Chemical Information Bulletin Vol. 62(3) Fall 2010

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Chemical Information Bulletin Vol. 62(3) Fall 2010

  1. 1. Chemical Information Bulletin Vol. 62(3) Fall 2010 1 Chemical Information Bulletin A Publication of the Division of Chemical Information of the ACS Volume 62 No. 3 (Fall) 2010 Dr. Svetla Baykoucheva Editor White Memorial Chemistry Library 1526 Chemistry Building, University of Maryland College Park, Maryland 20742 USA sbaykouc@umd.edu IN THIS ISSUE Message fromthe Chair 2 Letter from the Editor 3 CINF Sponsors 4 The Merck Index: Interview with Maryadele O’Neil 5 CINF Division Meetings and Social Events 10 Technical Program Highlights 11 Technical Program Schedule (Short) 12 Technical Program Schedule (Full) 13 Awards and Scholarships 19 Future ACS Meetings 22 Book Reviews 23 Abstracts 24 CINF 2010 Officers 55 CINF 2010 EXECUTIVE COMMITTEE ISSN: 0364-1910 Chemical Information Bulletin,  Copyright 2010 by the Division of Chemical Information of the American Chemical Society Photo on cover by Svetla Baykoucheva Chair: Chair Elect: Past Chair: Secretary: Treasurer: Program Chair: Membership Chair: Councilors: Alternate Councilors: Ms. Carmen Nitsche Dr. Gregory M. Banik Ms. Svetlana Korolev Ms. Leah R Solla (2010-2011) Ms. Meghan Lafferty (2009-2010) Dr. Rajarshi Guha (2009-2010) Ms. Jan Carver (2009-2011) Ms. Bonnie Lawlor (2010-2012) Ms. Andrea Twiss-Brooks (2009-2011) Dr. Guenter Grethe (2010-2012) Mr. Charles F Huber (2009-2011)
  2. 2. Chemical Information Bulletin Vol. 62(3) Fall 2010 2 MESSAGE FROM THE CHAIR Dear Colleagues, The Fall 2010 ACS National Meeting is just around the corner. In this issue you will find all the information you need to organize your schedule in Boston. Early Saturday morning we begin our Division business meetings with long range planning followed by committee and executive meetings. On Sunday the CINF and COMP Divisions invite you to the Joint CINF/COMP Welcoming Reception and CINF Scholarship for Scientific Excellence Posters. ACS Publications is generously sponsoring the event, in recognition of the 50th Carmen Nitsche anniversary of the Journal of Chemical Information and Modeling. The Program Committee has assembled a terrific technical program for us. We will be awarding a Best Presentation award once again at this meeting, thanks to an ACS Innovation Grant. Papers presented at the Data Intensive Drug Discovery session, organized by John Van Drie on Sunday afternoon will be eligible, and the author of the winning paper will receive the award at the CINF Luncheon on Tuesday. We also are trying an experiment on Monday afternoon. The CINFlash session offers speakers a chance to present truly new research and results. Tuesday will be dedicated to the Herman Skolnik awardee, our esteemed colleague Professor Anton Hopfinger. The all-day session is entitled “The Marriage, or at least Dating, of Molecular Simulation and Modeling with QSAR Analysis.” The celebration will be capped off with the Evening Reception at the Seaport Hotel. Make sure you reserve your seat at the Tuesday CINF Luncheon (order your tickets when you register, or see me at the meeting). We have lined up the journalist and author Mike Capuzzo as our luncheon speaker. His first book, Close to Shore, was a non-fictional account of the first US shark attacks off the shores of New Jersey. He will be speaking about his latest book, The Murder Room: The Heirs of Sherlock Holmes Gather to Solve the World's Most Perplexing Cold Cases, due out August 10th . In other Division news, I am pleased to report that CINF was granted a $5,000 innovation grant to work on web design of the eCIB (thanks to Bill Town for preparing the submission). This will help us as we consider the redesign of the entire CINF web presence. I can also report that we have submitted a grant proposal to support remote attendance/participation for our programming. To be more specific, we are requesting funds to allow live blogging and tweeting during our lightning sessions. Find out more about our current and future divisional activities by joining the CINF business meetings on Saturday. I see that 37 CINF Division members have joined the CINF group on the ACS Network. I encourage all of you to sign up before the meeting, so that we can use the network as our primary division communication mechanism as well as reduce our web infrastructure costs. All committee reports will be posted there in the Documents area in the next few weeks. See you in Boston! Carmen Nitsche Chair, ACS Division of Chemical Information Carmen.Nitsche@symyx.com
  3. 3. Chemical Information Bulletin Vol. 62(3) Fall 2010 3 LETTER FROM THE EDITOR Svetla Baykoucheva This issue of the Chemical Information Bulletin (CIB) is the third one we are publishing online. The first (Spring) issue was posted on the CINF web page (www.acscinf.org) before the ACS Spring National Meeting. It contained the technical program, the abstracts, awards information, book reviews, and three interviews. The second (Summer) issue, which is the equivalent of the former CINF eNews newsletter, was edited by Svetlana Korolev and contained information about the ACS Spring National Meeting. As you will notice, CIB is still in a period of transition from print to online format — the functionality of the product is not what we are used to seeing from the commercial publishers. I hope that for the next issues the process will become smoother and easier. Here in this issue you will find the usual categories — a Message from the Chair, Awards and Scholarships, Book Reviews, Technical and Social programs, Abstracts, and a list of the CINF functionaries. Rajarshi Guha, chair of Technical Program Committee highlights the technical program for the upcoming ACS Fall National Meeting (p. 11). Maryadele O’Neil, editor-in-chief of The Merck Index, discusses in an interview (p. 5) the history of this famous resource and what it takes to publish each new edition. The two book reviews (p. 23) were written by Bob Buntrock: (1) Bibliometrics and Citation Analysis: From the Science Citation Index to Cybermetrics, by Nicola De Bellis and (2) Patents for Chemicals,Pharmaceuticals, and Biotechnology, by Grubb & Thomsen. On p. 4 you will be able to see who the CINF sponsors are. As always, we highly appreciate their financial support for the Division. In the near future, the CINF Executive Committee will be looking for my replacement, and those who are interested and believe that they are qualified for this job should consider this exciting opportunity. Being the editor of CIB for five years has allowed me to become acquainted with many interesting people. The editor’s position is a voluntary one, and I have been greatly helped by many colleagues from the Division who submitted materials and proofread the issues. The journal is now published online, and it will be much easier for the next editor to put together the issues — there will be no strict deadlines, as there will be no need to send it to the printer. I hope you will find this issue useful and enjoyable. Svetla Baykoucheva,Editor sbaykouc@umd.edu
  4. 4. Chemical Information Bulletin Vol. 62(3) Fall 2010 4 CINF Sponsors Fall 2010 August 2010 The American Chemical Society Division of Chemical Information (CINF) is very fortunate to receive generous financial support from our sponsors to maintain the high quality of the Division’s programming, to promote communication between members at social functions at the ACS Fall 2010 National Meeting in Boston, and to support otherdivisional activities during the year, including scholarships to graduate students in Chemical Information. The Division gratefully acknowledges the contributions from the following sponsors: Platinum ACS Publications FIZ CHEMIE Berlin Gold Elsevierreaxys® Procter & Gamble Silver Bio-Rad Laboratories Bronze CambridgeSoft InfoChem RSC Publishing Thieme Publishers Opportunities are available to sponsorDivision of Chemical Information events,speakers, and materials. Our sponsors are acknowledged on the CINF web site, in the Chemical Information Bulletin,on printed meeting materials, and at any events for which we use their contribution.Please feel free to contact me if you would like more information about supporting the CINF. The ACS CINF Division is a non-profit tax-exempt organization with taxpayer ID no. 52-6054220. Graham Douglas Chair, Fundraising Committee Email: Fundraising@acscinf.org Tel: 510-407-0769 Please Join Us at These CINF Events! The ACS Division of Chemical Information (CINF) is pleased to host the following social networking events at the Fall 2010 ACS National Meeting in Boston, Massachusetts. CINF/COMP Welcoming Reception & CINF Scholarship for Scientific Excellence Posters & Awards Celebrating the 50th Anniversary of the Journal of Chemical Information & Modeling 6:30-8:30 pm: Sunday, August 22 (Harbor Ballroom I, Westin Boston Waterfront) Reception sponsored exclusively by ACS Publications Scholarships for Scientific Excellence sponsored by FIZ CHEMIE Berlin Harry's Party 5:30-8:00 pm: Monday,August 23 (Presidential Suite Westin Boston Waterfront) Sponsored exclusively by FIZ CHEMIE Berlin CINF Tuesday Luncheon (Ticketed Event); Speaker: Mike Capuzzo, author of “The Murder Room” 12:00-1:30 pm: Tuesday August 24, (Boston Convention and Exhibit Center 162A) Sponsored by Bio-Rad Laboratories, CambridgeSoft and Thieme CINF Herman Skolnik Award Reception honoring Dr. Anton Hopfinger 6:30-8:30 pm: Tuesday,August 23 (Seaport Boston Hotel, Plaza Ballroom C) Sponsored by ElsevierReaxys® & Procter & Gamble with InfoChem & RSC Publishing Division of Chemical Information American Chemical Society
  5. 5. Chemical Information Bulletin Vol. 62(3) Fall 2010 5 The Merck Index, an Encyclopedia of Chemicals and Natural Products: Interview with Maryadele O’Neil By Svetla Baykoucheva Maryadele O’Neil is the Senior Editor of The Merck Index and the Director of Scientific Nomenclature Services. She obtained her Master’s of Library Science from Rutgers University and her BA in Bacteriology (minor in Chemistry) from Douglass College at the same university. After working as a lab-bench researcher for several years, she became involved with The Merck Index. Now she directs all aspects of researching, writing, and publishing of this famous book and is responsible for its content and editorial style, as well as for the authorized product nomenclature and the development of official non- proprietary names for all Merck products. Ms O’Neil has founded the Women in Chemistry Scholarship Program to encourage women to pursue PhDs in medicinal or synthetic organic chemistry. This program has provided $5,000 scholarships, plus travel stipends for winners, to present their research at American Chemical Society national meeting s. She has started different initiatives to provide network ing opportunities for scholarship winners with their colleagues at the ACS. Maryadele O’Neil SB: The Merck Index has been an icon for chemists for decades, and it has served them very well. Could you tell our readers a little bit of its history and the people who have contributed to it? MO: The first edition, known as Merck’s Index, was published in 1889 by the German chemical company, E. Merck, in order to communicate with customers in the United States. The company’s American subsidiary was established 2 years later as Merck & Company. While the first edition was little more than a sales catalog, the second edition, published as Merck’s 1896 Index, grew in scope to include important medicines from the US Pharmacopeia and the National Formulary as well as common laboratory and manufacturing chemicals. Already, The Index was more of a reference handbook than a price list and included physical properties and medicinal uses for the compounds. Because of the popular demand, a Third Edition was published in 1907. Chemists were now an important part of the readership, and additional physical properties and line formulae were added for their use. Ties between the German and American companies were severed by the impact of World War I, but Merck & Co. continued to publish The Merck Index. An ever-growing number of compounds would be added in succeeding editions to increase the utility of the information for researchers. Still today, The Index is published on a not-for- profit basis as a service to the scientific community. The material in The Index has been written over the last 120+ years by generations of Merck scientists. No editors were specifically named until Paul G. Stecher was appointed as such for the Seventh Edition in 1960. Martha Windholz, also a Merck chemist, was named Editor for the Ninth Edition, followed by Susan Budavari, from whom I took over in 1999. The scientists of Merck Research Laboratories have always been very generous with their expertise and advice, and I am most grateful to them for their continued support.
  6. 6. Chemical Information Bulletin Vol. 62(3) Fall 2010 6 SB: As the editor of The Merck Index, what do your responsibilities include? MO: Most importantly, I author a significant amount of the material in the monograph section and tables. I am responsible for the selection of new compounds to be included as well as monographs that are retired from each edition. It is very difficult to select the compounds that will no longer appear in print, but it is necessary to maintain the single volume size. The retired monographs are still available in the online editions, although the information is no longer updated. If you look through previous print editions of The Index, you will notice that the contents are really an encapsulation of what was happening in science during a particular period of time. I so much enjoy reading and scanning journals and news articles for the latest developments, and I have been privileged to read and write about a number of significant scientific advancements. Perhaps the most enjoyable aspect of my role as editor is the opportunity to interact directly with those who use The Index in their daily work. Their specialties span a wide range of scientific disciplines and include researchers in the lab, emergency first responders, information professionals, educators, and, of course, students. It is most gratifying to speak with these individuals to learn how The Index has contributed to their ability to do their work. Many of them have great suggestions for us that they are willing to share. We try to incorporate their ideas into our workflow to continually improve both the information we provide and the way we deliver it. I and some of my team regularly attend the ACS National Meetings and would welcome everyone to stop by at our booth in the exhibition center. The title page of the First Edition of The Merck Index SB: With the many new resources available online, what is the niche that The Merck Index occupies nowand which is its audience today? What is unique about it? Why would people use it rather than go to other resources? MO: There is an overwhelming amount of information available now through the internet and some of it is very good. However, it is often difficult to find authoritative information while weeding through thousands of leads in your search engine of choice. Scientists have come to rely on the accuracy of the physical properties and chemical structures presented in The Index. It’s also viewed as a key to the literature — a first stop for an overview of a compound’s use or its significance. The Merck Index centralizes a lot of information that is critical to many different research disciplines. Approximately half of the monographs cover human and veterinary drugs, traditional and herbal medicines, and diagnostic aids. The remainder includes standard lab reagents, agricultural and commercial chemicals, plants and natural products, and compounds of environmental significance. We try to select the most important compounds across this broad sweep of science to retain the ready reference characteristic.
  7. 7. Chemical Information Bulletin Vol. 62(3) Fall 2010 7 In our user survey conducted last year, lab scientists surprisingly told us that they still prefer the printed handbook to keep nearby them at the bench. The encyclopedic organization of the data makes it easy for them to look up a particular compound and find all of the information together in a single monograph. SB: What is the publication process for the manual? How are new data added and how are these data verified? MO: All of the data included in The Index come from published sources, usually peer-reviewed journal articles that are cited within the monographs. We evaluate multiple sources before selecting the best values to report. If it is not possible to choose between varying data, both values are reported. Citations are also given so that our users may read the experimental details on their own. The online versions now include digital object identifiers (DOIs) and PubMed IDs for many of the cited articles to make it even easier to review the original sources. After a new compound has been selected for inclusion, the writer of the monograph performs a search of the scientific literature to immerse him or herself in the topic. Chemical names, trademarks, and generic names are gathered and verified as well as registry numbers and drug codes, if applicable. The chemical structure is drawn to TMI specifications and physical properties are gleaned as described above. Finally, literature citations, such as syntheses and analytical methods, are selected based on the information they provide and their applicability to our end users’ needs. As early as 1984, The Index has been available as an online database. We knew very early on that a publication cycle of 5-6 years had become too long for many of our readers to wait for new material. The online versions are updated twice per year with new and revised monographs. To accommodate this rapid cycle time, our manuscript is always publication-ready. Each monograph is written or updated and released into the manuscript as a completed entity. New monographs are appended in the order of completion, which is why they are not in alphabetical order in the electronic editions. Database extracts are prepared by our technical staff and exported to our online partners to be processed and published in their format. Publishing the print edition is somewhat more complicated. After the retired material is removed, monographs are re-alphabetized and re-numbered. The various indices for the printed edition are automatically created by the attributes assigned to specific data elements, such as registry number, formula, and synonyms. Extracts for each section and index are prepared and sent to the typesetter to produce the pages according to our specifications. Once the page proofs are reviewed to ensure accuracy, the work of the editorial staff is essentially done. Our good colleagues in the Merck Publishing Group take over and handle the printing and production. They also are responsible for the sales, marketing, and distribution of the new books. SB: Who are the people who are involved with The Merck Index now? MO: You may be surprised that the editorial staff of The Index is quite small. There are only 4 editors who write original content, each with a specific area of expertise. For example, Dr. Peter Dobbelaar is an experienced synthetic chemist who prepares the monographs on chemical reagents and is responsible for the Organic Name Reactions (ONR) section. We are fortunate to be able to call upon the expertise of chemists from outside of Merck as well. For the upcoming 15th edition, Dr. David MacMillan has been of great assistance in reviewing the ONRs. In previous editions, we have been privileged to work with Dr. David Evans and Dr. Barry Trost. Senior Associate Editor Patricia Heckelman has an advanced degree in toxicology. In addition to writing, she is responsible for all of the operational activities, manages the interactions with the typesetter and co-publishers, and ensures the accuracy of each of the electronic editions. Assistant Editor Kristin Roman utilizes her Masters Degree in Biotechnology to author new material pertaining to this field. Rounding out the team, we have excellent support from the senior editorial assistants, Catherine Kenny
  8. 8. Chemical Information Bulletin Vol. 62(3) Fall 2010 8 and Edwin Enraca, and the technical specialist, Linda Karaffa. We also have assistance from Merck’s nomenclature expert, Margaret Hill, who is always on-call to answer naming and structure questions. The Merck Index is part of a family of publications that include The Merck Manual of Diagnosis and Therapy, The Merck Veterinary Manual, and the Home Health and Pet Health editions. As publisher, Gary Zelko brings his years of experience in print publications to oversee the production and marketing of the entire set of handbooks. I would be remiss if I did not also mention my manager, Matthew Cahill, who also brings valuable expertise from the publishing world. SB: You have been passionate about creating opportunities for women to get involved and advance in science. What are the main issues women scientists are facing now? MO: I do believe that it is easier today for women to pursue a career in science than it was 30 or 40 years ago. While the number of women chemists at the master’s level continues to grow, the number of female PhD chemists is dropping precipitously. The choice to continue past the master’s level is a difficult one for women who continue to worry about balancing their work with a family. The availability of day care options is certainly more prevalent now, but it is still difficult for young mothers to cope with long hours in the laboratory. Experienced, successful women have a responsibility to mentor and encourage young talent. I have had the opportunity to speak with many young women as they are beginning their advanced studies. Overwhelmingly, they tell me that the opportunity to network with their female colleagues is invaluable. SB: Could you tell us what your background and professional and personal interests are? MO: My undergraduate degree is from Douglass College, which is part of Rutgers University and sister to the then all-male Rutgers College. While I had planned to pursue a career in the medical field, my professors convinced me that I had an aptitude for chemistry and I found myself spending more and more time in the chemistry building. I still maintained my love of the biological sciences and ended up with a degree in Microbiology. My first position at Merck was as a research assistant in the laboratories, working in the immunology department. There was an opening on The Index staff after the 10th Edition was published, and I thought that it would be the ideal job for someone like me who loved to read and write science. After joining the staff, I returned to Rutgers University part-time to pursue my Master’s Degree in Information Management, with two small children in tow. The decision to come to The Index wasabsolutely the right one for me. I have enjoyed my many years on the staff and have continued to learn something new every day. Not surprisingly, I do have a passion for reading, and enjoy non-fiction as well as novels of many different genres. One of my favorite hobbies is working in my perennial garden which is probably why I enjoy writing material on natural products and traditional medicines for The Index. I am an avid baseball fan and have been able to attend baseball games in the wonderful stadiums throughout the US, whenever my travel coincided with the home team’s schedule. SB: What is your relationship with the ACS? MO: I have personally been a member of ACS and the Chemical Information Division for many years and regularly attend the ACS national meetings. When not at the booth in the exhibit hall, you will more than likely find me attending one or more of the CINF sessions. I have also enjoyed being associated with the Women Chemists’ Committee and the great work they are doing to advance the careers of women in science.
  9. 9. Chemical Information Bulletin Vol. 62(3) Fall 2010 9 The Merck Index has had a long partnership with the ACS, particularly in support of various educational initiatives. Last year, in conjunction with National Chemistry Week, Merck donated 12,000 copies of The Index to local ACS sections to distribute to high school students and teachers across the country. I had the privilege of attending a science fair at Ballou High School in Washington DC with ACS President Tom Lane when the first books were distributed. The students and their teachers were most inspiring and I was delighted to be able to meet them and present them with copies of The Merck Index for use in their classrooms. SB: Why is the online version of The Merck Index accessible through different platforms rather than having it available like other similar resources directly from a web page? MO: The editorial staff prepares all of the material and maintains our content management system, but we do not have any search software with which to produce an online edition ourselves. Because of the richness of our indexing and the granularity of the data, The Merck Index Online is much more than a text-searchable eBook. Our co-publishers process our data and apply their specific tools to enhance the searchability of the material. The Merck Index has a diverse user base ranging from healthcare professionals, to engineers, to bench researchers. It is important to us that our end users are able to easily access the information, regardless of their discipline. The various platforms have been strategically selected based on the way the data are presented and/or paired with other resources to meet the needs of their specific target audience. SB: As science is becoming more and more interdisciplinary, how do you see the evolution of The Merck Index? MO: In the preface to the Tenth Edition (1983), Martha Windholz described her most important challenge as being able to “effectively report major developments at the forefront of the life sciences and to reflect the complex and inextricable interdependence of chemistry, biology, and medicine.” This began the incorporation of biologics into The Index to provide research chemists with access to a broader scope of information than they previously needed. Speaking selfishly, I was quite happy with this decision, since I was purposefully hired to bring my blended perspective of biology and chemistry to the staff. There is always the temptation to stray too far from our true niche, and we must not forget that our readers have relied on The Index as a key core reference for organic chemistry. Future editors of The Merck Index must balance the need for this interdisciplinary information without abandoning the original purpose set forth in the First Edition to provide a summary of whatever chemical products are today adjudged as being useful in either medicine or technology. SB: Thank you, Maryadele, for giving this interesting interview. Our readers will have a better idea now how this “icon” of chemical information is being published.
  10. 10. Chemical Information Bulletin Vol. 62(3) Fall 2010 10 ACS Chemical Information Division (CINF) Fall 2010 ACS National Meeting Boston, MA (August 22-26) CINF DIVISION MEETINGS AND SOCIAL EVENTS The CINF Executive Meeting is a closed meeting; if you wish to attend it, contact the division chair. CINF members are WELCOME AND ENCOURAGED to attend any of the other committee meetings and all social functions. All committee meetings will be held in the Boston Convention and Exhibit Center. Saturday, August 21, 2010 7:30 AM - 9:00 AM CINF: Long Range Planning & Breakfast Meeting (Room 156A) 9:00 AM - 10:00 AM CINF: Awards Committee Meeting (Room 156B) 10:00 AM - 11:00 AM CINF: Fundraising Committee Meeting (Room 156B) 11:00 AM - 12:00 PM CINF: Finance Committee Meeting (Room 156B) 9:00 AM - 10:30 AM CINF: Membership Committee Meeting (Room 155) 10:30 AM - 12:00 PM CINF: Careers Committee Meeting (Room 155) 9:00 AM - 12:00 PM Communications & Publications Committee Meeting (Room 156C) 9:00 AM - 12:00 PM CINF: Education Committee Meeting (Room 157A) 9:00 AM - 12:00 PM CINF: Program Committee Meeting (Room 156A) 12:00 PM - 1:00 PM CINF: Functionary Luncheon (Room 156A) 1:00 PM - 5:30 PM CINF: Executive Committee Meeting (Room 156A) Sunday, August 22, 2010 12:00 PM - 2:00 PM CINF - CSA Trust Group Meeting (Boston Convention and Exhibit Center, Room 153A) 6:30 PM - 8:30 PM Joint CINF/COMP Welcoming Reception, Sponsored Exclusively by ACS Publications and CINF Scholarship for Scientific Excellence Posters & Awards, Sponsored by FIZ CHEMIE Berlin Harbor Ballroom I, Westin Boston Waterfront Celebrating the 50th Anniversary of JCIM Monday, August 23, 2010 5:30 PM - 7:30 PM Harry’s Party, Sponsored Exclusively by FIZ CHEMIE Berlin Presidential Suite, Westin Boston Waterfront Tuesday, August 24, 2010 12:00 PM - 1:30 PM CINF: Luncheon – Boston Convention and Exhibit Center, Room 162A Speaker: Mike Capuzzo, author of “The Murder Room.” Sponsored by Bio-Rad Laboratories, CambridgeSoft and Thieme 6:30 PM - 8:30 PM CINF Herman Skolnik Award Reception honoring Dr. Anton Hopfinger Sponsored by ElsevierReaxys® & Procter & Gamble with InfoChem & RSC Publishing Plaza Ballroom C, Seaport Hotel Wednesday, August 25, 2010 12:00 PM - 5:00 PM CINF - CIC Collaborative Working Group Meeting Boston Convention and Exhibit Center 104A
  11. 11. Chemical Information Bulletin Vol. 62(3) Fall 2010 11 ACS Chemical Information Division (CINF) Fall 2010 ACS National Meeting Boston, MA (August 22-26) Technical Program Highlights By Rajarshi Guha, Program Chair The Fall ACS National meeting is nearly upon us and we are looking forward to attending an exciting line up of symposia and talks. As in recent meetings, we’ve got a packed program covering a diverse set of topics ranging from the Semantic Web to structure-activity relationships. Sunday starts off with a symposium on the use of the Semantic Web in chemistry, organized by Egon Willighagen and Martin Braendle. This is the first session of the three-session symposium that extends to Monday. Topics being covered range from tools & technologies for enabling the use of semantic concepts with chemical data, to actual chemical and biological applications of these concepts. In parallel, Sunday also is the day for the joint CINF-SLA symposium that will address how collections and information resources can be assessed — quantitatively and qualitatively. On Sunday afternoon we will also have the third session of the Best Presentation Award Symposium, organized by John Van Drie. It will focus on methods and approaches to handling the problems associated with the data deluge in drug discovery settings. The winner will receive an invitation to the CINF Luncheon, a plaque, as well as $1,000 towards registration and expenses. On Monday, we continue with the Semantic Web symposium and concurrently will have the first session of the symposium celebrating 50 years of the Journal of Chemical Information. This is being organized by Prof. William Jorgensen and has a lineup of chemical information luminaries who will be describing some of the pioneering work that was published in the journal. On Monday afternoon we will have a brand new symposium — CINFlash. This is an experimental symposium where we’ve tried to have people speak about recent work by allowing them to bypass the ACS abstract system. In addition, each talk is going to be strictly timed (with the help of a loud horn) for six minutes. So, you should expect some fun stuff! Tuesday is a day devoted to the Herman Skolnik Symposium, honoring Prof. Anton Hopfinger. This whole-day event features talks from his past students and collaborators covering a range of topics in molecular modeling. The symposium will be followed by the Skolnik Reception. On Wednesday, we will have a symposium to discuss recent developments in the structure-activity landscape (SAL) concept. Organized by Jurgen Bajorth, Gerry Maggiora and Mic Lajiness, it will cover topics ranging from novel descriptions of landscapes to new applications of the concept in molecular modeling. Wednesday also sees a symposium address recent developments in chemical structure representation, which is organized and run by Richard Apodaca; it will be covering new tools and applications that address traditional and novel chemical structure representations. I’m quite excited with the upcoming program and at the same time I am grateful for the contributions from the Program Committee members and symposium organizers. Thanks to everybody and I look forward to meeting you in Boston.
  12. 12. Chemical Information Bulletin Vol. 62(3) Fall 2010 12 Fall 2010 ACS National Meeting Boston, MA (August 22-27, 2010) Technical Program Schedule (Short Version) Rajarshi Guha, Chair SUNDAY MORNING Semantic Web in Chemistry E. Willighagen, Organizer; M. Braendle, Organizer; E. Willighagen, Presiding; Papers 1-5 Assessing Collections & Information Resources in Science & Technology E. Kajosalo, Organizer; E. Kajosalo, Presiding Papers 6-10 SUNDAY AFTERNOON Data-intensive Drug Design J. Van Drie, Organizer; J. Van Drie, Presiding; Papers 11-18 Assessing Collections & Information Resources in Science & Technology E. Kajosalo, Organizer; E. Kajosalo, Presiding Papers 19-22 SUNDAY EVENING 2010 CINF Scholarship for Scientific Excellence G. Grethe, Organizer; Papers 23-31 MONDAY MORNING Semantic Web in Chemistry E. Willighagen, Organizer; M. Braendle, Organizer; M. Braendle, Presiding; Papers 32-36 The Journal of Chemical Information and Modeling’s 50th Anniversary Symposium W. Jorgensen,Organizer; W. Jorgensen,Presiding Papers 37-42 MONDAY AFTERNOON Where's the Good Stuff - Consumer Health Information, and Social Networking Resources and Services A. Twiss-Brooks, Organizer; A. Twiss-Brooks, Presiding Papers 43-46 Semantic Web in Chemistry E. Willighagen, Organizer; M. Braendle, Organizer; E. Willighagen, Presiding; Papers 47-51 MONDAY EVENING Sci-Mix R. Guha, Organizer; Papers 2, 6, 78, 28, 91, 31, 20 TUESDAY MORNING Herman Skolnik Award Symposium A. Hopfinger, Organizer; E. X. Esposito, Organizer; A. Hopfinger, Presiding; Papers 52-55 TUESDAY AFTERNOON Herman Skolnik Award Symposium A. Hopfinger, Organizer; E. X. Esposito, Organizer; E. X. Esposito, Presiding; Papers 56-59 WEDNESDAY MORNING The Emerging Concepts of Activity Landscapes and Activity Cliffs and their Role in Drug Research G. Maggiora, Organizer; J. Bajorath, Organizer; M. Lajiness, Organizer; J. Bajorath, Presiding; Papers 60-64 Recent Progress in Chemical Structure Representation R. Apodaca,Organizer; R. Apodaca,Presiding; Papers 65-69 WEDNESDAY AFTERNOON The Emerging Concepts of Activity Landscapes and Activity Cliffs and their Role in Drug Research G. Maggiora, Organizer; J. Bajorath, Organizer; M. Lajiness, Organizer; G. Maggiora, Presiding Papers 70-73 Recent Progress in Chemical Structure Representation R. Apodaca,Organizer; R. Apodaca,Presiding; Papers 74-77 THURSDAY MORNING General Papers R. Guha, Organizer; R. Guha, Presiding; Papers 78-83 THURSDAY AFTERNOON General Papers R. Guha, Organizer; X. Wang,Presiding;Papers 84-91
  13. 13. Chemical Information Bulletin Vol. 62(3) Fall 2010 13 ACS Chemical Information Division (CINF) Fall 2010 ACS National Meeting Boston, MA (August 22-27, 2010) Full Technical Program Schedule Rajarshi Guha Chair, Technical Programming OTHER SYMPOSIA OF INTEREST: Data Analysis: Statistics on Chemicals (see COMP, Thu) The Journal of Chemical Information and Modeling’s 50th Anniversary Symposium (see COMP, Mon) Computer Modeling: The Wave of the Future and its Benefits for Small Business Owners (see SCHB, Thu) Drugging the Undruggable: Small Molecule Modulators of Protein-Protein Interactions (see MEDI, Mon) SOCIAL EVENTS CINF Welcoming Reception and Scholarship for Scientific Excellence Posters, 6:30-8:30pm: Sun Harry’s Party, 5:30-8pm: Mon Luncheon, 12-1:30pm: Tue Herman Skolnik Award Reception, 6:30-8:30pm: Tue SUNDAY MORNING Section A Boston Convention & Exhibition Center, Room 156A Semantic Web in Chemistry RDF & Computation E. Willighagen, Organizer, Presiding M. Braendle, Organizer Cosponsored by COMP 8:45 Introductory Remarks 8:55 1. Semantic envelopment of cheminformatics resources with SADI. L. L. Chepelev, E. Willighagen, M. Dumontier 9:40 2. RESTful RDF web services for predictive toxicology. N. Jeliazkova 10:10 Intermission 10:25 3. Linking the resource description framework to cheminformatics and proteochemometrics. E. L. Willighagen, J. E. Wikberg 10:55 4. Chemical e-Science Information Cloud (ChemCloud): A semantic web based eScience infrastructure. A. Paschke, S. Heineke 11:25 5. Use of semantic web services to access small molecule ligand database. A. P. Tamhankar, A. S. Ausekar Section B Boston Convention & Exhibition Center, Room 155 Assessing Collections & Information Resources in Science & Technology E. Kajosalo, Organizer, Presiding Cosponsored by SLA‡ 9:00 Introductory Remarks 9:05 6. Usage metrics: Tools for evaluating science monograph collections. M. M. Foss, V. Kisling, S. Haas 9:30 7. Happily ever after or not: E-book collection usage analysis and assessment at USC Library. N. Xiao 9:55 8. From Chemical Abstracts to SciFinder: Transitioning to SciFinder and assessing customerusage. S. Makar, S. Bruss 10:20 Intermission 10:35 9. Using Web of Knowledge to identify publishing and citation patterns of campus researchers at the University of Arkansas. L. Salisbury, J. S. Smith 11:00 10. Don’t forget the qualitative: Including focus groups in the collection assessment process.S.Shepherd, T. M. Vogel Social Networking: The Next Generation Sponsored by CHED, Cosponsored by CINF and YCC Tautomers and Biology Computer Handling of Tautomers Sponsored by COMP, Cosponsored by CINF, MEDI, and PHYS
  14. 14. Chemical Information Bulletin Vol. 62(3) Fall 2010 14 SUNDAY AFTERNOON Section A Boston Convention & Exhibition Center, Room 156A Data-intensive Drug Design J. Van Drie, Organizer, Presiding Cosponsored by COMP 1:45 Introductory Remarks 1:50 11. Strategies for the identification and generation of informative compound sets. M. S. Lajiness 2:15 12. Public-domain data resources at the European Bioinformatics Institute and their use in drug discovery. C. Steinbeck 2:40 13. Decision making in the face of complicated drug discovery data using the Novartis systemfor virtual medicinal chemistry (FOCUS). D. Chin 3:05 14. Integrating chemical and biological data: Insights from 10 years of VERDI. S. Roberts, W. P. Walters, R. McLoughlin, P. Gabriel, J. Willis, T. Kramer 3:30 Intermission 3:45 15. Collaborative database and computational models for tuberculosis drug discovery decision making. S. Ekins, J. Bradford, K. Dole, A. Spektor, K. Gregory, D. Blondeau, M. Hohman, B. A. Bunin 4:10 16. Data drive life sciences: The Pyramids meet the Tower of Babel. R. Guha 4:35 17. Design principles for diversity-oriented synthesis:Facilitating downstream discovery with upfront design.L. Marcaurelle 5:00 18. Overview: Data-intensive drug design. J. H. Van Drie Section B Boston Convention & Exhibition Center, Room 155 Assessing Collections & Information Resources in Science & Technology E. Kajosalo, Organizer, Presiding Cosponsored by SLA‡ 2:00 19. Data-driven development: How ACS Publications uses data to enhance products and services, and respond to customer needs.M. Blaney, S. Rouhi 2:25 20. Objective collections evaluation using statistics at the MIT Libraries. M. Willmott, E. Kajosalo 2:50 21. Getting the biggest bang for your buck: Methods and strategies for managing journal collections. G. Baysinger 3:15 22. Taking a collection down to its elements: Using various assessment techniques to revitalize a library. L. Solla 3:40 Panel Discussion Scripting & Programming HPC on the Cheap Sponsored by COMP, Cosponsored by CINF Social Networking: The Next Generation Sponsored by CHED, Cosponsored by CINF and YCC Using Waters Explicitly in Drug Discovery Theory and Methods Sponsored by COMP, Cosponsored by CINF and MEDI SUNDAY EVENING 2010 CINF Scholarship for Scientific Excellence G. Grethe, Organizer Financially supported by FIZ CHEMIE Berlin 6:30 - 9:30 23. Predicting specific inhibition of cyclophilins A and B using docking, growing, and free energy perturbation calculations. S. V. Sambasivarao, O. Acevedo 24. Using aggregative web services for drug discovery. Q. Zhu, M. S. Lajiness, D. J. Wild 25. Semantifying polymer science using ontologies. E. O. Cannon, A. Nico, P. Murray-Rust 26. Toxicity reference database (ToxRefDB) to develop predictive toxicity models and prioritize compounds for future toxicity testing. H. Tang, H. Zhu, L. Zhang, A. Sedykh, A. Richard, I. Rusyn, A. Tropsha 27. OrbDB: A database of molecular orbital interactions. M. A. Kayala, C. A. Azencott, J. H. Chen, P. F. Baldi 28. Novel approach to drug discovery integrating chemogenomics and QSAR modeling: Applications to anti-Alzheimer's agents. R. Hajjo, S. Wang, B. L. Roth, A. Tropsha 29. Cheminformatics improvements by combining semantic web technologies,cheminformatical representations,and chemometrics for statistical modeling and pattern recognition. E. L. Willighagen (withdrawn) 30. Prediction of consistent waternetworks in uncomplexed protein binding sites based on knowledge- based potentials. M. Betz, G. Neudert, G. Klebe (withdrawn) 31. Functional binders for non-specific binding: Evaluation of virtual screening methods for the elucidation of novel transthyretin amyloid inhibitors. C. J. Simões,T. Mukherjee, R. M. Jackson, R. M. Brito
  15. 15. Chemical Information Bulletin Vol. 62(3) Fall 2010 15 MONDAY MORNING Section B Boston Convention & Exhibition Center, Room 155 Semantic Web in Chemistry OWL Chemical Ontologies M. Braendle, Organizer, Presiding E. Willighagen, Organizer Cosponsored by COMP 8:30 32. Using the oreChemexperiments ontology: Planning and enacting chemistry. J. G. Frey, M. I. Borkum, C. Lagoze, S. J. Coles 9:15 33. CHEMINF: Community-developed ontology of chemical information and algorithms. L. L. Chepelev, J. Hastings,E. Willighagen, N. Adams, C. Steinbeck, P. Murray-Rust, M. Dumontier 9:45 Intermission 10:00 34. Chemical entity semantic specification: Knowledge representation for efficient semantic cheminformatics and facile data integration. L. L. Chepelev, M. Dumontier 10:30 35. Semantic assistant for lipidomics researchers. A. Kouznetsov, R. Witte, C. J. Baker 11:00 36. ChemicalTagger: A tool for semantic text- mining in chemistry. L. Hawizy, D. M. Jessop, P. Murray-Rust Section A Boston Convention & Exhibition Center, Room 156A The Journal of Chemical Information and Modeling's 50th Anniversary Symposium W. Jorgensen,Organizer, Presiding Cosponsored by COMP 8:45 Introductory Remarks 8:55 37. From canonical numbering to the analysis of enzyme-catalyzed reactions: 32 years of publishing in JCIM (JCICS). J. Gasteiger 9:55 39. Fifteen years in chemical informatics: Lessons from the past,ideas for the future. D. Agrafiotis 10:25 Intermission 10:40 40. Applications of wavelets in virtual screening. V. Gillet, R. Martin, E. Gardiner, S. Senger 11:10 41. Privileged substructures revisited:Target community-selective scaffolds. J. Bajorath 11:40 42. Automated retrosynthetic analysis: An old flame rekindled. P. Johnson, A. P. Cook, J. Law, M. Mirzazadeh, A. Simon Tautomers and Biology Predictions of Tautomer Ratios Sponsored by COMP, Cosponsored by CINF, MEDI, and PHYS The Community Structure-Activity Resource (CSAR) Scoring Challenge Sponsored by COMP, Cosponsored by BIOL, CINF, and MEDI MONDAY AFTERNOON Section B Boston Convention & Exhibition Center, Room 155 Where’s the Good Stuff? Consumer Health Information, and Social Networking Resources and Services A. Twiss-Brooks, Organizer, Presiding Cosponsored by CHED 1:00 43. Dietary supplements: Free evidence-based resources for the cautious consumer. B. Erb 1:25 44. What lessons learned can we generalize from evaluation and usability of a health website designed for lower literacy consumers? M. J. Moore, R. G. Bias 1:50 45. National Library of Medicine resources for consumer health information. M. Eberle 2:15 46. Better prescription for information: Dietary supplements online. G. Y. Hendler Section A Boston Convention & Exhibition Center, Room 156A Semantic Web in Chemistry RDF/OWL Applications E. Willighagen, Organizer, Presiding M. Braendle, Organizer Cosponsored by COMP 1:15 47. Overview of the linking open drug data task. E. Prudhommeaux, E. Willighagen, S. Stephens 2:00 48. Control, monitoring, analysis and dissemination of laboratory physicalchemistry experiments using semantic web and broker technologies. J. G. Frey, S. Wilson
  16. 16. Chemical Information Bulletin Vol. 62(3) Fall 2010 16 2:30 Intermission 2:45 49. Semantic analysis of chemical patents. D. M. Jessop, L. Hawizy, P. Murray-Rust, R. C. Glen 3:15 50. Data mining and querying of integrated chemical and biological information using Chem2Bio2RDF. D. J. Wild, B. Chen, Y. Ding, X. Dong, H. Wang, D. Jiao, Q. Zhu, M. Sankaranarayanan 3:45 51. Mining and visualizing chemical compound- specific chemical-gene/disease/pathway/literature relationships. Q. Zhu, P. Purohit, J. Youl Choi, S. Bae, J. Qiu, Y. Ding, D. Wild 4:15 Intermission 4:20 CINF Open Meeting 4:30 Open Meeting. Committees on Publications and Chemical Abstracts Service Section B Boston Convention & Exhibition Center, Room 155 CINFlash Can You Present Faster Than a Femtosecond Laser? R. Guha, Organizer, Presiding 2:45 Panel Discussion The Community Structure-Activity Resource (CSAR) Scoring Challenge Sponsored by COMP, Cosponsored by BIOL, CINF, and MEDI The Journal of Chemical Information and Modeling's 50th Anniversary Symposium Sponsored by COMP, Cosponsored by CINF Using Waters Explicitly in Drug Discovery Characterization and Applications Sponsored by COMP, Cosponsored by CINF and MEDI MONDAY EVENING Sci-Mix R. Guha, Organizer 8:00 - 10:00 2, 6, 20, 28, 31. See previous listings. 78, 91. See subsequent listings. TUESDAY MORNING Section A Boston Convention & Exhibition Center, Room 156A Herman Skolnik Award Symposium The Marriage, or at Least Dating, of Molecular Simulation and Modeling with QSAR Analysis: Exploring Chemometric Methods A. Hopfinger, Organizer, Presiding E. X. Esposito, Organizer 8:15 Introductory Remarks 8:30 52. What makes polyphenols good antioxidants? Alton Brown, you should take notes... E. X. Esposito 9:15 53. Engineering and 3D protein-ligand interaction scaling of 2D fingerprints. J. Bajorath 10:00 Intermission 10:15 54. In silico binary QSAR models based on 4D- fingerprints and MOE descriptors for prediction of hERG blockage. Y. Tseng 11:00 55. Telling the good from the bad and the ugly: The challenge of evaluating pharmacophore model performance. R. D. Clark Tautomers and Biology Tautomers and Macromolecule-ligand Complexes Sponsored by COMP, Cosponsored by CINF, MEDI, and PHYS The Community Structure-Activity Resource (CSAR) Scoring Challenge Sponsored by COMP, Cosponsored by BIOL, CINF, and MEDI TUESDAY AFTERNOON Section A Boston Convention & Exhibition Center, Room 156A Herman Skolnik Award Symposium The Marriage, or at Least Dating, of Molecular Simulation and Modeling with QSAR Analysis: Exploring Chemical Systems E. X. Esposito, Organizer, Presiding A. Hopfinger, Organizer 2:00 56. Creative application of ligand-based methods to solve structure-based problems: Using QSAR approaches to learn from protein crystal structures. C. M. Breneman, S. Das, M. Sundling, M. Krein, S. Cramer, K. P. Bennett, C. Bergeron, J. Zaretzki
  17. 17. Chemical Information Bulletin Vol. 62(3) Fall 2010 17 2:45 57. Computer-aided drug discovery. W. L. Jorgensen 3:30 Intermission 3:45 58. Structure-based discovery and QSAR methods: A marriage of convenience. J. S. Duca 4:30 59. Extending the QSAR Paradigm using molecular modeling and simulation. A. J. Hopfinger 5:15 Presentation of Award Using Waters Explicitly in Drug Discovery Hybrid Explicit/Implicit Methods Sponsored by COMP, Cosponsored by CINF and MEDI WEDNESDAY MORNING Section A Boston Convention & Exhibition Center, Room 156A The Emerging Concepts of Activity Landscapes and Activity Cliffs and their Role in Drug Research J. Bajorath, Organizer, Presiding G. Maggiora, M. Lajiness, Organizers Cosponsored by COMP and MEDI 8:50 Introductory Remarks 9:00 60. Overview of activity landscapes and activity cliffs: Prospects and problems. G. M. Maggiora 9:30 61. Exploring and exploiting the potential of structure-activity cliffs. G. M. Maggiora, M. S. Lajiness 10:00 62. What makes a good structure activity landscape? Network metrics and structure representations as a way of exploring activity landscapes. R. Guha 10:30 Intermission 10:45 63. Consensus model of activity landscapes and consensusactivity cliffs. J. L. Medina-Franco, K. Martinez-Mayorga, F. Lopez-Vallejo 11:15 64. R-Cliffs: Activity cliffs within a single analog series. D. Agrafiotis Section B Boston Convention & Exhibition Center, Room 155 Recent Progress in Chemical Structure Representation Applications and Tools R. Apodaca, Organizer, Presiding 9:00 Introductory Remarks 9:05 65. Chemical structure representation in the DuPont Chemical Information Management Solutions database: Challenges posed by complex materials in a diversified science company. M. A. Andrews, E. S. Wilks 9:35 66. From deposition to application: Technologies for storing and exploiting crystal structure data. C. R. Groom, J. Cole, S. Bowden, T. Olsson 10:05 67. Recent IUPAC recommendations for chemical structure representation: An overview. J. Brecher 10:35 Intermission 10:50 68. Orbital development kit. E. L. Willighagen 11:20 69. Line notations as unique identifiers. K. Boda WEDNESDAY AFTERNOON Section A Boston Convention & Exhibition Center, Room 156A The Emerging Concepts of Activity Landscapes and Activity Cliffs and their Role in Drug Research G. Maggiora, Organizer, Presiding J. Bajorath, M. Lajiness, Organizers Cosponsored by COMP and MEDI 2:00 70. Analysis of activity landscapes,activity cliffs, and selectivity cliffs. J. Bajorath 2:30 71. Using Activity Cliff Information in structure- based design approaches. B. Seebeck, M. Wagener, M. Rarey 3:00 72. Exploring activity cliffs using large scale semantic analysis of PubChem. D. J. Wild, B. Chen, Q. Zhu 3:30 73. Quantifying the usefulness of a model of a structure-activity relationship: The SALI Curve Integral. J. H. Van Drie, R. Guha 4:00 Concluding Remarks Section B Boston Convention & Exhibition Center, Room 155 Recent Progress in Chemical Structure Representation File Formats and Line Notations R. Apodaca, Organizer, Presiding 2:00 74. Status of the InChI and InChIKey algorithms. S. Heller 2:30 75. Self-contained sequence representation (SCSR): Bridging the gap between bioinformatics and cheminformatics . K. T. Taylor, W. L. Chen, B. D. Christie, J. L. Durant, D. L. Grier, B. A. Leland, J. G. Nourse 3:00 Intermission 3:15 76. Representation of Markush structures:From molecules toward patents. S.Csepregi, N. Máté, R. Wágner,T. Csizmazia, S. Dóránt, E. Bíró, T. Dudgeon, A. Baharev, F. Csizmadia
  18. 18. Chemical Information Bulletin Vol. 62(3) Fall 2010 18 3:45 77. CSRML: A new markup language definition for chemical substructure representation. C. H. Schwab, B. Bienfait, J. Gasteiger, T. Kleinoeder, J. Marucszyk, O. Sacher, A. Tarkhov, L. Terfloth, C. Yang THURSDAY MORNING Section A Boston Convention & Exhibition Center, Room 156A General Papers Characterization and Prediction R. Guha, Organizer, Presiding 8:45 78. Prediction of solvent physical properties using the hierarchical clustering method. T. M. Martin, D. M. Young 9:10 79. Scaffold diversity analysis using scaffold retrieval curves and an entropy-based measure. J. L. Medina-Franco, K. Martinez-Mayorga, A. Bender, T. Scior 9:35 80. Nonsubjective clustering scheme for multiconformer databases. A. B. Yongye, A. Bender, K. Martinez-Mayorga 10:00 Intermission 10:10 81. Finding drug discovery “rules of thumb”with bump hunting. T. Hashimoto, M. Segall 10:35 82. Machine learning in discovery research: Polypharmacology predictions as a use case. N. Wale, K. McConnell, E. M. Gifford 11:00 83. Interpretable correlation descriptors for quantitative structure-activity relationships. J. D. Hirst Computer Modeling: The Wave of the Future and its Benefits for Small Business Owners Sponsored by SCHB, Cosponsored by CINF, COMP, and PROF Targeting Gram-Negative Pathogens Sponsored by COMP, Cosponsored by CINF and MEDI THURSDAY AFTERNOON Section A Boston Convention & Exhibition Center, Room 156A General Papers Extraction and Integration X. Wang, Presiding R. Guha, Organizer 1:30 84. Chemistry in your hand: Using mobile devices to access public chemistry compound data. A. J. Williams, V. Tkachenko 1:55 85. Feature analysis of ToxCastTM compounds. P. Volarath, S. Little, C. Yang, M. Martin, D. Reif, A. Richard 2:20 86. Extracting information from the IUPAC Green Book. J. G. Frey, M. I. Borkum 2:45 87. Biologics and biosimilars: One and the same? R. Schenck 3:10 Intermission 3:20 88. Intelligent mining of drug information resources. R. Jain, A. Tamhankar, A. Ausekar, Y. Dixit 3:45 89. Cheminformatics semantic grid for neglected diseases.P. J. Kowalczyk 4:10 90. Extraction and integration of chemical information from documents. H. O. Villar, J. Betancort, M. R. Hansen 4:35 91. SAR and the role of active-site waters in blood coagulating serine proteases:A thermodynamic analysis of ligand-protein binding. N. K. Salam, W. Sherman, R. Abel Data Analysis: Statistics on Chemicals Sponsored by COMP, Cosponsored by CINF Targeting Gram-Negative Pathogens Sponsored by COMP, Cosponsored by CINF and MEDI
  19. 19. Chemical Information Bulletin Vol. 62(3) Fall 2010 19 AWARDS AND SCHOLARSHIPS 2010 Herman Skolnik Award to Tony J. Hopfinger Anton (Tony) J. Hopfinger Anton (Tony) J. Hopfinger, Distinguished Research Professor of Pharmacy, University of New Mexico, Professor Emeritus of Medicinal Chemistry and Pharmacognosy, University of Illinois, and co-Founder and Chief Science Officer of The Chem21 Group, Inc., is the recipient of the 2010 Herman Skolnik Award presented by the ACS Division of Chemical Information (CINF). The award recognizes outstanding contributions to and achievements in the theory and practice of chemical information science and related disciplines. The prize consists of a $3,000 honorarium and a plaque. At the ACS Fall National Meeting there will be a Skolnik Award Symposium entitled The Marriage, or at Least Dating, of Molecular Simulation and Modeling with QSAR Analysis: Exploring Chemometric Methods, organized by Tony Hopfinger and Emilio Esposito. It will be held on Tuesday,August 24th, and abstracts of the papers to be presented are listed under “Abstracts” in this issue. Tony Hopfinger is recognized as a pioneer and major contributor in the fields of quantitative structure activity relationship (QSAR) and quantitative structure property relationship (QSPR) techniques employing three and higher dimensional levels of information derived from modeling and simulation. Tony has addressed chemical information and modeling problems in the pharmaceutical, polymer and materials sciences, in both industry and academia, and he is generally acknowledged as having fathered the development of QSPR modeling in polymer and materials science, including coining the acronym QSPR. The breadth of his interests and the applicability of the techniques he has developed are reflected in the topics covered in some of his recent papers, including drug discovery, ADME-Tox property prediction, nanotoxicity, cheminformatic descriptors and molecular similarity analysis. Tony has made many contributions to the field of cheminformatics through his publications, teaching, mentoring, advising and organizing. He has authored or co-authored more than 270 peer-reviewed (and highly cited) papers and delivered almost 360 invited lectures. He has served on many journal editorial boards and has been an associate editor of the Journal of Chemical Information and Modeling (previously Journal of Chemical Information and Computer Sciences) for the past 16 years. He has been a member of government and industrial advisory boards, and he chaired a Gordon Research Confe rence on Quantitative Structure-Activity Relationships in Biology. He has coordinated and taught at short courses in North and South America and Europe; more than 50 computational scientists earned their Ph.D. degrees under Tony ’s mentoring; and he has also provided advanced training to more than 70 postdoctoral students. Tony Hopfinger received a B.S. in Math and Physics from the University of Wisconsin in 1966, and a Ph.D. in Biophysical Chemistry from Case Western Reserve University in 1969. He started his career in 1969 as an NIH Postdoctoral Fellow, Department of Biological Chemistry, Harvard Medical School, and from there moved to Case Western Reserve University in 1970 as Assistant Professor of Macromolecular Science. He held increasingly senior positions at Case Western, eventually becoming Professor of Macromolecular Science in 1978 and Director, Research Computing Laboratory, in 1979. In 1981 he moved from academia to industry, joining G.D. Searle (now part of Pfizer) as Director, Department of Drug Design , and later Director, Department of Medicinal Chemistry. Tony maintained links with academia, holding several adjunct and visiting professorships, and in his spare time founded, or co-founded, a number of software and pharmaceutical companies, including Intersoft, ChemLab, Receptor Laboratories and DNACodes. He returned to academia in 1985 and was Professor of Bioengineering, Chemistry and Medicinal Chemistry, University of Illinois at Chicago until 2005. Since then he divides his time as Distinguished Research Professor of Pharmacy, University of New Mexico; Chief Science Officer of The Chem21 Group, Inc.; and Professor Emeritus of Medicinal Chemistry and Pharmacognosy, University of Illinois. Tony Hopfinger is highly respected by all of his colleagues worldwide and this Award is a well-deserved recognition of the outstanding career of an unstinting and generous pioneer and practitioner of cheminformatics. Phil McHale, Chair, CINF Awards Committee pmchale@cambridgesoft.com
  20. 20. Chemical Information Bulletin Vol. 62(3) Fall 2010 20 CINF Scholarship for Scientific Excellence Sponsored by Accelrys® The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by Accelrys is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to two scholarships valued at $1,000 each will be presented at the 241th ACS National Meeting in Anaheim, CA, March 27 – 31, 2011. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the new abstract submission systemof ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe@comcast.net, that you are applying for a scholarship. Submit your abstract at http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract for “CINF Scholarship for Scientific Excellence”. PACS will be open for abstract submissions on August 3, 2010, and close on October 18, 2010. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by January 31, 2011. Any questions related to applying for one of the scholarships should be directed to the s ame e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the student’s work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked “Winner of Accelrys-CINF Scholarship for Scientific Excellence” at the poster session. Guenter Grethe ggrethe@comcast.net
  21. 21. Chemical Information Bulletin Vol. 62(3) Fall 2010 21 Chemical Structure Association Trust Applications Invited for CSA Trust Jacques-Émile Dubois Grants for 2011 The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research. In support of its charter, the Trust has creat ed a unique Grant Program, renamed in honor of Professor Jacques-Émile Dubois who made significant contributions to the field of cheminformatics. The Trust is currently inviting the submission of grant applications for 2011. Purpose of the Grants: The Grant Program has been created to provide funding for the career development of young researchers who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, process and retrieve information about chemical structures, reactions and compounds. A Grant will be awarded annually up to a maximum of four thousand U.S. dollars ($4,000). Grants are awarded for specific purposes, and within one year each grantee is required to submit a brief written report detailing how the grant funds were allocated. Grantees are also requested to recognize the support of the Trust in any paper or presentation that is given as a result of that support. Who is Eligible? Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information related research and who are developing careers that have the potential to have a positive impact on the utility of chemical information relevant to chemical structures, reactions and compounds, are invited to submit applications. While the primary focus of the Grant Program is the career development of young researchers, additional bursaries may be made available at the discretion of the Trust. All requests must follow the application procedures noted below and will be weighed against the same criteria. What ActivitiesAre Eligible? Grants may be awarded to acquire the experience and education necessary to support research activities; e.g. for travel to collaborate with research groups, to attend a conference relevant to one’s area of research, to gain access to special computational facilities, or to acquire unique research techniques in support of one’s research. ApplicationRequirements: Applications must include the following documentation: 1. A letter that details the work upon which the Grant application is to be evaluated as well as details on research recently completed by the applicant; 2. The amount of Grant funds being requested and the details regarding the purpose for which the Grant will be used (e.g. cost of equipment, travel expenses if the request is for financial support of meeting attendance, etc.). The relevance of the above-stated purpose to the Trust’s objectives and the clarity of this statement are essential in the evaluation of the application); 3. A brief biographical sketch, including a statement of academic qualifications; 4. Two reference letters in support of the application. Additional materials may be supplied at the discretion of the applicant only if relevant to the application and if such materials provide information not already included in items 1-4. Three copies of the complete application document must be supplied for distribution to the Grants Committee. Deadline for Applications: Applications must be received no later than March 14, 2011. Successfulapplicants will be notified no later than May 2, 2011.
  22. 22. Chemical Information Bulletin Vol. 62(3) Fall 2010 22 Address for Submission of Applications: Two copies of the application documentation should be forwarded to: Bonnie Lawlor CSA Trust Grant Committee Chair 276 Upper Gulph Road, Radnor, PA 19087, USA. If you wish to enter your application by e-mail, please contact Bonnie Lawlor at blawlor@nfais.org prior to submission so that she can contact you if the e-mail does not arrive. 2011 Lucille M. Wert Scholarship Call for Applications Deadline: February 1, 2011 Designed to help persons with an interest in the fields of Chemistry and Information to pursue graduate study in Library, Information, or Computer Science, the Scholarship consists of a $1,500 honorarium. This scholarship is given yearly by the Division of Chemical Information of the American Chemical Society. The applicant must have a bachelor’s degree with a major in Chemistry or related disciplines (related disciplines are, for example, Biochemistry or Chemical Informatics). The applicant must have been accepted (or currently enrolled) into a graduate Library, Information, or Computer Science program in an accredited institution. Work experience in Library, Information or Computer Science preferred. The deadline to apply for the 2011 Lucille M. Wert Scholarship is February 1, 2011. Details on the application procedures can be found at: http://www.acscinf.org and once there click on “Awards” and then click on “Lucille M. Wert Student Scholarship”. Applications (e-mail preferred) can be sent to: margaret.matthews@thomsonreuters.com Contact: Marge Matthews CINF Awards Committee 633 Dayton Rd. Bryn Mawr, PA 19010-3801 Phone: 215-823-3922 SCHEDULE OF FUTURE ACS NATIONAL MEETINGS 240th Fall 2010 August 22-26 Boston,Massachusetts 241st Spring 2011 March 27-31 Anaheim, California 242nd Fall 2011 August 28- September 1 Denver, Colorado 243rd Spring 2012 March 25-29 San Diego, California 244th Fall 2012 September 9-13 Philadelphia, Pennsylvania
  23. 23. Chemical Information Bulletin Vol. 62(3) Fall 2010 23 Book Reviews By Robert E. Buntrock buntrock16@myfairpoint.net De Bellis, Nicola. Bibliometrics and Citation Analysis: From the Science Citation Index to Cybermetrics; Scarecrow Press: Lanham, MD, 2009, $55.00 (Paperback). 394 pp. ISBN: 978-0-8108-6713-0. This rather massive monograph is the outgrowth of a research project on a related topic and is an English translat ion, encouraged by Eugene Garfield, of the Italian original. The history and philosophy behind citation indexing and other bibliometric measures are documented in chapters one and three. The empirical basis, the literary antecedents, and comparisons with concept indexing and other full text retrieval are described in chapter two, including some discussion of Salton’s work. The work of the giants in these portions of the information industry — Bernal, Merton, Price, Garfield, and Small — are documented in detail. The mathematics of bibliometrics are described in chapter four including skewness, Lotka’s Law, Bradford’s Law, Zipf’s Law, and the work of Mandelbrot. A chapter titled “Maps and Paradigms” discusses involvement of bibliographic citation with the history and sociology of science using co-citation analysis and other methods. Another chapter, titled “Impact Factor and the Evaluation of Scientists: Bibliographic Citation at the Service of Science Policy and Management,” probably has the most relevance to most scientists. The various metrics are discussed including the Hirsch (h) index. Chapter seven, with the intriguing title, “On the Shoulders of Dwarfs: Citation as a Rhetorical Device …,” describes reasons for citation, professed and actual. Chapter eight evolves the discussion into cybermetrics, including the involvement of citation or linking in the performance of search engines. Errors and omissions do occur. Reference 5 for the introduction is missing. Recall and relevance are only discussed briefly in the context of “improvement” of results from concept indexing (manual) and retrieval by means of Salton’s geometric machine indexing and other full text indexing methods. No mention is made in chapter seven (or apparently elsewhere) of the relevance of citation retrieval since it should be commonly known among searchers that authors don’t always cite other references for the same reasons that the searcher is interested in. Due to the multitude of topics and concepts that can app ear in a single article, many of us searchers can cite instances where a citation was made for a non-relevant concept. Curiously, the discussion of citation searching in patents is the last section of chapter six and has no discussion of the validity of t he bibliometric value of citations in patents. The work of Narin is described and referenced, but that of critics of the method, including Edlyn Simmons, Stu Kaback, and Nancy Lambert, is missing. The existence of other uses of citation indexing and searching, e.g. in the CA file on versions of STN, is not mentioned. In the Conclusions, the author provides an either/or summation of the evaluation controversy. Either you believe that citations are “Mertonian” or you don’t. If the former, researchers, organization, and journals can be evaluated. If you don’t, none of the evaluations can be made and the Citation Index itself may not be of value. This reviewer instead t akes an intermediate attitude. Bibliometric evaluations can be a valuable supplement in a larger, more personal evaluation scheme. As for searching, use of citation indexes is a valuable supplement to other methods of searching (index, full text, etc.) and all methods should be used, none exclusively. This book will be useful to those interested in or doing research in the fields of information science or history of science. Chapter six should be made available to the management of academic and other organizations that use citation analysis for personnel evaluation. Grubb, Philip W., Thomsen, Peter R. Patents for Chemicals, Pharmaceuticals,and Biotechnology; Oxford University Press: New York, 2010, $190.00 (Hardcover). 592 pp. ISBN: 987-0-19-957523-7. This exhaustive monograph covers the whole of the field of patents on an international scale. History, patent law and procedure, patentability, patenting in practice (including drafting), and commercial exploitation are covered in depth in 25 chapters. However, it is directed at patent agents and other practitioners in patent law including portfolio manag ement. Significantly, the chapter in previous editions on patents and information (chapter 20 in the 4th edition) has been eliminated. For a treatment of the field of patent information, including a good primer on patents in general, the interested reader is referred to, among others,“Information Sources in Patents”* by Stephen Adams. *Adams, S. R. Information Sources in Patents, 2nd ed.; K. G. Saur, Munich, 2006.
  24. 24. Chemical Information Bulletin Vol. 62(3) Fall 2010 24 ACS Chemical Information Division (CINF) Fall 2010 ACS National Meeting Boston, MA (August 22-26) ABSTRACTS CINF 1 Semantic envelopment of cheminformatics resources with SADI Leonid L Chepelev(1) ,leonid.chepelev@gmail.com,1125 Colonel By Drive, Ottawa Ontario K1S 5B6, Canada ; Egon Willighagen(2) ;Michel Dumontier(1) .(1) Department of Biology,School of Computer Science,and Institute of Biochemistry, Carleton University, Ottawa Ontario K1S 5B6, Canada (2) Department of Pharmaceutical Sciences,Uppsala University, Uppsala, Sweden The distribution of computational resources as web services and their execution as workflows has enabled facile computation and data integration for bio- and cheminformatics. The Semantic Automated Discovery and Integration (SADI) framework addresses many shortcomings of similar frameworks, such as SSWAP and BioMoby, while allowing for more efficient semantic envelopment of computational chemistry services, resource discovery, and automated workflow organization. In this work, we apply the CHEMINF ontology and Chemical Entity Semantic Specification and demonstrate the usability of the SADI framework in solving common cheminformatics problems starting from RDF-based chemical entity representations. Our eventual goal is to convert all of the functions and functionalities of the Chemistry Development Kit (CDK) into distinct SADI services. This would enable the formulation of all cheminformatics problems currently addressed by CDK, as SPARQL queries, returning meaningful RDF output which can then be easily integrated with existing RDF- based knowledgebases or used for further processing. CINF 2 RESTful RDF web services for predictive toxicology Nina Jeliazkova(1) ,jeliazkova.nina@gmail.com,4 A.Kanchev str., Sofia - 1000,Bulgaria . (1) Ideaconsult Ltd., Sofia 1000,Bulgaria The Open Source Predictive Toxicology Framework http://www.opentox.org, developed by partners of the EC FP7 OpenTox project , aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology http://www.opentox.org/api/1.1/opentox.owl ii) flexibility by linking with related ontologies; iii) availability of data and algorithms via a standardized REST web services interface, where every compound, data set or predictive method has an unique web address, used to retrieve its RDF representation, or initiate the calculations. The OpenTox framework allows building user-friendly applications for toxicological experts or model developers, or direct access by an application programming interface for development, integration and validation of new algorithms. The work presented describes the experience of building RESTful web services, based on RDF representation of resources, to incorporate diverse IT solutions into a distributed and interoperable system. CINF 3 Linking the resource description framework to cheminformatics and proteochemometrics Egon L. Willighagen(1) , egon.willighagen@farmbio.uu.se,Box 591,Uppsala Uppland SE-75124;Jarl E.S. Wikberg(1) .(1) Department of Pharmaceutical Biosciences,Uppsala University, Uppala, Sweden Background Semantic web technologies are finding their way into the life sciences.Ontologies and semantic markup have already been used for more than a decade in molecular sciences,but have not found widespread use yet. The semantic web technology Resource Description Framework (RDF) and related methods showto be sufficiently versatile to change that situation. Results The work presented here focuses on linking RDF approaches to existing molecular chemometrics fields, including cheminformatics, QSAR modeling and proteochemometrics. Applications are presented that link RDF technologies to methods from statistics and
  25. 25. Chemical Information Bulletin Vol. 62(3) Fall 2010 25 cheminformatics, including data aggregation, visualization, chemical identification, and property prediction. They demonstrate how this can be done using various existing RDF standards and cheminformatics libraries. For example, we showhow IC50 and Ki values are modeled for a number of biological targets using data from the chEMBL database. Conclusions We have shown that existing RDF standards can suitably be integrated into existing molecular chemometrics methods. Platforms that unite these technologies,like Bioclipse, makes this even simpler and more transparent. Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility. The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows. CINF 4 Chemical e-Science Information Cloud (ChemCloud): A semantic web based eScience infrastructure Stephan Heineke(1) ,heineke@fiz-chemie.de,Franklinstr. 11, Berlin Berlin, Germany ; Adrian Paschke(2) .(1) FIZ CHEMIE, Berlin 10587,Germany (2) Department of Mathematicsand ComputerScience, FU Berlin, Berlin 14195,Germany Our Chemical e-Science Information Cloud (ChemCloud) – a Semantic Web based eScience infrastructure – integrates and automates a multitude of databases,tools and services in the domain of chemistry, pharmacy and bio-chemistry available at the Fachinformationszentrum Chemie (FIZ CHEMIE), at the Freie Universitaet Berlin (FUB), and on the public Web. Based on the approach of the W3C Linked Open Data initiative and the W3C Semantic Web technologies for ontologies and rules it semantically links and integrates knowledge from our W3C HCLS knowledge base hosted at the FUB, our multi-domain knowledge base DBpedia (Deutschland) implemented at FUB, which is extracted from Wikipedia (De) providing a public semantic resource for chemistry, and our well-established databases at FIZ Chemie such as ChemInform for organic reaction data, InfoTherm the leading source for thermophysical data, Chemisches Zentralblatt, the complete chemistry knowledge from 1830 to 1969, and ChemgaPedia the largest and most frequented e-Learning platform for Chemistry and related sciences in German language. CINF 5 Use of semantic web services to access small molecule ligand database Anay P Tamhankar(1) ,anay@evolvus.com,88 Shukrawar Peth, Pune Maharashtra 411002,India ; Aniket S Ausekar(1) .(1) Software Solutions Group,Evolvus, Pune Maharashtra 411002,India Resource Description Framework (RDF) and a set of associated technologies like OWL, SPARQL etc..., which form the W3C's semantic web technology stack, are renewing interest in semantic chemistry. Semantic Web Services not only specify syntactic interoperability but also specify and enforce the semantic constraints of messages being transmitted and objects being accessed. Liceptor database is a small molecule ligand database consisting of approximately 4 million compounds.The database schema consists offields like molecular properties (2D-structure, molecular weight, molecular formula etc...), molecular descriptors (H-donors, H- acceptors,logP, logD number of rotational bonds etc...) and pharmacological properties (bio-assays,receptors, enzymes, parameters, animal models, therapeutic indications etc...). Pharmaceutical and Bio-Technology companies use this database to mine chemical space for internal research, to prioritize QSAR and pharmacophore studies,for synthetic chemistry endeavors and for advancing hit-to-lead patterns. The database records are available in multiple formats (relational database,XML, Rdfile etc...) as well as available online through an interactive web application (html format). The soon to be released version of the database includes access using semantic web services. The ontology is expressed in OWL and RDF defines the overall
  26. 26. Chemical Information Bulletin Vol. 62(3) Fall 2010 26 framework. Typical consumers of the data using this access mechanism are expected to be third-party tool vendors and data aggregators. Use of semantic web services allows evolution of the schema over time without explicitly communicating the change as well as requiring all data consumers to be changed. CINF 6 Usage metrics: Tools for evaluating science monograph collections Michelle M Foss(1) ,micfoss@uflib.ufl.edu, PO Box 117011,Gainesville FL 32611,United States ; Vernon Kisling(1) ;Stephanie Haas(1) .(1) Department of Marston Science Library, University of Florida, Gainesville FL 32611,United States As academic libraries are increasingly supported by a matrix of databases functions, the use of data mining and visualization techniques offer significant potential for future collection development based on quantifiable data. While data collection techniques are not standardized and results may be skewed because of granularity problems, or faulty algorithms, useful baseline data is extractable and broad trends identified. The purpose of the study is to provide an initial assessment of data associated with the science monograph collection at the Marston Science Library (MSL), University of Florida. The sciences fall within the major Library of Congress Classification schedules of Q, S, and T, excluding TN, TR, TT, and R. The overall strategy of this project is to analyze audience- based circulation patterns, e-book usage, purchases, and interlibrary loan statistics from the academic year July 1, 2008 to June 30, 2009. Such analyses provide an evidence-based framework for future collection decisions. CINF 6 Usage metrics: Tools for evaluating science monograph collections Michelle M Foss(1) ,micfoss@uflib.ufl.edu, PO Box 117011,Gainesville FL 32611,United States ; Vernon Kisling(1) ;Stephanie Haas(1) .(1) Department of Marston Science Library, University of Florida, Gainesville FL 32611,United States As academic libraries are increasingly supported by a matrix of databases functions, the use of data mining and visualization techniques offer significant potential for future collection development based on quantifiable data. While data collection techniques are not standardized and results may be skewed because of granularity problems, or faulty algorithms, useful baseline data is extractable and broad trends identified. The purpose of the study is to provide an initial assessment of data associated with the science monograph collection at the Marston Science Library (MSL), University of Florida. The sciences fall within the major Library of Congress Classification schedules of Q, S, and T, excluding TN, TR, TT, and R. The overall strategy of this project is to analyze audience- based circulation patterns, e-book usage, purchases, and interlibrary loan statistics from the academic year July 1, 2008 to June 30, 2009. Such analyses provide an evidence-based framework for future collection decisions. CINF 7 Happily ever after or not: E-book collection usage analysis and assessment at USC Library Norah Xiao(1) ,nxiao@usc.edu,910 BloomWalk, Los Angeles CA 90089-0481,United States . (1) University of Southern California,United States With more and more e-book collections being launched by publishers, USC Science and Engineering Library initiated its e-book collection acquisition since late 2008, and one of first and biggest acquired collections is Springer e-books. Now after two years, are users satisfied with this e-book collection? Are they accessing and using it? Like any other e-collection, how well have we, librarians and staff, been coping with this collection in collection development (e.g. e-book packages from other publishers), access services (e.g. interlibrary loan, off-campus access, e-books technical issues), outreach (e.g. e-book market strategies), and information literacy? This presentation will overview our assessment of this e-book collection after 2 years. What have we learned from the usage data? And by analyzing the data, how did and can we improve our services to users? It is hoped to our experience can present a proactive implementation plan for others considering comprehensive digital migration of their content, with the goal of not only better coping with the current economic environment, but of spurring development, innovation, and efficiency in the long run.
  27. 27. Chemical Information Bulletin Vol. 62(3) Fall 2010 27 CINF 8 From Chemical Abstracts to SciFinder: Transitioning to SciFinder and assessing customer usage Susan Makar(1) ,susan.makar@nist.gov,100 Bureau Drive, MS 2500, Gaithersburg MD 20899-2500,United States; Stacy Bruss(1) , stacy.bruss@nist.gov,100 Bureau Drive, MS 2500, Gaithersburg MD 20899-2500,United States. (1) National Institute of Standardsand Technology, United States The Research Library of the National Institute of Standards and Technology (NIST) monitors SciFinder usage to ensure customers have ready access to the database and to determine who uses it. Usage statistics played a critical role in determining whether to increase the number of seats and which heavy users should help pay for those additional seats. While most NIST researchers were very excited to acquire access to this product, many, who were well acquainted with using the print version of Chemical Abstracts, needed to learn best techniques for searching and browsing the chemistry literature using SciFinder. Transitioning from the printed Chemical Abstracts to SciFinder posed significant challenges to one research project. This presentation will describe how the NIST Research Library used SciFinder usage statistics to make collection development decisions and how library staff worked with NIST researchers to successfully transition from the printed Chemical Abstracts to SciFinder. CINF 9 Using Web of Knowledge to identify publishing and citation patterns of campus researchers at the University of Arkansas Lutishoor Salisbury(1) ,lsalisbu@uark.edu,365 N. McIlroy Ave.,Fayetteville AR 72701-4002,United States; Jeremy S. Smith(1) .(1) University of Arkansas,United States This presentation will provide information on a project undertaken at the University of Arkansas in Fayetteville to study publications by the campus researchers with an emphasis on the STEM (agricultural sciences, physical science, biological sciences, engineering and mathematics, etc.) disciplines at the macro-level for a three-year period. The overall objective of the study was (1) to provide an overview of the productivity of faculty and researchers in the various departments which could be used in allocating resources for collection development and (2) to provide evidence-based data of periodical use to assist with collection decisions and to identify collection strengths at the university level. We used the Web of Knowledge database (Science Citation Index, Social Science Citation Index and Arts and Humanities Citation Index) to identify the periodical literature in which our researchers published and those that they cite in their publications to do several analysis including determining the extent to which our researchers are publishing in and citing periodicals from the Elsevier, Wiley and IEEE journal packages. A methodology for extracting citations from Web of Knowledge into an Excel spreadsheet will also be presented. The strengths and weaknesses of the Web of Knowledge for this study will also be highlighted. CINF 10 Don't forget the qualitative: Including focus groups in the collection assessmentprocess Teri M. Vogel(1) ,tmvogel@ucsd.edu,9500 Gilman Dr #0175E,La Jolla CA 92093,United States ; Susan Shepherd(1) .(1) University of California San Diego, United States To complement our ongoing quantitative collection evaluations based on cost and usage data,the UC San Diego Science & Engineering Library conducted a series of focus groups with graduate students and faculty in our core departments. Our objective was to learn more about how they use the collection for research and teaching,so that we could make more informed decisions about collection management, as well as how best to deploy our staff resources for increased promotion, outreach and instruction. Participants were asked about the resources they use, how they use them, and what gaps they perceived. We also probed their familiarity with the top licensed resources in their fields. In this presentation we will discuss ourfocus group methods, results and the next steps we have taken in this assessment,including a follow-up survey to the same departments to obtain more quantitative information about usage of the collection.
  28. 28. Chemical Information Bulletin Vol. 62(3) Fall 2010 28 CINF 11 Strategies for the identification and generation of informative compound sets Michael S Lajiness(1) ,LajinessMS@Lilly.com, 1 Corporate Center, DC:1930, Indianapolis,IN IN 46285, United States. (1) ComputerAided Drug Discovery, Eli Lilly & Company,Indianapolis,IN IN 46285,United States Mounting pressures in drug discovery research dictate more efficient methods of picking the winners: molecules that actually have a chance to be the drugs of the future. Clearly, these methods need to navigate a highly, multi- dimensional landscape. It is also clear that hard filters should never be used and that a more continuous treatment or prioritization has clear advantages. Further, structural diversity needs to be considered in order for the best structural ideas to be found most efficiently. In addition, history and external sources of information also must be examined. This presentation will describe some of the methods, techniques, and strategies that have been employed by the author over the past 25 years working in cheminformatic that attempt to identify compounds that are likely to provide the most useful information so that one might discover solid leads more rapidly. CINF 12 Public-domain data resources at the European Bioinformatics Institute and their use in drug discovery Christoph Steinbeck(1) ,steinbeck@ebi.ac.uk,Welcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, United Kingdom. (1) European BioinformaticsInstitute, EMBL Outstation - Hinxton,Hinxton Cambridge CB10 1SD, United Kingdom Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open chemistry databases into the public domain calls for flexible, open toolkits to process them. These databases and tools will, for the first time, create opportunities for academia and third-world countries to perform state-of-the-art open drug discovery and translational research – endeavors so far a domain of the pharmaceutical industry.This talk will describe a couple of relevant data resources at the European Bioinformatics Institute and will also outline our research on and development of toolkits such as the Chemistry Development Kit and CDK-Taverna to support the exploitation of these data sources. CINF 13 Decision making in the face of complicated drug discovery data using the Novartis system for virtual medicinal chemistry (FOCUS) Donovan Chin(1) ,donovan_chin@novartis.com,250 Mass Ave, Cambridge MA 02139,United States. (1) Global Discovery Chemistry, Novartis Institutesfor BioMedical Research, Cambridge MA 02139,United States This talk will describe some of the broad concepts that led to the development of the Novartis software system for data analysis & virtual medicinal chemistry (FOCUS). The system, which is routinely used globally, is designed to present the scientist with an accessible interface that permits iterative hypothesis testing of many possible chemical candidates while accounting for undesirable ADMET properties. Some of the key principles are to present the data in a way that reflects stored knowledge and facilitates the decision about what compound to make next. We will highlight some of these concepts in applications spanning the range from target identification to drug optimization. CINF 14 Integrating chemical and biological data: Insights from 10 years of VERDI Susan Roberts(1) ,susan_roberts@vrtx.com,130 Waverly St, Cambridge MA 02139,United States ; W. Patrick Walters(1) ;Ryan McLoughlin(1) ;Philppe Gabriel(1) ; Jonathan Willis(1) ;Trevor Kramer(1) .(1) Vertex Pharmaceuticals,Cambridge MA 02139,United States VERDI is a software system, originally developed in 2000 at Vertex Pharmaceuticals, for integrating chemical and biological data and delivering this information to drug discovery teams. In addition to traditional table views, VERDI incorporated a number of modules designed to enable scientists to understand relationships between chemical structure and biological data. Over the last 10 years, VERDI has been the primary data access tool for hundreds of scientists at multiple sites around the world. A retrospective evaluation of VERDI has provided us with a number of 'lessons-learned', which come from a multitude of revisions, improvements and new feature additions. Some of these lessons, which are being used as the basis for development of the next generation of data analysis and visualization tools at Vertex, will be presented and discussed in detail.
  29. 29. Chemical Information Bulletin Vol. 62(3) Fall 2010 29 CINF 15 Collaborative database and computational models for tuberculosis drug discovery decision making Sean Ekins(1)(2)(3)(4) ,sekins@collaborativedrug.com,601 Runnymede Ave, Jenkintown PA 19046,United States ; Justin Bradford(1) ;Krishna Dole(1) ;Anna Spektor(1) ; Kellan Gregory(1) ;David Blondeau(1) ;MosesHohman(2) ; Barry A Bunin(1) .(1) Collaborative Drug Discovery, Burlingame CA 94403,United States (2) Collaborations in Chemistry, Burlingame CA 94403,United States (3) Department of Pharmaceutical Sciences,University of Maryland,Burlingame CA 94403,United States (4) Department of Pharmacology,Robert Wood Johnson Medical School,University of Medicine & Dentistry of New Jersey, Burlingame CA 94403, United States Drug discovery is being re-shaped involving large scale collaborations that connect individual researchers using collaborative computational approaches and crowdsourcing. Future drug discovery decisions will ultimately still be made based on massive multidimensional datasets. As an example, the search for molecules with activity against Mycobacterium tuberculosis (Mtb) is employing many approaches in collaborating national and international laboratories. We have developed a database (CDD TB) to capture public and private Mtb data while enabling data mining and collaborations with other researchers. We have also used the public data along with several computational approaches including Bayesian classification models for 220,463 molecules and tested them with external molecules, enabling the discrimination of active or inactive substructures from other datasets in CDD TB. The combination of the database, dataset analysis, and computational models provides new insights into molecular properties and features that are determinants of whole cell activity, allowing prioritization and decision making around molecules. CINF 16 Data drive life sciences:The Pyramids meet the Tower of Babel Rajarshi Guha(1) , guhar@mail.nih.gov,9800 Medical Center Drive, Rockville MD 20852,United States . (1) Department of Informatics, NIH Chemical Genomics Center, Rockville MD 20852,United States A characteristic feature of modern life science research is the fact that it has become data intensive. As a result we are faced with datasets of massive size and wide variety in terms of the type of data. Examples include massive datasets from next generation sequencing to more complex datasets of chemical structure and activity from high-throughput small molecule screens. In this talk I will discuss some aspects of how one can handle datasets of such size and variability. I will consider examples from computational science and distributed services that allow us to easily and cheaply handle massive datasets to integration approaches that attempt to merge data from multiple sources to obtain a systems level view of the biological effects of small molecules. In all cases, the focus will be data generated from and for small molecule studies. CINF 17 Design principles for diversity-oriented synthesis: Facilitating downstream discovery with upfront design Lisa Marcaurelle(1) ,lisa@broadinstitute.org,7 Cambridge Center, Cambridge MA 02139,United States. (1) Chemical Biology Platform, Broad Institute, Cambridge MA 02139,United States To expand the diversity of our screening collection to access a broad range of biological targets, we aspire to produce libraries of small-molecules that combine the structural complexity of natural products and the efficiency of high-throughput processes. Moreover, we aim to synthesize the complete matrix of stereoisomers for all library members. We reason that this unique collection will enable the rapid development of stereo-structure/activity relationships (SSAR) upon biological testing providing valuable information for the prioritization and optimization of hit compounds. Although our library products may be distinct compared to traditional compound collections, we are faced with fundamental questions relevant to library design: How do you prioritize scaffolds for synthesis? How do you select products with desirable physicochemical properties? In designing DOS libraries we employ a number of cheminformatic methods to tackle such issues and select compounds for synthesis/screening. An overview of our design criteria and decision-making process will be presented.
  30. 30. Chemical Information Bulletin Vol. 62(3) Fall 2010 30 CINF 18 Overview: Data-intensive drug design John H Van Drie(1) ,johnvandrie@mindspring.com,34 Stinson Rd, Andover MA 01810,United States. (1) R&D, Van Drie Research, AndoverMA 01810,United States How do we best make med chem decisions in the face of a lot of data? This is an issue that confronts us at many stages of the drug discovery process: screening, hit-to- lead, early lead optimization, and late-stage lead optimization. In this session, speakers representing each of these stages will describe how they have successfully tackled these issues, emphasizing general principles over specific computational tools. Our brains can conveniently handle only about 7 things at a time, and most traditional med chem. decision-making processes reflect that. Already when the number of molecules being considered is in the range of dozens, things get tricky; when that number is in the thousands to hundreds of thousands, one must re-orient one's perspective CINF 19 Data-driven development: How ACS Publications uses data to enhance products and services, and respond to customer needs Sara Rouhi(1) ,s_rouhi@acs.org, 1155 16th St., NW, Washington DC 20036,United States; Melissa Blaney(1) . (1) ACS Publications,United States As the scholarly publishing landscape continues to rapidly transform in unprecedented ways, publishers and libraries have had to quickly pivot to accommodate the changing preferences that users have for accessing, collecting, and consuming digital information. ACS Publications has used a data-driven approach to handle these changing customer and end-user needs. Everything from our ACS Mobile iPhone application to our transition from print to online Web products has been shaped by this approach. This presentation will address the role of data in developing new products, enhancing our web presence, and responding to user behavior on the ACS Web Editions Platform. CINF 20 Objective collections evaluation using statistics at the MIT Libraries Mathew Willmott(1) ,willmott@mit.edu,Building 14S-134, 77 MassachusettsAve, Cambridge MA 02139-4307, United States ; Erja Kajosalo(1) .(1) Engineering & Science Libraries, Massachusetts Institute of Technology, United States Recent budget pressures have forced many libraries to reevaluate their collections and substantially cut back on their subscription spending.The task of evaluating a large collection of subscription-based materials, however, is a difficult one. Journals from different subject areas are used differently, and journals from different publishers have their usage measured differently. Evaluating each individual journal subscription separately would be a monumental task bordering on infeasibility. This paper will discuss the approach taken by the MIT Engineering and Science Libraries in the spring of 2009 and 2010 to evaluate their journal collections, specifically for Springer, Elsevier, and Wiley-Blackwell, the three journal publishers with which these libraries hold the most subscriptions.Discussion will include the gathering and analysis of usage data,publication data, and citation data, as well as the process by which these data were combined to create an objective ranking for each journal. These objective rankings were not final decisions; librarians with subject expertise then evaluated the lower-ranked journals to determine if they were appropriate choices for cancellation, often taking into consideration many additional factors. However, these objective evaluations helped librarians to more efficiently use their time by indicating which journals may be strong candidates for cancellation, and they helped department liaisons to defend final cancellation choices to a very data-driven faculty. The end result was a more efficient cancellation process as well as a more comprehensive understanding of the library's journal collections. CINF 21 Getting the biggest bang for your buck: Methods and strategies for managing journal collections Grace Baysinger(1) ,graceb@stanford.edu,364 Lomita Drive, Stanford 94305-5081,United States . (1) Stanford University, United States Chemistry journals have the highest average cost per title of all subject areas. Library collection budgets have not kept pace with price increases and funds to acquire new titles are scarce. Signing big deals for journals has limited flexibility in adapting to changes.These factors have made acquiring journals to support programmatic needs more of a challenge than ever before. This presentation will cover methods, strategies,and tools than can be used to help assess howresources are allocated when

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