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Seth Godin’s Big Ideas, the InChiKey and Structure Searching the Web

13 Sep

Seth Godin is a mentor to many marketers out there today. I’ve read a number of his books over the years and he has many comments. He is a self-professed “idea-giver” …read his latest blog posting. I specifically like his comment “ideas are easy, doing stuff is hard”. How true that is. Over the years I’ve had lots of ideas. I’ve shared many “beverage-based conversations” where big ideas have been put out. The trick is in the “money where your mouth is” execution of these ideas. Over the years I’ve had the pleasure of working with people who tend to deliver as well as talk. WAY more motivating than just listening to the promises of what could be.

A few years ago at a meeting in Washington I sat in on probably the earliest public forum discussion on the potential of InChI. As a result of excellent teamwork between NIST and IUPAC, and doing rather than just talking they got it done. There was some negativity expressed during the initial meetings about InChI but it did not distract the team from producing the prototype versions, initial release and now the latest update with InChIKey support.

Now, I’ll guarantee that Seth Godin doesn’t know what an InChIKey is (Seth, if you’re reading this prove me wrong 🙂 ). But I want to take the position of supporting the Big Idea of structure searching the web and suggesting InChI key as one way execute on this now. There is a lot of passion around doing this and it has shown up in a number of postings by Rich, by Joerg (in regards to Wikipedia in this discussion), by Egon (discussing RDF’ing molecular space) and Jim, among others.

I am reading and hearing exchanges about the web being made structure searchable and my mind drifts immediately to the “it’s not enough” stance. The InChIKey should address some of the issues seen with InChI string searches and likely will be way more popular with the search engines. As commented last night on ChemSpider news the InChI keys on ChemSpider now link directly to a Google search.

The challenge remains, once all of those keys are out there how will the web be SUBstructure searchable or SIMILARITY searchable. The solution would appear to be a centralized repository of structures with their associated InChI strings and InChIKeys. The InChIKey cannot be reversed to the structure. A centralized repository of millions of structures and associated InChI strings and keys would allow that repository to be searched by substructure/similarity and then when a structure(s) of interest is identified then the Google search on that string/key could be kicked off. Maybe the discussion regarding the creation of such a centralized repository has happened already so I’d be interested in hearing what the path forward for that is. If it’s happening then the questions are who will host, how will it be funded, is there a timeline etc. If it’s not happening or is way in the future then I have an interest in opening the discussion regarding using the ChemSpider database and appropriate services (presently under development) to provide an interim service.

Structure searching of the web is of course going to provide high value. It should not stop there of course. let’s have the proactive dialog now about the next phase to facilitate substructure and similarity searching. If the conversations are going on elsewhere please post the links as comments so that the readers can follow them. I’m sure that Egon, Joerg, Rich, PMR will all have thoughts about how this should look. The bottom line out there is if this is the path the underlying system needs to be able to handle at least 25 million structures (ChemSpider has 17 million already) in the short term and be scalable to many tens of millions. There aren’t too many open platforms that can do that yet. I am aware of commercial platforms supporting many millions but no Open Source platforms yet…

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on September 13, 2007 in Vision

 

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