Exchangeable molecular and analytical data formats and their importance in facilitating data exchange
Are you interested in exchangeable molecular and analytical data formats and their importance in facilitating data exchange? Do you have experience in this area? If you do, and if you are attending the ACS meeting in Indianapolis in the Fall, then please come and discuss your experiences in a session on this topic. Robert Lancashire, known for his contributions to JCAMP as well as the development of the JSpecView applet, will be co-hosting the session with me. The session outline is listed below. Please note the submission of abstracts deadline is March 18th. Thanks
“There are a myriad number of tools supporting cheminformatics and the generation and analysis of analytical data. These two areas of scientific data in particular have benefitted from the efforts that have been invested to develop exchange formats and standards enabling data to be exchanged between software packages and to be used to transfer via the web. Examples of such data formats include MOL, InChI, JCAMP-DX, NetCDF, AniML and many others. This symposium will discuss the benefits of such standards, their robustness and the need for enhanced coverage to further facilitate the chemical sciences.”
If you believe there is a role for social networking in advancing the chemical sciences, and it has brought you value we’d like to hear about it. If you are attending the ACS meeting in Indianapolis this fall it would be great if you would present on your work and experiences. This is a Division of Chemical Information session (CINF) and we are already open for abstracts so please submit before the deadline of March 18th!
“There is no shortage of social networking tools available to the scientific community to embrace and, in theory, use to advance the chemical sciences. From YouTube videos for demonstrating lab procedures, to personal blogs or blogging communities, to crowdsourced wikis and Twitter. These tools allow for sharing, for community engagement and collaboration, and many other opportunities to connect scientists (and others) to science. This symposium will examine whether social networking tools offer value to the chemical sciences. We will review how these tools are presently being used and what the opportunities are for the future for improved engagement with the existing systems or the development of new and improved tools.”
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.
It has been a pleasure working with Alex Clark and Sean Ekins on mobilizing chemistry in the past couple of years. It was only fitting that RSC sponsored the mobile apps known as Green Solvents and Lab Solvents. We hope that chemists around the world take the benefit from these apps and get great value from them in their work!!! This adds to the array of Chemistry apps that RSC is involved with delivering to the community including our ChemSpider Mobile app on Android and iOS, our Natural Product Updates Alerts app. We also continue to work on the ChemGoggles app for optical structure recognition.
The Royal Society of Chemistry (RSC) announced they have sponsored the Green Solvents and Lab Solvents mobile apps for a year.
Green Solvents and Lab Solvents are innovative apps for the iOS and Android platforms that list solvents and their scores versus various environmentally relevant properties. They are based on published data that had not been widely disseminated in conveniently available media. The apps are freely available and were developed by Dr. Alex M. Clark at Molecular Materials Informatics (MMI, Montreal, Canada) after an initial idea from Dr. Sean Ekins at Collaborations in Chemistry (CIC, Fuquay Varina, USA).
“These apps are first class examples of how green chemistry data can be delivered to a mobile device and complement other apps such as ChemSpider Mobile, which we have developed with Alex.” said Antony J. Williams, VP Strategic Development for Royal Society of Chemistry. “We are honoured to support such efforts that raise awareness of green chemistry and educate the public and serve a need for scientists in the lab”.
“It is really wonderful validation of these apps that an organisation such as the RSC would sponsor Green Solvents and Lab Solvents and this will help to further raise their visibility to scientists globally” said Alex Clark, owner of Molecular Materials Informatics. “Our recent publication in ACS Sustainable Chemistry and Engineering on the development of these apps has provoked a great deal of interest in how such datasets can be appified”.
ACS Sustainable Chem. Eng., 2013, 1 (1), pp 8–13
As announced in a recent post to the CHMINF list server the XCITR resource has been transferred to the Royal Society of Chemistry as its new home. If you are interested in finding chemical information teaching resources, and hopefully posting your own (!) then you will now find XCITR at http://www.xcitr.org. We look forward to supporting the XCITR advisory board as we reinvigorate the site in terms of hosting new content and look forward to your feedback as to what we can do to improve the service. My thanks to my colleagues Valery Tkachenko, Dan Ging and James Stevens especially for all of the work they did to make the transfer work. I work with great people!
XCITR – Explore Chemical Information Teaching Resources
I am delighted to announce that XCITR has found a new home. After a successful transfer from FIZ Chemie Berlin, the program is now hosted and maintained by the eScience group of the Royal Society of Chemistry and is accessible at http://www.xcitr.org.
We are very grateful and thank FIZ Chemie, especially Prof. Rene Deplanque, Dr. Gregor Zimmermann and Dr. Ira Fresen, for hosting and maintaining the program in the past. Their efforts in the development of XCITR are very much appreciated.
The purpose is to alleviate the availability and distribution of instructional material in chemical information. XCITR is a hub in which librarians, instructors and information providers deposit and access important and useful teaching materials. Additionally, one can find educational materials about library services and collections.
The open source system uses Drupal to make full use of Web 2.0 functionalities. Contents can be provided as documents (Word, PowerPoint, Excel, and PDF files), embedded videos (from www.youtube.com) or slideshows (from www.slideshare.net), and as external web based instructional materials by providing a link. At present, over 50 documents have been submitted. All submissions are evaluated by an Editorial Committee to make sure that they are within the scope of the collection. The system is available at http://www.xcitr.org and can be accessed without a password for browsing.
We urge readers to become familiar with XCITR and its content and to submit instructional material that may be of interest and help to other information specialists.
Pull-down menus help make it quick and easy to supply metadata for a resource. When finished, please choose “Review” on the Workflow tab to initiate the submission process with the editorial board.
Details of the program and its history are available in the Fall 2011 CCCE Newsletter at http://www.ccce.divched.org/P1Fall2011CCCENL.
Please contact me if you have any questions at email@example.com.
The RSC is involved in the project as a result of our skills in hosting chemicals in a publicly accessible database as well as integrating data. ChemSpider also has a rich collection of natural products already in the database and we are developing approaches to segregate the collection for use by the project. We also have the RSC Natural Product Updates database that we have already integrated with ChemSpider. There are various other aspects of work that we will be doing to support the project including developing approaches to perform “dereplication” – determining whether or not a particular chemical has been previously isolated/identified/elucidated, in this case by searching the ChemSpider database using spectral features (NMR shifts, multiplicities, mass, fragment ions etc). If the actual compound itself is not identified then dereplication approaches can certainly hint at a particular chemical class and substructures. We do NOT have spectral data for the majority of compounds in ChemSpider so spectral prediction approaches will be useful in this regard. We will be working with some very skilled scientists who have experience with the structure elucidation of novel natural products and will have the opportunity to collaborate with ACD/Labs, a company I worked for for over a decade on their Computer-Assisted Structure Elucidation software program, Structure Elucidator, one of the tools that will be used in this project.
Its going to be an exciting project, I am REALLY looking forward to it and heck, if we can help identify new classes of antibiotics we might contribute to some of the challenges we have ahead of us!!!!
We at RSC are fully committed to a mobile vision in terms of access to articles, data, our databases, services and…well…let’s see what the future brings! I’ve been fascinated with mobile chemistry for a couple of years now and co-authored a number of relevant articles in this area…
A.J. Williams and H. Pence, Smart Phones, a Powerful Tool in the Chemistry Classroom, J. Chem. Educ. 2011, 88 (6), pp 683–686. Link
Mobilizing Chemistry in the World of Drug Discovery, A.J. Williams, S. Ekins, R. Apodaca, A.Clark and J. Jack, Drug Discovery Today, 16:928-939
Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration, S. Ekins, A.M. Clark, A.J. Williams, Molecular Informatics 31 (8), 585-597, 2012 Link
Redefining Cheminformatics with Intuitive Collaborative Mobile Apps, A.M. Clark, S. Ekins, A.J. Williams, Molecular Informatics 31 (8), 569-584, 2012 Link
Incorporating Green Chemistry Concepts into Mobile Chemistry Applications and Their Potential Uses, S. Ekins, A.M.Clark and A.J. Williams, ACS Sustainable Chem. Eng., 2013, 1 (1), pp 8–13, http://pubs.acs.org/doi/abs/10.1021/sc3000509
Cheminformatics workflows using mobile apps, A. Clark, A.J. Williams and S. Ekins, Chem-Bio Informatic Journal, Vol. 13, pp.1-18 (2013) https://www.jstage.jst.go.jp/article/cbij/13/0/13_1/_pdf
In parallel we have been VERY active in supporting the delivery of Mobile Apps such as ChemSpider mobile for BOTH iOS and Android written by Alex Clark. In parallel we have been working on a couple of new apps and now we release, for Android only at present, our new NPU Alerts application. NPU stands for Natural Product Updates, one of the RSC graphical Databases as shown here: LINK.
What Dmitry Ivanov, one of our team, has produced is an Android App that displays the latest batch of structures in an “issue” of the database, produced monthly. It displays up to 200 compound structures and the links out to both ChemSpider and the relevant record on the graphical abstracts database. It is MUCH easier for a scientist to recognize structure class by looking at a structure representation compared with a chemical name like hexamethylchickenwire. A user of the app can quickly browse the chemical structures and click on the relevant compound for more information.
This is the first example of us displaying “structure flows” like this from a graphical abstract database. The first of many. it is not difficult to envisage extending this to supporting structure flows for each issue of a journal…right!?
Please go and try out the app and give us your feedback….it can be downloaded here: LINK
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.
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.
This week/weekend I will attend the ScienceOnline2013 conference here in Raleigh, North Carolina. This is my favorite conference of the year, bar none. I feel privileged every time I attend to be surrounded by people who are challenging the status quo and are passionate about making science more available and consumable to their peers and the community. I have met some great people at this conference and every year I walk away tired yet invigorated. I walk away feeling that my own contributions to science, especially my work to enable access to chemistry data, is coherent with the efforts of many of the crowd attending this meeting. The meeting has a commitment to scientific truth, collaboration, communication and openness. YES!!!
While I am a chemist by training what I enjoy so much about the meeting is meeting NON-chemists and learning about their world, their interests, their adventures and challenges. By keeping my head in my own box at many other conferences, primarily chemistry of course, I limit what I can learn from the experiences outside of my domain. ScienceOnline frees me up from these boundaries by throwing me into a mix of wildly different engagement. It is, quite simply, a joy! And coming at the beginning of the year it is the first conference I attend…always good!
The conference is well organized, wall to wall entertainment in various forms (including science comedians!), is socially engaging (lots of opportunities for after hours play!) and is full of “my kind of people”. I am lucky to be so close and, this year, to be able to share space with one of my closest friends. Sean Ekins (@collabchem) and I will host a discussion on “Leading Chemists Into Openness“. Sean and I hung out at the conference last year and it had a good impact on him as he describes here.
If you are attending ScienceOnline2013, are interested in Open Science and the advantages, challenges and “unknowns” of how to get there, then please come and join the conversation. We are the hosts…you define where we go! The slides below are for you to review/consider/digest in advance of the session. See you there???!!!