Participation of the RSC Cheminformatics Team in Presentations at the ACS San Francisco Meeting

It has been a busy few months for us this year and this will be represented at the ACS meeting in San Francisco where our team will be connected to over 20 presentations at this Fall Meeting. We have been working hard on a number of grant-based projects and specifically working on the development of the RSC Data Repository. The lists below are the papers that I will be presenting as well as others that members of the cheminformatics team will be involved with.

Papers that I will be presenting:

  1. PAPER ID: 24594
    PAPER TITLE: “Applying Royal Society of Chemistry cheminformatics skills to support the PharmaSEA project” (final paper number: 1)
    DAY & TIME OF PRESENTATION: August 10, 2014 from 9:45 am to 10:15 am
    LOCATION: Palace Hotel, Room: Marina
  2. PAPER ID: 18831
    PAPER TITLE: “How the InChI identifier is used to underpin our online chemistry databases at the Royal Society of Chemistry” (final paper number: 32)
    DAY & TIME OF PRESENTATION: August 10, 2014 from 2:00 pm to 2:35 pm
    LOCATION: Palace Hotel, Room: California Parlor
  3. PAPER ID: 20185
    PAPER TITLE: “Dealing with the complex challenge of managing diverse chemistry data online” (final paper number: 46)
    DAY & TIME OF PRESENTATION: August 11, 2014 from 9:40 am to 10:10 am
    LOCATION: Palace Hotel, Room: Marina
  4. PAPER ID: 24677
    PAPER TITLE: “Encouraging undergraduate students to participate as authors of scientific publications” (final paper number: 184)
    DAY & TIME OF PRESENTATION: August 11, 2014 from 2:00 pm to 2:25 pm
    LOCATION: Moscone Center, North Bldg., Room: 123
  5. PAPER ID: 24417
    PAPER TITLE: “Teaching analytical spectroscopy using online spectroscopic data” (final paper number: 104)
    DAY & TIME OF PRESENTATION: August 11, 2014 from 4:30 pm to 4:50 pm
    LOCATION: Moscone Center, North Bldg., Room: 111
  6. PAPER ID: 25726
    PAPER TITLE: “Who knew I would get here from there: How I became the ChemConnector” (final paper number: 103)
    DAY & TIME OF PRESENTATION: August 13, 2014 from 9:55 am to 10:20 am
    LOCATION: Palace Hotel, Room: Presidio
  7. PAPER ID: 24536
    PAPER TITLE: “Open innovation and chemistry data management contributions from the Royal Society of Chemistry resulting from the Open PHACTS project” (final paper number: 137)
    DAY & TIME OF PRESENTATION: August 14, 2014 from 10:15 am to 10:35 am
    LOCATION: Palace Hotel, Room: Presidio
  8. PAPER ID: 24515
    PAPER TITLE: “Using an online database of chemical compounds for the purpose of structure identification” (final paper number: 354)
    DAY & TIME OF PRESENTATION: August 14, 2014 from 11:30 am to 11:50 am
    LOCATION: Moscone Center, North Bldg. , Room: 125
  9. PAPER ID: 25640
    PAPER TITLE: “The Royal Society of Chemistry and its adoption of semantic web technologies for chemistry at the epoch of a federated world” (final paper number: 144)
    DAY & TIME OF PRESENTATION: August 14, 2014 from 1:50 pm to 2:10 pm
    LOCATION: Palace Hotel, Room: Marina

Other presentations that the Cheminformatics team is involved with, but for which I do not yet have times and room numbers, are as follows (the bolded name indicates the presenter):

  1. Accessing 3D printable chemical structures online. V. F. Scalfani, A. J. Williams, R. M. Hanson, J. E. Bara, A. Day, V. Tkachenko
  2. Using the BRAIN, biorelations and intelligence network, for knowledge discovery. A. Mons, B. Mons, A. Krol, A.Baak, A. Williams, V. Tkachenko
  3. Navigating chemistry requirements for data management and electronic notebooks: A case study. L. R. McEwen, A. J. Williams, V. Tkachenko, J. G. Frey, S. J. Coles, A. E. Day, C. Willoughby, W. R. Dichtel
  4. Integrating Jmol/JSpecView into the Eureka Research Workbench. S. Chalk, M. Morse, I. Hurst, A. Williams, V.Tkachenko, A. Pshenichnov, R. Hanson
  5. Clustering the Royal Society of Chemistry chemical repository to enable enhanced navigation across millions of chemicals. K. Karapetyan, V. Tkachenko, A. J. Williams, O. Kohlbacher, P. Thiel
  6. Experiences and adventures with noSQL and its applications to cheminformatics data. V. Tkachenko, A. Williams, K. Karapetyan, A. Pshenichnov, M. Rybalkin
  7. Building an online data repository for 100,000 dyes. D. Hinks, V. Tkachenko, A.J. Williams
  8. Faculty profiling and searching in the Eureka Research Workbench using VIVO and ScientistsDB. S. Chalk, M.Morse, I. Hurst, A. Williams, V. Tkachenko, A. Pshenichnov
  9. Semantic enrichment of ChemSpider data: Usage and applications. V. Tkachenko and A.J. Williams
  10. Supporting the exploding dimensions of the chemical sciences via global networking. V. Tkachenko, A. Williams, S. Vatsadze
  11. Toward extracting analytical science metrics from the RSC archives. S. Chalk, A. Williams, V. Tkachenko, C.Batchelor
  12. Dereplication applications for computer-assisted structure elucidation (CASE) and the ChemSpider database. P.Wheeler, A. Moser, J. DiMartio, M. Elyashberg, K. Blinov, S. Molodstov, A.J. Williams
  13. Real structures for real natural products − really getting them right and getting them faster. P. Wheeler, A.J. Williams, M. Elyashberg, R. Pol, A. Moser

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European Memorial Symposium on July 14th to Honor Jean-Claude Bradley

Many of us are still recovering from the tragic loss of Jean-Claude Bradley from the world. There have been a number of additional blog posts regarding JC… and I might have missed some (1,2,3,4)….and these express our shock and appreciation for who JC was as a man, a collaborator, an innovator and agent of change.

There will be a memorial symposium for JC at Drexel University on September 8th but Andy and I, selfishly I admit, wanted to take advantage of the the fact that we will both be in the UK during the week of July 14th, to try and pull together a symposium in Europe to celebrate JC’s contributions to Open Science.

Thanks to the kindness of Bobby Glen, outstanding advocate of Open Science, we have a venue for the symposium at Cambridge University. When Peter Murray-Rust heard that we were intending to host a symposium at Cambridge University he willingly jumped into the fray at short notice to help us co-host the gathering.

We admit that things are moving very quickly at present because of the short time until the meeting but we believe that the Open Science field, in particular, is fast-moving, flexible and more than willing to assemble to honor JC and discuss Open Science. The day-long meeting is on Monday July 14th and registration has just opened up so please do sign up to attend. A symposium page has been set up here by Andy on the InMemoriamJCB wiki and this will be updated regularly as we get the list of speakers squared away.

If you are interested in contributing a talk please contact me offline at tony27587ATgmailDOTcom. We are presently assembling titles and abstracts and will start listing them shortly. We are working on this in our off hours (early mornings and evenings) so please bear with us through the crunch of bringing this gathering together.

What is most critical at present is for us to get an estimate of numbers of attendees. There are two rooms available to us at the university and we need to firm up quite quickly an estimate of the numbers of attendees so we can choose which room to lock down for the meeting. With this in mind registration (and with a firm commitment to attend please) is encouraged early. Once again…sign up here.

 

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Beyond the paper CV and developing a scientific profile through social media, altmetrics and micropublication

This is a presentation that I will have delivered twice here in the UK this week…

Beyond the paper CV and developing a scientific profile through social media, altmetrics and micropublication

Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools. However, despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our future careers. We are being indexed and exposed on the internet via our publications, presentations and data. We also have many more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. Many of these can ultimately contribute to the developing measures of you as a scientist as identified in the new world of alternative metrics. Participating offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career.

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In Memory of Jean-Claude Bradley

My friend Jean-Claude Bradley was a dreamer. To lose him is a nightmare, a tragedy ….

My friend JC Bradley - leader, evangelist and practitioner of Open Science...to the max.

My friend JC Bradley – leader, evangelist and practitioner of Open Science…to the max.

When I received the sad news that JC had passed I went into the sad, dark place that losing family and friends sends me. And I went there fast. As we age we all need to face the challenge of increasing loss around us..it is inevitable. And in recent years it is with increasing frequency. In two weeks time I turn fifty years old and for sure I am more conscious of my time on this planet than ever. My priorities have shifted over the years to more balance between life and work, WAY more quality time with the people I love and especially to my twin boys (while they still want me around!) and yet I am still driven to leave my mark in my domain of science. It doesn’t have to be dramatic, it doesn’t have to glorious…but I would like it to be catalytic and, hopefully, important. And someone pointing at it with a “Tony was involved with that”…will make me happy. Likely for less than a generation…but nevertheless. We should all be pointing at JC and LISTING the “JC was involved with that…”. I believe it would make him happy.

JC Bradley did something important. He did something catalytic. Actually he did a lot that was important and catalytic. And even though he has gone he will not be forgotten by his peers, his collaborators and his followers for a long time. And I believe his legacy will survive and flourish. JC was, for me, and many others, the father of Open Notebook Science. Fortunately he is remembered in this way on Wikipedia as coining the term.

I first met JC as a PhD student while I was at Ottawa University. I used to run 2D NMR for him in the days when walk-up 2DNMR wasn’t available….300MHz XL-300 Varian instrument. The good old days. We used to spread out spectra on the floor of my apartment and assigned data. Many a long night. Even then it was clear JC was a character…an interesting character. Driven. Focused. Serious..about his science. With a laugh for all the right reasons.

I lost track of JC until he got to Drexel but since we reconnected we have spent many, many long hours on phone calls, worked on many projects together for the sake of Open Science, and I have sat and laughed and visited the many trials and tribulations of openness with JC and people including Cameron Neylon, Andy Lang and many others. JC was driven, he was humble, he was a doer. He challenged the status quo with the spirit of a change agent but without the arrogance and brutality of some in the world of openness in chemistry.

I am not going to belabor the contributions he has made to Open Science. Many others will do that in the next few days. I will do it in presentations and in my writings for sure. His legacy will live on. For now I am going to grieve the loss of an evangelist, a driven practitioner in the world of Open Science, a humble man and my friend.

He traveled the world of Second Life while here  and wherever he is now, and I am making no judgments of peoples views of where that might be, I hope Horace Moody, the cat JC was in Second Life, is purring somewhere. In my head he is smiling, he is purring and he is proud. He should be. As Mays tells us….it is a calamity not to dream…and JC did….

“The tragedy of life doesn’t lie in not reaching your goal. The tragedy lies in having no goal to reach. It isn’t a calamity to die with dreams unfilled, but it is a calamity not to dream. It is not disgrace not to reach the stars, but it is a disgrace to have no stars to reach for.” -Benjamin E. Mays (American educator, Clergyman, 1895-1984)-

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The Importance of the InChI Identifier as a Foundation Technology for eScience Platforms at the Royal Society of Chemistry

This is a presentation I gave today at Bio-IT 2014 here in Boston. I was in the company of a number of my favorite people to be o the agenda with… Steve Heller, Steve Boyer, Evan Bolton and Chris Southan.

The Importance of the InChI Identifier as a Foundation Technology for eScience Platforms at the Royal Society of Chemistry

The Royal Society of Chemistry hosts one of the largest online chemistry databases containing almost 30 million unique chemical structures. The database, ChemSpider, provides the underpinning for a series of eScience projects allowing for the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it specifically in the ChemSpider project to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a Global Chemistry Network encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.

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The potential benefits of making yourself visible online as a scientist

The potential benefits of making yourself visible online as a scientist

This is a presentation I gave at MIT to the Boston ACS Young Chemists regarding how they can take advantage of some of the online tools to spread the message about their activities, their interests, get engaged with collaborative science and participate now to gain benefits from the growing world of AltMetrics

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Presentation at the 2014 Allen Press Emerging Trends in Scholarly Publishin Seminar

Today I gave a presentation at the 2014 Allen Press Emerging Trends in Scholarly Publishing™ Seminar here in Washington DC. Over coffee I had very positive feedback about what we are doing at RSC and various comments about “real science exposed by a publisher”. The abstract and Slideshare presentation are below.

The Application of Text and Data Mining to Enhance the Royal Society of Chemistry Publication Archive

The Royal Society of Chemistry (RSC) is one of the world’s most prominent scientific societies and STM publishers. Our contributions to the scientific community include the delivery of a myriad of resources to support the chemistry community to access chemistry-related data, information and knowledge. This includes ChemSpider, a compound centric platform linking together over 30 million chemical compounds with internet-based resources. Using this compound database and its associated chemical identifiers as a basis the RSC is utilizing text and data mining approaches to data enable our published archive of scientific publications. This presentation will provide an overview of our technical approaches to text and data enable our archive of scientific articles, how we are developing an integrated database of chemical compounds, reactions, physical and analytical data and how it will be used to facilitate scientific discovery.

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Accessing Royal Society of Chemistry resources and making chemistry mobile

This is a presentation I gave at the ACS Dallas meeting on March 19th 2014

Accessing Royal Society of Chemistry resources and making chemistry mobile

The ongoing drive towards mobile devices is now simply one of generic ubiquity. It is less an issue of whether a scientist has a mobile device but rather what brand, what generation and what apps do they have installed. Chemistry has fast been moving to mobile devices for a number of years now and today is it possible to draw chemical compounds, perform searches of databases both on device and in the cloud. Modeling of data using server based platforms is increasing in scope and capabilities. The Royal Society of Chemistry was early in recognizing the potential power of mobile platforms in terms to allowing scientists to access data and the benefits of such devices to allowing students access to data and content. This presentation will provide an overview of our efforts to date in supporting chemistry technologies on mobile devices and our recent developments in this domain.

 

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Data enhancing the Royal Society of Chemistry publication archive

This is a presentation I gave at the ACS Dallas meeting on March 19th 2014

Data enhancing the Royal Society of Chemistry publication archive

The Royal Society of Chemistry has an archive of hundreds of thousands of published articles containing various types of chemistry related data – compounds, reactions, property data, spectral data etc. RSC has a vision of extracting as much of these data as possible and providing access via ChemSpider and its related projects. To this end we have applied a combination of text-mining extraction, image conversion and chemical validation and standardization approaches. The outcome of this project will result in new chemistry related data being added to our chemical and reaction databases and in the ability to more tightly couple web-based versions of the articles with these extracted data. The ability to search across the archive will be enhanced as a result. This presentation will report on our progress in this data extraction project and discuss how we will ultimately use similar approaches in our publishing pipeline to enhance article markup for new publications.

 

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The UK National Chemical Database Service as an integration of commercial and public chemistry services to support chemists in the United Kingdom

This is a presentation I gave at the ACS National Meeting in Dallas on Wednesday 19th March 2014

The UK National Chemical Database Service – an integration of commercial and public chemistry services to support chemists in the United Kingdom

At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types associated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined.

 

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