Last day at the Royal Society of Chemistry – So long and thanks for all the spuds

Today is my last day of employment for the Royal Society of Chemistry. It will be almost six years since I joined RSC when ChemSpider was acquired. While ChemSpider was initially a “hobby project” and attempt to create a disruption in terms of access to chemistry data, crowdsourced contribution and data validation, it has gone from strength to strength and now serves ca. 40,000 unique users a day from around the world. It won three awards in the first few months that we joined RSC and was catalytic in RSC winning three grants to allow us to participate in the Open PHACTS project, the PharmaSea project and become the host of the UK National Chemical Database Service. Based on the feedback I have received over the years ChemSpider is much-loved and appreciated as a contribution to the scientific community and is recognized as one of the key players in the free chemistry resources arena. I am proud to have been associated with it.

We also got to set up the ChemSpider SyntheticPages micropublishing site and tried to get the community sharing syntheses that would likely not make it into mainstream papers but were still of value to science.

During my six years at RSC I have been involved with many discussions regarding the following areas of work, study and research and how they would benefit publishing, the society and, of course, the chemistry community at large. The list includes, in particularly random order:

  • Chemistry databases – both commercial and free- and how to best mesh, commercialize and license data
  • Data quality in publications and databases and development of tools for data validation
  • Open Data, Open Access and Open Notebook Science
  • Text-mining of the RSC archive to extract & mark up compounds, reactions, property data and analytical data.
  • The potential of semantic web applications to scientific publishing
  • Encouraging the use of Open Identifiers – especially ORCID and InChI
  • The future of Micropublishing in the chemical sciences
  • Analytical data and building an open spectral database for the community
  • Social networking approaches to build online profiles – especially for young scientists

There are many, many more things of course but these are the big ones and, for me, bring clarity to what my interests are – chemistry data and making it available to the appropriate communities. It is with this in mind that I am excited to join the Environmental Protection Agency next week in the National Center of Computational Toxicology.

With every move forward into a new job we leave behind our old one. And I leave RSC with some sadness that I am leaving and excitement for the new opportunities. I have had the chance to work with so many good people at RSC, to engage with collaborators such as ACD/Labs, Mestre, NextMove, EBI, ChemAxon, Accelrys (as they were then), iChemLabs, Dotmatics and on and on. Apologies if you are not named but the list is very long. Thanks to everyone for your support, encouragement and opportunities to engage. It has been a blast.

And for everyone at RSC who catered to my strange diet of potatoes only…so long, and thanks for all the spuds.

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Beyond the Paper CV (or how to build an online profile as a scientist)

Beyond the Paper CV (or how to build an online profile as a scientist)

This presentation was given at the UKICRS meeting (http://www.ukicrs.org/2015-symposium.html) on April 16th 2015 at the University of Nottingham. This presentation was in a workshop and focused on trying to inform attendees in the postgraduate phases of their careers how to use online tools to start building a reputation and profile in their field. It was good to get positive feedback from some of the attendees. Generally the comments were in regards to the number of different online tools they could use that I highlighted as well as them getting an understanding that they must take responsibility for their reputation and do it soon…there are benefits to starting early!

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Our dire need to mandate data standards and expectations for scientific publishing

This is a presentation that I delivered at the ACS Division of Chemical Information meeting regarding “Reproducibility, Reporting, Sharing & Plagiarism” at ACS Denver on 23rd March 2015.

I took the opportunity to remove my hat that has me be the VP of Strategic Development at RSC, and a member of the cheminformatics group that built ChemSpider and works on other RSC projects related to it. Instead I presented on how a LACK OF MANDATES from publishers on me in terms of submission of data accompanying articles I am involved with writing is actually weakening my scientific record as data is not getting shared in the most useful forms possible to the benefit of the community. I think there would be benefits for publishers to start pushing me for MORE data, in fairly general standards, and allowing me (and others) to download the data in the form of molecules (and collections), spectral data, CSV files etc.

 

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Providing Access to a Million NMR Spectra via the web

This presentation was given at the ACS Denver meeting on March 22nd 2015 in a CHED Division symposium

Providing Access to a Million NMR Spectra via the web

Antony Williams, Alexey Pshenichnov, Peter Corbett, Daniel Lowe, Carlos Coba

Access to large scale NMR collections of spectral data can be used for a number of purposes in terms of teaching spectroscopy to students. The data can be used for teaching purposes in lectures, as training data sets for spectral interpretation and structure elucidation, and to underpin educational resources such as the Royal Society of Chemistry’s Learn Chemistry. These resources have been available for a number of years but have been limited to rather small collections of spectral data and specifically only about 3000 spectra. In order to expand the data collection and provide richer resources for the community we have been gathering data from various laboratories and, as part of a research project, we have used text-mining approaches to extract spectral data from articles and patents in the form of textual strings and utilized algorithms to convert the data into spectral representations. While these spectra are reconstructions of text representations of the original spectral data we are investigating their value in terms of utilizing for the purpose of structure identification. This presentation will report on the processes of extracting structure-spectral pairs from text, approaches to performing automated spectral verification and our intention to assemble a spectral collection of a million NMR spectra and make them available online.

 

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Give me kudos for taking responsibility for self-marketing my scientific publications and increase impact

This presentation was given at the ACS Denver meeting on March 22nd 2015 in a CINF Division symposium

Give me kudos for taking responsibility for self-marketing my scientific publications and increase impact.

Antony Williams, Will Russell, Melinda Kenneway and Louise Peck

The authoring of a scientific publication can represent the culmination of many tens if not 100s of hours of data collection and analysis. The authoring and peer-review process itself often represents a major undertaking in terms of assembling the publication and passing through review. Considering the amount of work invested in the production of a scientific article it is therefore quite surprising that authors, post-publication, invest very little effort in communicating the value and potential impact of their article to the community. Social networking has clearly demonstrated the ability to self-market and drive attention. At the same time, the increasing volume of literature (over a million new articles are published every year), requires authors to take on a more direct role in ensuring their work gets read and cited. This requirement may grow with the emergence of a range of metrics at the article level, shifting attention away from where a researcher publishes to the performance of their individual articles. Therefore, a separate platform to facilitate social networking and other discovery tools to communicate the value of published science to the community would be of value. In parallel the possibility to enhance an article by linking to additional information (presentations, videos, blog posts etc) allows for enrichment of the article post-publication, a capability not available via the publishers platform. This presentation will provide a personal overview of the experiences of using the Kudos Platform and how it ultimately benefits my ability to communicate an integrated view of my research to the community.

 

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PITTCON poster: Dealing with the complex challenge of managing diverse analytical chemistry data online

This is a talk I presented at Pittcon on Wednesday March 13th, 2015

Dealing with the complex challenge of managing diverse analytical chemistry data online

The Royal Society of Chemistry provides open access to data associated with tens of millions of chemical compounds. The richness and complexity of the data has continued to expand dramatically and the original vision for providing an integrated hub for structure-centric data has been delivered across the world to hundreds of thousands of users. With an intention of expanding the reach to cover more diverse aspects of chemistry-related data including compounds, reactions and analytical data, to name just a few data-types, we are in the process delivering a Chemistry Data Repository. The data repository will manage the challenges of associated metadata, the various levels of required security (private, shared and public) and exposing the data as appropriate using semantic web technologies. Ultimately this platform will become the host for all chemicals, reactions and analytical data contained within RSC publications and specifically supplementary information. This presentation will report on the challenges of managing “Big Data” for chemists around the world and providing access to tools for structure dereplication, spectral database searching and the crowdsourcing of the worlds’ largest spectral database.

 

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PITTCON Poster: Using an online database of chemical compounds for the purpose of structure identification

This is a poster I presented at Pittcon on Wednesday March 9th, 2015

Using an online database of chemical compounds for the purpose of structure identification

Online databases can be used for the purposes of structure identification. The Royal Society of Chemistry provides access to an online database containing tens of millions of compounds and this has been shown to be a very effective platform for the development of tools for structure identification. Since in many cases an unknown to an investigator is known in the chemical literature or reference database, these “known unknowns” are commonly available now on aggregated internet resources. The identification of these types of compounds in commercial, environmental, forensic, and natural product samples can be identified by searching against these large aggregated databases querying by either elemental composition or monoisotopic mass. Searching by elemental composition is the preferred approach as it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results can be refined by appropriate filtering to identify the compounds. We will report on integrated filtering and search approaches on our aggregated compound database for the purpose of structure identification and review our progress in using the platform for natural product dereplication purposes.

 

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PITTCON Poster: ChemSpider – building an online database of open spectra

This is a poster I presented at Pittcon on Wednesday March 11th, 2015

ChemSpider – building an online database of open spectra

ChemSpider is an online database of over 30 million chemical compounds sourced from over 500 different sources including government laboratories, chemical vendors, public resources and publications. Developed with the intention of building community for chemists ChemSpider allows its users to deposit data including structures, properties, links to external resources and various forms of spectral data. Over the past few years ChemSpider has aggregated almost 20000 high quality NMR and IR spectra and continues to expand as the community deposits additional types of data. The majority of spectral data is licensed as Open Data allowing it to be downloaded and reused in presentations, lesson plans and for teaching purposes. This poster will present our existing technology and our plans to host a million spectra in our developing online data repository.

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Presentations at the ACS Meeting in Denver

Having just returned from Pittcon late last night I am now turning my attention to the next set of presentations to be given at the ACS Denver meeting. These are listed below. If any of the blog readers will be at the ACS meeting it would be great to catch-up. See you there.

PAPER TITLE: Importance of data standards for large scale data integration in chemistry (final paper number: CINF 39)
DAY & TIME OF PRESENTATION: Wednesday, March, 25, 2015 from 11:20 AM – 11:50 AM
ROOM & LOCATION: Room 110 – Colorado Convention Center

ABSTRACT
Increasingly online databases are being used for the purpose of structure identification. In many cases an unknown to an investigator is known in the chemical literature or online database and these “known unknowns” are commonly available in these aggregated internet resources. The identification of these types of compounds in commercial, environmental, forensic, and natural product samples can be identified by searching against these large aggregated databases querying by either elemental composition or monoisotopic mass. We will report on the search approaches that we offer on aggregated compound databases hosted by the Royal Society of Chemistry and how these resources can be used for the purpose of structure identification. We will also report on our progress in the area of hosting interactive spectral data, including assignments, on our data repository and how we are using our analytical data platform for the purpose of natural product dereplication.

 

PAPER TITLE: Give me kudos for taking responsibility for self-marketing my scientific publications and increase impact (final paper number: CINF 8)
DAY & TIME OF PRESENTATION: Sunday, March, 22, 2015 from 2:15 PM – 2:40 PM
ROOM & LOCATION: Room 110 – Colorado Convention Center

ABSTRACT
The authoring of a scientific publication can represent the culmination of many tens if not 100s of hours of data collection and analysis. The authoring and peer-review process itself often represents a major undertaking in terms of assembling the publication and passing through review. Considering the amount of work invested in the production of a scientific article it is therefore quite surprising that authors, post-publication, invest very little effort in communicating the value and potential impact of their article to the community. Social networking has clearly demonstrated the ability to self-market and drive attention. At the same time, the increasing volume of literature (over a million new articles are published every year), requires authors to take on a more direct role in ensuring their work gets read and cited. This requirement may grow with the emergence of a range of metrics at the article level, shifting attention away from where a researcher publishes to the performance of their individual articles. Therefore, a separate platform to facilitate social networking and other discovery tools to communicate the value of published science to the community would be of value. In parallel the possibility to enhance an article by linking to additional information (presentations, videos, blog posts etc) allows for enrichment of the article post-publication, a capability not available via the publishers platform. This presentation will provide a personal overview of the experiences of using the Kudos Platform and how it ultimately benefits my ability to communicate an integrated view of my research to the community.

 

 

PAPER TITLE: Providing access to a million NMR spectra via the web (final paper number: CHED 91)
SESSION: NMR Spectroscopy in the Undergraduate Curriculum
DAY & TIME OF PRESENTATION: Sunday, March, 22, 2015 from 4:15 PM – 4:35 PM
ROOM & LOCATION: Gold – Sheraton Denver Downtown Hotel

ABSTRACT
Access to large scale NMR collections of spectral data can be used for a number of purposes in terms of teaching spectroscopy to students. The data can be used for teaching purposes in lectures, as training data sets for spectral interpretation and structure elucidation, and to underpin educational resources such as the Royal Society of Chemistry’s SpectralGame (www.spectralgame.com). These resources have been available for a number of years but have been limited to rather small collections of spectral data and specifically only about 3000 spectra. In order to expand the data collection and provide richer resources for the community we have been gathering data from various laboratories and, as part of a research project, we have used text-mining approaches to extract spectral data from articles and patents in the form of textual strings and utilized algorithms to convert the data into spectral representations. While these spectra are reconstructions of text representations of the original spectral data we are investigating their value in terms of utilizing for the purpose of structure identification. This presentation will report on the processes of extracting structure-spectral pairs from text, approaches to performing automated spectral verification and our intention to assemble a spectral collection of a million NMR spectra and make them available online.

 

PAPER TITLE: Using online chemistry databases to facilitate structure identification in mass spectral data (final paper number: ANYL 45)
SESSION: Advances in Mass Spectrometry
DAY & TIME OF PRESENTATION: Tuesday, March, 24, 2015 from 8:45 AM – 9:05 AM
ROOM & LOCATION: Aspen Room A – Embassy Suites Denver – Downtown Convention Center

ABSTRACT
The Royal Society of Chemistry hosts large scale data collections and provides access to the data to the chemistry community. The largest RSC data set of wide scale interest to the community offers access to tens of millions of compounds. The host platform, ChemSpider, is limited as it is a structure centric hub only. A new architecture, the RSC data repository, has been developed that extends support to reactions, spectral data, crystallography data and related property data. It is also the architecture underlying a series of exemplar projects for managing data for a number of diverse laboratories. The adoption of data standards for the integration and distribution of data has been essential. Specific standards include molecular structure formats such as molfiles and InChIs, and spectral data formats such as JCAMP. This presentation will report on our development of the data repository, the importance of utilizing standards for data integration, the flexible nature of the architecture to deliver solutions for various laboratories and our efforts to develop new large data collections. This includes text-mining efforts to extract large spectrum-structure collections from large corpuses.

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Micropublishing of 200 words isn’t new but the Journal of Brief Ideas is

Nature recently posted about a Journal that Publishes 200 Word Articles. The reporter commented “it is the latest online journal promises to bring a little brevity to science by accepting submissions of 200 words or less”. Initially I thought it was a Nature experiment but it isn’t. The intention around this new Journal of Brief Ideas is outlined here : http://beta.briefideas.org/about.

Some of the comments on the Nature post are interesting. This one from Bob Buntrock, who I know well from the Chemical Information list server probably represents a large number of people:

“200 words is not even a good abstract in most cases. Sop to the Twitter crowd. Since I do not nor plan to use social media for scientific communication, I’ll never use it and I’ll tend not to respect it.”

Personally, I BELIEVE in micropublishing. That’s why when I joined RSC over 5 years ago and we unveiled ChemSpider at our first conference in Glasgow the NEW idea that Valery Tkachenko and I pitched was to take advantage of our knowledge of cheminformatics, chemical data handling in ChemSpider and the increasing activities in blogging and microblogging and apply them to something called “ChemSpider Syntheses”. The ChemSpider Journal of Chemistry had been run as an experiment already, and is still online. We had already shown that Open Access articles such as those from MDPI Molecules could be hosted in the ChemMantis platform and marked up with interactive chemical widgets. We were already aware of the great work done by the SyntheticPages group and we chose to collaborate to create ChemSpider SyntheticPages (CSSP) as announced here.

Since then CSSP has accepted many articles and became the host of all of the Olympicene synthetic steps. The story of Olympicene is in this YouTube video and the list of synthetic steps is here. Peter Scott has told his story about CSSP and submissions have continued.

I took a look at some of these articles and if I exclude the Title, data such as NMR list of shifts and Chemicals Used then MANY ChemSpider SyntheticPages articles are about 200-250 words (i.e. the Procedure and the Authors Comments). All articles submitted to CSSP go through a fairly light review process from one of the editorial team, generally in about 24 hours, then are published and the community can comment on them – open peer review.

I also believe in the possibilities associated with Nanopublishing and nanopublications and there is work afoot to unveil some of these from text-mining efforts.

While our micropublishing efforts are focused on chemistry and syntheses specifically I believe there are other opportunities. Certainly Figshare, Slideshare and Dryad can all host micropublications already. The efforts of the Journal of Brief Ideas is a new approach and an experiment worth watching!  Good luck to them!

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