ChemSpider Blog

Last a week I had a pleasant chat with a reporter from Nature magazine, a Mr Geoff Brumfiel. Geoff was interested in ChemSpider…what it was, how it ran, who used it, who supported it, who liked it, who curated it, who didn’t like it and so on.

The results of that discussion, and others he spoke to about ChemSpider, are here in his article.

Chemists spin a web of data p139
Chemspider website provides free information on millions of molecules.
Geoff Brumfiel
doi:10.1038/453139a
Full Text | PDF

It is a rule at Nature, at least for this type of article, that I could not see the article before it went to press and therefore I didn’t get the chance to proofread and comment. Geoff has accurately captured the spirit of our discussions but a few detailed clarifications are needed too. I have pasted in black the article content and in italics the clarification.

“providing the community with an open-access source of chemical information”

I giggled and commented please don’t say it’s Open Access. Say it’s Free Access. Say there are Open Data. And now we have Creative Commons licenses. But don’t say it’s Open Access, not Strong, not weak, not gold, not green. Just Free Access. No price barriers to usage.

“Chemist Antony Williams is hoping to change this in a move likely to ruffle the feathers of the American Chemical Society.”

I commented that we are not purposely in competition with anyone. It’s not what drives us to do this. Whether others see us to be competitive is for them not us. We don’t intentionally try to ruffle feathers. It doesn’t mean that what we are doing won’t ruffle feathers of course. Whether it’s ACS or others. It’s not the goal..it might be an outcome.

“The modest project has made chemists interested in open access take notice — last week, the number of daily users of the site surpassed 5,000.”

We have crossed 5500 users for the past two nights. The trend is positive.

“Other potential sources of information, such as Wikipedia, lack the algorithms needed to search chemicals according to their structure. “

Structure searching is “feasible” of course with InChI Strings. But substructure isn’t and Wikipedia is treated as a text-based search by almost all of its users

“The site is maintained with modest profits from advertising and the work of about 30 active volunteers who double-check the data pulled in from outside.”

The original investment in hardware and software costs has finally been recouped. Modest profits? No one gets paid for the work we do. There is a phenomenal sweat equity investment in the platform numbering many thousands of hours to get here. We are indebted to the many software collaborators, providers of tools and the people curating and depositing to the system. There have BEEN about 30 active volunteers. RIght now I would say the number of active depositors and curators is around 10. But it is growing. I hadn’t checked the number of REGISTERED users for a long time. We have over 1150 registered users…those who CAN login and curate data, deposit data, see new features etc. People do NOT have to register to use the site…but >1150 did. Wow. I didn’t know it was that many until i just checked (BIG SMILE)

““There’s an awful lot of chemical information, but there’s an awful lot of rubbish as well,” says Barrie Walker, a retired industrial chemist in Yorkshire, UK, who helps maintain the site.”

Don’t know whether Marrie said this or not. He IS an honest guy and he is our QUALITY GURU and we are proud that he is willing to give us his fine eyes. There IS garbage on the site still. But, after a year online and active curating it has been much reduced. About 200 edits a day are made to the site: names changed/deleted/added, spectra/structures/URLs/Publications added etc. It’s quite the pace. We have cleaned up 100s of thousands of incorrect associations from the external data sources. It’s been and will remain an enormous task with an enormous payback for the community

“Williams adds that the site still has problems with certain searches. For example, it struggles to distinguish between isomers: molecules with the same chemical formula arranged in different structures.”

We  can distinguish isomers no problem. The PROBLEM is that there is a mixture of isomeric species submitted from multiple data sources and data are mixed and intermingled in way that the user cannot get to the correct structure. Search taxol or Ginkgolide on the ChemSpider blog and read the mutliple blog posts about this. We can of course search all isomers for a particular chemical formula…

“But Williams nevertheless believes that the service may be able to compete with for-profit services. “What I’m doing is highly disruptive,” he says. “I think it can be done and it needs to be done.””

I think what WE are doing…its not me..it’s we…is disruptive. In a good way. Many chemists will benefit. Will it have an impact on for-profit services? Yes, maybe. As an outcome but not as the target. Our team of people, both internal to ChemSpider’s development and Advisory Group, and the people we don’t even know who are cleaning and depositing into the system for their colleagues in the community, are creating a powerful resource for Chemists. The FOCUS of this effort is to Build a Structure Centric Community for Chemists. We will change that soon…the focus on Structure-Centric will be to cover Chemistry in general and to Build a Community for Chemists.

We are well on our way and thanks to Nature, and Geoff in particular for exposing it. My comments above are not meant to detract from Geoff’s reporting abilities but it was a long discussion and some clarification statements are of value i believe.

Over the past few weeks I have had a few discussions with a member of the ChemSpider Advisory group regarding a concept to create WiChempedia. I’ve enjoyed these conversations with Alex Tropsha (professor and Chair in the Division of Medicinal Chemistry and Natural Products in the School of Pharmacy, UNC-Chapel Hill.) We are like-minded in a number of ways but specifically in what can be done to facilitate delivery of quality information to the chemistry community.

As you will notice if you frequent this blog I am rather a stickler for accuracy and quality (1,2,3). I think it’s important (4). Over the past few weeks I’ve spent more time looking at the quality of data on Wikipedia and trying to figure out the best way to bring together our efforts on ChemSpider to enhance the capabilities of integrated information and to support the quality efforts being made by the WP:CHEM team and help them. I also intend to facilitate the development of our own Wiki environment for chemistry and to generally enhance the tools available to chemists not only for Wikipedia type annotation but also to support Open notebook Science.

Now, I don’t want to reinvent the wheel. Wikipedia has a lot of what is necessary in terms of being a known system, a following of people and committed supporters in the WP:CHEM team. What I have been hoping for was a shift around structure and substructure searching on the MediaWiki platform but I know that is a tough request as the platform is not built for that type of thing, The InChKey holds some promise for exact structure searching but does not offer an opportunity for substructure searching without a lookup across a larger database. I want to facilitate information and data sharing further. I do want to provide the type of service that Wikipedia does in terms of general information but also layer cheminformatics tools onto that knowledge and information, allow addition of analytical data, analysis tools, real time predictions and analysis ultimately. This platform should certainly be wiki-enabled.

Decision made. Our intention is to deliver wiki-capabilities in ChemSpider and to use the Open Content associated with chemicals and drugs on Wikipedia inside the system. We will then provide an environment for people to continue to add to, enhance and curate the Wikipedia content as well as add their own. Last night (and well into the early morning) I spent some time talking to Martin Walker from WP:CHEM regarding my concerns that we might offend the Wikipedians with our efforts and that I did not want them to feel that we were ripping off their hard work but rather have our efforts seen as supportive and enabling. My intention as we work through downloading the data and to check, validate and correct what is sitting on Wikipedia directly for benefit to the community. Also, we will of course need to leave all Wikipedia content under the appropriate licensing for others to use. Martin commented that there are tens of mirrors of Wikipedia out there ripped purely with the purpose of exposing and getting ads revenue. We are not working from that model….our intention, as usual, is to build a structure centric community for chemists and with so much excellent work done on Wikipedia I want to take advantage of it and give back also by the work we will do.

Two domain names have been grabbed for this project : WiChempedia, for compatibility with Wikipedia, and also WeChempedia, to emphasize the community aspects of the project.

If you frequent this blog you will recall that we have made a commitment to Microsoft Sharepoint as our future platform for wiki’ing ChemSpider. That is where we believe this work will be done ultimately but we don’t have the platform in our hands yet.

The Xmas vacation is going to be full of holiday movies and manual examination and curation of the Wikipedia data. Wish us luck!

Yesterday I announced the availability of the MassSpec web services for ChemSpider and, less than 24 hours later, I am happy to announce that it is already integrated. Egon Willighagen, one of the members of our Advisory Group, has already reported on his integration to ChemSpider with the intention of speeding up metabolomics analysis. He has used Taverna, a workflow and pipelining tool to set up his workflows. What’s good to see is how easy this was for him to do …well, I assume it was easy since he didn’t need to consult with us. We released the MassSpec web service and voila, he was integrated.

This is what is happening with our other web services too. A number of organizations are now integrated to ChemSpider and using the services on a daily basis.

Recently there was a commentary made about the “highly curated data” on Wikipedia. To me curators are heroes. They are detail oriented, committed to the cause and simply “care”.

As a result of reading that post you saw me go off and check on Taxol, post a few comments and come out the other end of the work with a “more highly curated record” on Wikipedia.

Then I commented on there are better ways to ensure the quality of structure drawings than redrawing them…specifically dictionary look-up and optical structure recognition.

I don’t mind being taken to task on my opinions. As my late father said…”Opinions are like nostrils, everybody has them”. Okay, the body cavity was a little more south but you get the point. However, this opinion stirred me…

“If you wish to spend your life recording typos in chemical documents, I hope it is fulfilling.”

Now, sometimes when you are stirred emotionally, it helps to sit down and think about it.

So, I’ve thought about it… and I’m happy about where I’ve ended up.

My life IS fulfilling. I might need therapy for this particular passion but I DO actually enjoy checking typos in “documents” - of course our conversations are about chemical documents (structures) and I DO confess I like it. Why? I care about Quality.

When I see an acknowledgment that Wikipedia is highly curated and I know I have contributed to that I have a certain pride to having contributed to community science. Those of us cleaning up the historical record for others to benefit are doing a lot of the grunt work that others talk about being necessary and espouse the need for platforms to do so. You can throw a palette of colors and a brush on a floor but someone has to pick it up and do something with it. Platforms, tools, visions are great…we need thinkers but we also need doers. Doers are important and necessary and people who find typos in chemical documents likely do find it fulfilling. I’m a thinker and a doer. until I have experienced the challenges of curating historical records I do not feel I am sufficiently immersed in the challenge. Oh…there’s another nostril (opinion).

So, who are my heroes? Some of them in this domain are:

1) Barrie Walker, ChemSpider Advisory Group member and our KING OF QUALITY.

2) Ann Richards, EPA, founder of the DSSTox effort and quality guru extraordinaire. Ann and her team have taken on the task of assembling, from various sources (and of various quality levels), a public resource of incredible value to the Tox community. This paper explains in detail. With her fine eye for detail, commitment to detail (checking CAS numbers to the digit, stereochemistry of each bond and the accuracy of the chemical names) her databases are likely the cleanest and most highly curated databases from any government labs (no intention to offend others here and if your DB is as good as DSSTox you are my heroes too!) In particular I acknowledge Marti Wolf from Ann’s lab who has spent thousands of hours assembling data, “recording typos in chemical documents” and correcting them to the benefit of the community.

3) People like Peter Corbett. He really seems to care about what’s in a database and the quality of what’s there. He is discovering these issues by observation and checking. His careful eye, clearly necessary for the development of OSCAR, makes him a hero (I look forward to meeting him!)

4) The people I worked with at ACD/Labs in the database compilation office are heroes. This group of 10s of individuals over the years, have manually curated 100s of thousands of structures and associated properties (Physchem parameters, NMR shifts, name-structure pairs). They have done it with a fine eye. THEIR efforts were the basis of what led to industry leading NMR prediction algorithms which were used recently to provide feedback to the Blue Obelisk team member, Christoph Steinbeck, to help clean up errors in the NMRSHIFTDB. While others were attacking the open data effort those of us concerned with the details helped curate the data.

5) The curators at CAS, at MDL (now Symyx), at GVKBio, and in software houses and labs all over the world who manually curate data, and, from their experience, build robots to help their processes and improve the data for all.

For all of you who wish to spend your life recording typos in chemical documents, it is likely very fulfilling if you care about quality.

I find it fulfilling. It’s a necessary part of understanding the problem. Quality is hard to define. But, we’ve been challenged on the quality of our science on ChemSpider enough. We’ve been challenged for sodium chloride dimers and shown it’s valid science. We’ve been challenged for logP prediction of Calcium Carbonate and had an industry great acknowledge our attention to detail. We’ve been challenged on inorganic chemistry and compared ourselves to others.

We Monkeys have been told to close the gates of ChemZoo. We didn’t. Instead we are doing great things for the community I hope. We have opened up a series of services that the Open Access world likes (specifically the Blue obelisk players..), we are donating our database to PubChem shortly, and we are working with some of the best people on our advisory group to satiate their needs. It’s pretty damn fulfilling.

* I will acknowledge that the comment “If you wish to spend your life recording typos in chemical documents, I hope it is fulfilling.” is removed from the context of the entire post. So read the post. Then read all the others I’ve mentioned. I made my interpretation of the comment based on the ongoing flavor. Maybe my nostril was clogged…

The ChemSpider team is a small group of passionate individuals. We all have day jobs. ChemSpider is innovated, extended and maintained during evenings and weekends, with the support of friends, family, collaborators and chemists wanting to make a difference.Here’s a disclaimer regarding one member of the team from the recent Press Release when ChemSpider integrated ACD/Labs properties “Disclaimer: ChemZoo, Inc., is founded by Dr. Antony Williams, who is also serving as VP and Chief Science Officer for ACD/Labs. ChemZoo and ChemSpider services are not affiliated with Advanced Chemistry Development, Inc., (ACD/Labs) and are developed independently of ACD/Labs initiatives.”