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

I just found the video of my presentation given at the 2014 Emerging Trends in Scholarly Publishing™ Seminar

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.

Both the SLideshare presentation and my presentation are posted below:

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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 gave during a UK tour in Sept/Oct 2014 at a number of UK universities

Beyond the paper CV and developing a scientific profile through social media, AltMetrics and micropublications

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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Who knew I would get here from there and how I became the ChemConnector. #ACSsanfran

This was my fifth talk at the ACS meeting in San Francisco…..

Who knew I would get here from there. How I became the ChemConnector.

As the ChemConnector and one of the people responsible for creating ChemSpider I have become well known in the chemical information world. I get to connect with some of the brightest minds in the domain, have participated in meetings with Microsoft, Google, various government institutions and with some of the top chemical and pharmaceutical companies. While my path to this point feels at some times like a random walk, and certainly I never set a trajectory to become a chemical information specialist as I am a spectroscopist by training, I look back upon my career with a lot of satisfaction. We are now at a time when information is becoming so important to support and guide the discovery process. At the same time the opportunity to communicate your science to the masses is upon us. I will discuss how I became the ChemConnector, my Twitter handle, and why I believe entering the field of cheminformatics at this time holds incredible potential for influence.

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RSC eScience heroes rewarded through Microsoft prize

A press release from today….I hope to say more after the week at ACS New Orleans….

Last year, the Royal Society of Chemistry’s Antony Williams was given the Microsoft Jim Gray eScience Award, recognising his pioneering contribution to ChemSpider, the free chemical structure database.

Now, Tony has chosen to pass on the $20,000 prize money to recognise eight colleagues who have made contributions to eScience through their own research.

Tony explains that, as the first non-academic to win the award, where traditionally the monetary prize has gone to the winner’s institution to invest in research, as he works in the publishing wing of his organisation, this needed a different approach.

Tony says: “I wanted to reward and recognise the efforts of the many people I’ve worked with and whose data, systems and services I have used over the years – every one of them has contributed in some ways to my own work in this area.

“In science you commonly stand on the shoulders of the giants that come before you. In eScience it is very possible to benefit from the efforts of others and implement, and I am fortunate to be able to take advantage of the brilliance of others.

“This is my giveaway in recognition of what they do and my thank you to them.”

One of Tony’s choices is Jean-Claude Bradley, Associate Professor at Drexel University in Philadelphia, who has pioneered work on Open Notebook Science. Tony Williams is deeply impressed with Jean-Claude’s approach, saying “I believe we will look back at what he’s doing as being hugely important – he really has his finger on the pulse of the future”.

Jean Claude feels equally strongly that a more open approach to science is vital for the acceleration of science and chemical projects. When asked about the importance of receiving the extra financial support, he said: “It’s fantastic, I’m very honoured by the award and certainly we don’t have any government funding for this so it’s very encouraging.

“Crowd funding and these kinds of initiatives, I think there are situations where it really works, so it definitely means a lot.

“ChemSpider itself has been key in the technical components of our work because we use ChemSpider IDs as our primary key for the molecules that we track and it has a lot of useful web services you can use, so working with Tony and the tools available from ChemSpider has been fantastic”.

Another recipient is Professor Martin Walker who, as well as teaching organic chemistry at the State University of New York at Potsdam has worked on improving the chemical compound pages on Wikipedia Chemistry. That work is “incredibly important”, according to Tony Williams. He adds: “Martin came in to work with the RSC for a year, so he’s someone I know and respect hugely. I also worked with him at Wikipedia Chemistry and he’s co-ordinated some incredibly important work”.

In turn, Martin Walker says “I admire Tony Williams immensely, and his award was certainly well deserved. I feel very honoured that he has chosen to recognise my work in this way.”

The award winners are recognised for their contributions as described in Tony’s own words below:

1) JC Bradley –Open Notebook Science: He coined the term Open Notebook Science and has set the vision for its applications to chemistry. http://www.drexel.edu/chemistry/contact/facultyDirectory/Jean-Claude%20Bradley/

2) Martin Walker – Wikipedia Chemistry. Leads and coordinates many efforts around Chemistry on Wikipedia contributing a significant number of the chemistry articles: http://www2.potsdam.edu/walkerma/

3) Bob Hanson – Jmol: Leads development of the Jmol applet, one of the most useful tools for chemistry on the web: http://www.stolaf.edu/people/hansonr/

4) Robert Lancashire – JSpecView: Project lead for the JSpecView Applet, an enabling component to allow for display of spectra data on the web: http://wwwchem.uwimona.edu.jm/chrl.html

5) Egon Willighagen – Open Source Chemistry: A contributor to the world of Open Code for Chemistry, especially to the Chemistry Development Kit and semantics for chemistry.: http://egonw.github.com/

6) Igor Pletnev – InChI: the InChI software manager and sole developer of all enhancements to the original InChI software code: http://analyt.chem.msu.ru/eng/preconcentration/pletnev/default.htm

7) Daniel Lowe – Nomenclature conversion and Open Reactions. Daniel managed the development of the OPSIN name-to-structure conversion software for 3 years and has contributed hundreds of thousands of chemical reactions to the world of Open Data. http://www-ucc.ch.cam.ac.uk/members/dl387

8) Peter Corbett – Text-mining: Peter developed the OSCAR3 open source package for chemistry text mining and also was the original developer of OPSIN. http://scholar.google.co.uk/citations?user=RSDcspMAAAAJ&hl=en

Press release online

http://www.rsc.org/AboutUs/News/PressReleases/2013/escience-heroes-award.asp

More information

Edwin Silvester

Media Relations Executive

Royal Society of Chemistry,

Thomas Graham House, Science Park,

Milton Road, Cambridge CB4 0WF, UK
Tel +44 (0)1223 432294, Mob +44 (0)7825 186342

www.rsc.org

 

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How ACDLabs Software Tools are used by the Royal Society of Chemistry

At RSC we are involved with a number of projects utilizing components of Advanced Chemistry Development software including nomenclature, physchem prediction and spectroscopy integration. This presentation was given at a small ACD/Labs user meeting in Loughborough, England in February 2013. I couldn’t make it and the presentation was given by Valery Tkachenko.The slide deck is on SlideShare here.

An associated movie is available on YouTube here: http://youtu.be/2kAsyRU7lRg.

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Division of Chemical Information Webinar with Jason Priem from #ImpactStory

We are pleased to announce the third in a series of webinars from the ACS Division of Chemical Information. On February 20, 11 am EST (US), Jason Priem, a PhD candidate at the University of North Carolina, will be giving a presentation entitled “Telling a fuller story of research impact with altmetrics and ImpactStory”. Jason originated the term “altmetrics”, and is very prominent in the research effort to measure scholarly impact over the social web instead of through traditional citation. For more information and details on joining the webinar, see http://www.acscinf.org/about/news/20130131.php.

 

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NERDS – a show for nerds, geeks and anyone who survived the computer boom…so, me.

Tonight I went to see NERDS, a musical comedy about Bill Gates and Steve Jobs. It was playing at the Progress Energy Center here in Raleigh and it was super, light-hearted, TOTALLY factual…even down to Steve and Bill rapping together, offered really deep insights into the minds of two of the most interesting men of the past few decades (uh…not really) and had some very memorable songs and tunes (what no CD on Amazon???).

It is showing pre-Broadway here in Raleigh and has a few days left. If you have a chance go see it…you will laugh, you will snort, you will giggle, you will cover your eyes. And for whatever reason Bill’s last little speech about Steve Jobs in his last months brought a tear to my eye. And Myrtle…oh Myrtle…if only.

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Teaching 10 Year Old Kids about Inside Magnets and Magnetic Resonance Imaging

While people think of me as a chemist and cheminformatician I am actually an NMR spectroscopist by training. The majority of my publications are about NMR…

My boys have been learning about magnetism recently so I took the opportunity to go into their class and teach 10 year olds about “inside magnets”. I was warned off of discussing nuclei but was able, I hope, to get across about hydrogen atoms being magnetic, that water inside us gives us lots of “inside magnets” and that MRIs and X-rays are way different. All this while navigating the discussions of metabonomics, “gas”, urine and how we are ALL magnetic…with more magnets inside us than the number of stars in the universe.

I might have stretched some of the analogies, might have missed out some of the details, but I hope what I tried to teach was at least educational to this class at Franklin Academy.

My thanks to Dr Matthew Crilley at Team Chiropractic in Wake Forest for lending me a light box to display X-rays he provided to me. Also to Franklin Academy, and especially Ms Miller, for hosting me.

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The International Star Registry want MORE money from me!

Yesterday I commented on “The International Star Registry while doing a nice thing for my family??“. For how corrupt things seem to be see this article on the Discover Magazine blog by @badastronomer. To quote him

“the International Star Registry, was issued a violation by the New York City Department of Consumer Affairs for using deceptive practices”.

This was capped off by an email today offering me a chance to get Volume 9 of a book submitted to  the Copyright office. See below. Not only can they create “black holes” from “white dwarfs”…i.e. black spots on a page from white paper…but they create new spellings too! Sweet. Good go buy a planet from them next….

 

StarRegistry

PS…my 10 year old son Tyler wishes to point out that this all started when he noticed that his mom’s star wasn’t on his map! And neither was his brothers or his Dad’s. And he was pretty upset about it!

Tyler and his doubtful look

 

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An interesting experience with the International Star Registry while doing a nice thing for my family

I have a certain aspect of my personality that wakes up at the opportunity to doing fun and rewarding for my family. So, when I saw the International Start Registry Living Social offer I bought four…one for me, my wife and two for my boys. A cool Xmas gift.

star_livingsocial

It was advertised as follows.

Catch the twinkle in their eyes as they look to the skies with this deal from the International Star Registry: Give the gift of a personalized star for $20 (a $65 value). Lucky recipients can join the ranks of celebrities, dignitaries, and even royalty who have their own celestial sparklers.

  • Each star comes with a 16″ x 12″ full-color parchment certificate, personalized with the star’s name, date, and coordinates
  • Create a cluster of stars for the whole family in the same constellation, or make personalized corporate gifts
  • Identification is easy with a custom 16″ x 12″ sky chart that features the star’s name, date, constellation, and location circled in red
  • A booklet on astronomy written by a professional astronomer includes additional sky charts
  • Celebrate the moment with a letter of congratulations/memorial for the recipient
  • The new star name will be published in book form for registration in the US Copyright Office

Based on what I see 31,157 were purchased

numberI chose to put our stars all close to Perseus so that we could be clustered as a family. And here we all are…slices of our own individual star maps overlaid for comparison.

allstars

On each section I have marked our individual stars. There are large stars and small stars then the ones flagged as ours. So here is my question….why do we not see each others stars on each others maps? Are these stars actually fictitious and simply inserted on the star map for effect?

A quick search online and I found this….

“The outfits that “sell” the right to name a star are out and out frauds.  The fact that there are several “selling” these rights should tell you something.  They don’t coordinate with one another, so two companies could sell the same star.”

WONDERFUL! I am scientist and got caught up with the fun for my family, allowed myself to be scammed as did 31,000 other people…There are days when I am a fool….shame on me, shame on LivingSocial and shame on the International Star Registry. HAH!

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