underlying technologies associated with the InChI resolver, and how the resolver is being used, integrated and enhanced to provide additional value to the chemistry community. We will discuss present limitations to application of the resolver for providing access to databases and chemistry information distributed across the internet and define our vision for enhancing interconnectivity across Open databases using the InChI resolver as the glue.

ChemSpider: Building a knowledge-based community for chemists using social and data networking technologies (Link to Slideshare)

In less than 2 years ChemSpider has become one of the primary online resources for chemists providing access to an unsurpassed aggregate of free-access knowledge and data. ChemSpider was developed with the intention of providing a structure centric community for chemists that would be enhanced by data depositions, curations and annotations by the community. The system presently hosts over 21.5 million chemical compounds from over 200 data sources. Working with a network of advisors, collaborators and data providers ChemSpider has created a unique resource of integrated information for chemists. These efforts have enabled us to support the curation of the Wikipedia chemistry pages, the production of a community supported Open Access chemistry journal and provision of web services integrated to spectrometer systems distributed around the world. This talk will provide an overview of how ChemSpider utilized social and data networking to create a community for chemistry.

Building an integrated system for chemistry markup and online publishing integrated to online chemistry resources (Link to Slideshare)

The extraction of chemical entities from documents such as patents and publications has been pursued for a number of years. We wish to report on ChemMantis, an integrated system for chemistry-based entity extraction and document mark-up enabling access to the rich resource of online chemistry know as ChemSpider. We will discuss the development of the platform from its inception as a series of dictionaries to the integration of an entity extraction algorithm and its expansion to a public deposition and publishing platform for chemistry. Chemistry articles can now be deposited, marked-up and exposed to the public within a few minutes in many cases making it an ideal platform for communicating research and providing integrated access to data sources including PubChem, ChEBI, Wikipedia and Entrez.

“…Nature Chemistry articles are annotated to identify all of the chemical compounds mentioned throughout the text. Users can choose to view the article with all of the compounds highlighted, and find out more about those compounds by linking out to other information resources including PubChem and ChemSpider.”

It’s great to be seen as a database of value to be linked to! Neil Withers highlighted it in his blogpost too.

Egon has already given a good overview of the markup and semantic nature of the articles so I won’t repeat that. Egon did comment in his post: “Like many other chemistry journals, Nature Chemistry does not consider properties of the molecule interesting, and NMR spectra are hidden in the Supplementary Information. This paper in particular, disregards a lot of machine readable facts by putting all experimental section bits in a PDF document. So, the next challenge for Nature Chemistry will be to get the authors of papers contribute the original spectra (JCAMP-DX, CMLSpect, etc) in the supplementary information section. Better, have the raw data or even the NMR peak-atom annotations deposited in public repositories such ”

We have done this on the ChemSPider Journal of Chemistry already for this example.

In the Editorial Comment David Wild writes about “Grand challenges for cheminformatics” and comments:

“We have seen huge leaps forward in the provision of freely accessible chemical databases such as PubChem [3] and ChemSpider [4]. A wealth
of information is buried in these databases as well as many other related sources.”

To be listed with alongside PubChem is very humbling. PubChem is an incredible contribution to the community and we wish to deliver similar, though additional contributions.

One of the papers is a commentary

Chemistry publication – making the revolution
Steven M Bachrach
Journal of Cheminformatics 2009, 1:2

Steven touches my heart with his two references to our works

ChemSpider “Publishers should welcome the additional supporting materials and make then available under the Open Data principle. Furthermore, publishers should encourage the mining of these supporting materials, like the CrystalEye [42] and ChemSpider [43] projects.”

ChemMantis “There are two fledgling experiments that attempt to put into place some of these enhanced-publication/datument ideas: Project Prospect [51] from the Royal Chemical Society and ChemMantis from the ChemSpider [43] group.”

And he states… “We need to encourage these projects and the development of more tools. We need to encourage our colleagues to adopt a new model for publication. We can revolutionize how we perform our science. This is the real hope of the internet for scientists.”

Amen Steve…Amen.

With the RSC depositions came many beautiful structures – highly symmetric, complex and just plain “pretty” to a chemist. But a high level of complexity also arrived with the collection and while many InChIs could be converted to their associated connection tables the act of converting the InChIs could add additional stereochemistry and structure cleaning could change stereochemistry so this was a long, tedious and mostly manual process I’m afraid. Nevertheless, a wonderul addition to the ChemSpider database and our sincere thanks, on behalf of the community too, to the Royal Society of Chemistry for sharing their data with us. The InChIs will be deposited into the InChI Resolver shortly.

Where could we go from here? Some potential ideas….

1) provide the ability to switch on/off each individual entity in the paper.

2) select a name and highlight it across the paper

3) export the list(s) to text files

4) Link each of the names out to ChemSpider/Wikipedi/others

What else…we welcome your suggestions.

The eight articles are provided at www.chemmantis.com or at the alternative redirect from www.chemspider.com/journal.

We welcome your feedback. The authors of the articles welcome your feedback. At the bottom of each article is a “post new comment” button. Please do so provide us with your thoughts.

Markup has been performed using our ChemMantis markup platform. ChemMantis stands for Chemical Markup And Nomenclature Integrated System. Markup is fully automated and then manual curation of the markup is performed. In general markup is taking less than 60 seconds and curation of course depends on the complexity of the content.

Over the next few days I will provide more detail about the platform and we will rollout a stack of articles. For now there is a teaser article here. This article is taken from Chemistry Central, with their permission, and my thanks to Jan Kuras for his support. This article is of the “Christmas tree Light” type of markup where we have chemical names, species, elements, chemical reactions, chemical groups, hardware vendors and software vendors all highlighted!!! Whoa…TOO colorful you say???? Simply switch off the “offending” entity classes using the checkboxes as shown in the image below (Click on the Thumbnail to see the full effect please)!

We are continuing to welcome submissions for the ChemSpider Journal of Chemistry. Please contact us at infoATchemspiderDOTcom if you want to submit an article to the journal.