Skip navigation

Accelrys Blog

6 Posts authored by: Carmen.Nitsche
0

Now that I have been back from the American Chemical Society (ACS) meeting for a few weeks I wanted to take a moment to reflect on my three year term as  Chair Elect/Chair/Past Chair of the Chemical Information  Division (CINF) of ACS.  The single year of actual chairmanship does not give one a tremendous amount of time, but I am satisfied that  during my tenure we improved the communications infrastructure, we adopted the ACS Network for member and functionary communication,  we became supporters of InChI, and we were able to secure innovations grants to fund a new website and the CINFlash experiment.  We also had strong, multidisciplinary technical programming and an abundance of networking opportunities at our national meeting, thanks to our program and fundraising committees.

 

The  term was  not without its challenges. Probably the single largest issue we faced and continue to face is retaining the membership.  Finding volunteers for our various committees is like pulling teeth, and our overall membership, who in large part remain quite unengaged, continues to decline.  While these issues are not unique to our division, our relative small size means we get affected by these dynamics more drastically  than other groups.  However  I left Denver energized, and excited about the next few years for CINF.  Despite our membership challenges, I see a lot of creative and engaged members focusing on shaping CINF to continue to be relevant in the years to come. And to top it off, we have a strong line-up in the top leadership.  As Greg Banik and I move on, Rajarshi Guha and Antony Williams are moving into the Chair and Chair Elect positions, two folks with lots of ideas and plenty of energy to execute.   I look forward to supporting their efforts, in part through my participation on the communications and publications committee, as we experiment with more virtual and local activities and other initiatives so we can  keep CINF relevant and critical to librarians and cheminformaticians alike. 

 

Thanks for all the support I received during my term.  It was an experience I will always remember warmly.    Sincerely,  --Carmen

623 Views 0 References Permalink Categories: Cheminformatics, Scientific Databases Tags: statistics, acs, american_chemical_society, chemical_information_division, cinf, cheminformaticians, chemistry_librarian, science_librarian
0

 

This fall’s ACS meeting in Boston seemed lower key than the spring meeting in San Francisco. But maybe it was just that I was insanely busy with Chemical Information Division (CINF) activities, as my term as chair of the division ended at this meeting. I was really thrilled to be able to present Tony (Anton J. Hopfinger) with the 2010 Herman Skolnik award. I do not have a computational chemistry background, but I worked with Tony on my first MDL business development project, and his reasonable, fair, and generous nature left me with a long-term respect and affection for him.

 

I also quite enjoyed the speaker we had at the CINF luncheon. Michael Capuzzo, former Philadelphia enquirer reporter, joined us to talk about his most recent book, The Murder Room: The Heirs of Sherlock Holmes Gather to Solve the World's Most Perplexing Cold Cases. While, yes, he doesn’t work directly in cheminformatics, Capuzzo painted a picture of information gathering and relationship extraction that mapped very closely to the challenges we information professionals face every day.

 

Capuzzo noted that over meals not unlike the one we had shared prior to his talk, a team of dedicated and skilled detectives known as the Vidocq Society pore over gruesome crime scene photos of corpses and cannibalism and detailed police investigative reports to try to bring serial killers to justice. Good thing we had finished eating before Michael took to the podium! Michael explained that the Vidocq Society has handled hundreds of cases over the years and made significant contributions leading to new arrests and/or exonerations. Michael noted there is still a big difference between knowing who committed the crime and being able to secure justice—and so Vidocq Society is very strict about only getting involved if family members and the local law enforcement invite them to participate

 

CINF sponsored several symposia, from a thorough overview of semantic web applications for chemistry to developing chemistry collections in this challenging economic climate.  CINF also had two “celebratory” symposia, the first for the 50th anniversary of the Journal of Chemical Information and Modelling (edited by Bill Jorgensen) and the Herman Skolnik award presentation that I mentioned previously.

 

My colleague Keith Taylor participated in a session dedicated to chemical representation, which Wendy Warr reviewed recently. The session showed that work in this area is by no means finished. One talk covered the recent IUPAC recommendations for chemical structure representation and another covered advances with InChI—both are true community projects that bring together vendors, academics, and publishers. I’ll admit I held my breath when Keith, who spoke on our new flexible sequence representation, launched a live demo—but it worked splendidly, really showing off the flexibility and power of this new approach. You can view Keith’s slides below.


Finally, the ACS exhibition allowed the Accelrys content group to showcase all the database content that is now part of the Accelrys product family. We continue to focus on chemical sourcing, reactions, and bioactivity information, offering multiple in-house and hosted options. We also demoed the All New DiscoveryGate at ACS and are looking for beta testers to come on board as we begin adding reaction content to the sourcing data currently delivered through that system. If you’d like to participate, please email feedback@discoverygate.com or comment on this post.

522 Views 0 References Permalink Categories: Bioinformatics, Cheminformatics, Scientific Databases Tags: conferences, biologics, discoverygate, chemical-representation
0

The well traveled Wendy Warr offered to provide a review of some of the talks she attended at the Boston meeting of the American Chemical Society last week. Below are her thoughts:

 

WW smaller.gifOn August 25 at the ACS meeting in Boston, CINF Division ran a session on recent progress in chemical structure representation. I was particularly interested because I have just written a review on structure representation for Wiley Interdisciplinary Reviews in Computational Molecular Science.

 

The day began with some really complex structures from Mark Andrews of DuPont. It reminded me a bit of the good old days of polymer representation at MDL before MDL shifted focus largely to life sciences--all those brackets and attached data and stuff--but things have moved on since then, and DuPont have done painstaking work on “no structures” and mixtures and all sorts of polymers. Most impressive. In contrast, Jonathan Brecher’s structures were “beautiful”. Jonathan has ensured that ChemDraw structures follow IUPAC’s standards for graphical representation of chemical structure diagrams.

 

Steve Heller gave a status report on InChI and InChIKey. There was not a lot of new material in his talk since the one he gave at the spring ACS meeting, but I was intrigued that Steve was much lower key, much less challenging than in previous talks. I got the feeling that InChI has now entered the mainstream.

 

Keith Taylor described Accelrys’s hybrid representation for biological sequence information. It is a “best of both worlds” approach combining the compactness of a sequence with detailed connectivity information for modified regions. While Symyx was beavering away on self-contained sequence representation (SCSR), Accelrys was touting BioReg, its biological registration system. Now that the two companies are united, there could be genuine synergies between BioReg and SCSR, with resultant user benefits.

 

Szabolcs Csepregi talked about Markush structures: I won’t say more since I hope that anyone interested will be able to find most of this on the ChemAxon website. The work is not new to me but Molecular Networks’ work was. Christof Schwab described CSRML, a new markup language for chemical substructure representation. At first I wondered why we need this if we trust chemical markup language (CML) but I learned that CML does not handle query structures.

 

My apologies to anyone who reads this post and wonders why I did not mention his or her talk. And anyone who wants lots of detail can always buy my report on the meeting, which I'll be publishing in January.

443 Views 1 References Permalink Categories: Cheminformatics Tags: conferences, compound-management, guest-authors, accelrys-draw, chemical-representation
0

Counting up the compounds in a database should be as easy as, well, 1, 2, 3… But a recent thread on the Chemical Information Sources Discussion List (login required) pointed out that what counts is how (and what) vendors count. In this post, I'd like to comment on this confusion and explain how we count compounds for our premiere sourcing databases: the Available Chemicals Directory (ACD) and the Screening Compounds Directory (SCD).

 

The discussion on CHMINF is far from the first time that scientists have complained about vendors providing apparently misleading database counts. That’s because of the perception in the database market that size matters. If you’re selling a database, it looks good to boast that you have more compounds or reactions or suppliers than everyone else. So it shouldn’t be surprising that vendors will jockey for position.

 

As this thread indicated, so much goes into a compound database that it’s possible to count in many different ways, which is why things get so confusing. In sourcing, for instance, a chemical supplier may sell a given unique chemical as many different products (HPLC grade, reagent grade, etc.) and offer various packages of each (10 g, 500 g, 1 Kg, etc.). So as a database vendor, do you size up your database by counting the number of unique chemicals, or do you count each instance of that chemical separately, or do you count each package? All would be accurate! But for any comparisons between databases to be accurate, customers need to know what is being counted.

 

Sourcing databases present another challenge in the numbers game as well. If a compound was available once, but isn’t available now, should it still count? With ACD, our intent is to emphasize the word available. Sure, we have a few older catalogs in the database, but those are the exception. Our goal is to provide the most comprehensive database of available chemicals. So for us, size may not matter as much as utility.

 

So with that said, our aim is to provide all the relevant statistics about what our databases contain so that you can see exactly what you are getting. Here is where ACD and SCD stand today:

 

ACD (2010.07)

 

Chemicals                             2,962,241

 

Products                               6,037,389

 

Packages                               13,929,578

 

Catalogs                               897

 

New Chemicals                    286,407

 

New Catalogs                       5

 

Updated Catalogs                77

 

SCD (2010.02)

 

Chemicals          9,648,480

 

Products           20,990,755

 

Packages           26,114,574

 

Vendors            53

 

With these numbers in hand you should be able to make the comparisons yourself.

321 Views 0 References Permalink Categories: Scientific Databases Tags: content-in-context, available-chemicals-directory, chemical-sourcing
0

ACS members love to come to San Francisco and this spring was no exception. While I have not seen report of the final numbers, attendance was expected to be near the all-time high, with almost 18,000 people registered to attend.

 

We had very good turnout for the CINF sessions and presented several sessions virtually for those who were unable to attend. I found of particular personal interest many of the papers in the Wednesday morning session titled "The Future of Scholarly Publishing." Microsoft gave a couple of talks during which they, among other things, introduced the Chem4Word add-in for Microsoft Word, and Peter Murray-Rust was not struck by lightning after he predicted the demise of all abstracting and indexing services.

 

Our terrific sponsors ensured that CINF continued its tradition of excellent networking opportunities, including three receptions and a luncheon. Now that I am CINF Chair these activities are not as carefree for me as they used to be. I worry that we’ll run out of food or Anchor Steam Beer or that the microphone won’t be on. But I still had a wonderful time catching up with old colleagues and meeting new ones. In keeping with the green chemistry theme of the overall ACS meeting, we opted for recycled/recyclable materials at our receptions.

 

Symyx was pleased to be able to once again offer two scholarships to students pursuing advanced degrees in chemical information and related sciences. [Editor's note: In July 2010 Symyx merged with Accelrys, Inc.) We had a record number of applicants; we’ll tell you more about the winners in future entries. Strolling through the poster session at the Sunday reception, I was very impressed with all the student submissions.

 

For those who held down the forts at home, I urge you to visit the CINF Web site to catch up on what you missed.

428 Views 0 References Permalink Categories: Cheminformatics, Scientific Databases Tags: conferences
0

Conference review: NFAIS

Posted by Carmen.Nitsche Mar 12, 2010

I recently returned from the National Federation of Advanced Information Services (NFAIS) conference, a meeting devoted to discussing the role of information and content in business and research, and would like to share with you my impressions of the conference and a summary of my talk.

 

The theme of this year’s meeting was Redefining the Value of Information—Exploring the New Equation. Most of the attendees and speakers were vendors—creators of content or content-supporting technologies—though there were some representatives from university and industry information centers too. A full agenda and links to slides are available.

 

My talk was titled Does Volume Really Equal Value? I reviewed the buying behaviors of corporate and academic institutions, which have dramatically shifted from a “buy for a rainy day” mode to buying to, well, get by. The reality today is that scientists have little patience for hard-to-use systems. For just about any other type of information, they can Google and find immediate answers. So why does scientific information require them to navigate complicated interfaces—and pay for that “privilege”?

 

I offered vendors two ways to deliver value. We can practice agile development to involve scientists more directly in developing the solutions we offer. We can also provide flexibility through “containerless” content—service-oriented systems that provide content in context with common workflows such as experiment planning and sourcing.  I concluded with some thoughts on the business models we content providers need to explore given the challenges of the economy and the current “Frenzy of Free.” The positive comments I received afterwards suggested that I hit a resonant chord.

 

I found it interesting that despite all the discussions and talks centered on ROI and value propositions, no one has really cracked the nut on how to overcome the overwhelming economic and user behavioral changes facing our industry. I would argue that as an information community we did a poor job in the past of communicating quality and value and educating users to be discerning consumers of content, which is now exacerbating the current challenges facing our industry.

 

The general consensus among attendees was that end-user driven knowledge gathering is here to stay, ease and speed are prerequisites, and vendors need to experiment with social networks and media, mobile technologies, and other mechanisms to create some sort of alliance with “free.” I’d be curious what our blog readers think. How are you using content today, and what can vendors do to help you use it more productively? And what are you really willing to pay for?

420 Views 0 References Permalink Categories: Scientific Databases Tags: conferences, content-in-context