Archive for category Community Building
This is the second presentation I gave at the ACS Meeting in Indianapolis
Accessing chemical health and safety data online using Royal Society of Chemistry resources
The internet has opened up access to large amounts of chemistry related data that can be harvested and assembled into rich resources of value to chemists. The Royal Society of Chemistry’s ChemSpider database has assembled an electronic collection of over 28 million chemicals from over 400 data sources and some of the assembled data is certainly of value to those searching for chemical health and safety information. Since ChemSpider is a text and structure searchable database chemists are able to find relevant information using both of their general search approaches. This presentation will provide an overview of the types of chemical health and safety data and information made available via ChemSpider and discuss how the data are sourced, aggregated and validated. We will examine how the data can be made available via mobile devices and examine the issue of data quality and its potential impacts on such a database.
The future of scientific information & communication presented at the SUNY Potsdam Academic Festival
This is a LONG presentation….I talk about the “It’s All About Me” attitude that can positively feed science….we want to share OUR science, we want people to know about our opinions, our activities, our collaborators, we want to get funding, recognition and attribution. And why not…it can all be to the benefit of science.
This presentation was given at the SUNY Potsdam Academic Festival
The future of scientific information & communication
Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content continues to expand while the pace of change does not appear to be slowing. While scientists now have access to the enormous capacities and capability of the internet the vast majority of scientific communication continues to be through peer-reviewed scientific journals. The measure of a scientist’s contribution is primarily represented by their publication profile and the citations to their published works and offers an incomplete view of their activities. However, we are at the beginning of a new revolution where the ability to communicate offers the opportunity to embrace new forms of publishing and where scientific participation and influence will be measured in new ways. This presentation will provide an overview of our new generation of “openness” in which open source, open standards, open access and open data are proliferating. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.
The story about Olympicene was released earlier this week to great fanfare online. I discussed the details here. There has been so much press with comments made online on the websites of Popular Science, Scientific American, BBC News, the Huffington Post and many others that I wondered whether it would be appropriate to suggest an article get written for Wikipedia.
Now, I am VERY concerned with notability on Wikipedia, as evidenced by my post here about notability. I think Olympicene is “notable”. I am also concerned with being flagged with conflict of interest as I was involved with the Olympicene project. My intention was to ask the community to participate in writing the article. However, after checking Wikipedia I was happy to find that the community already got to it. In two days 9 authors had already worked on the article! I checked the View History logs…I don’t know who ANY of them are….so I am not in conflict of interest there either by asking someone to write it!
The Wikipedia article on Olympicene is here. It would be ideal to get the color image up there for dramatic effect as well as the original concept details when Olympicene was introduced, as well as at least some representatives of the synthetic path on ChemSpider SyntheticPages. I can’t add them…I’ll get flagged probably. I’d also link to the ScientistsDB article about Graham Richards as it is much richer than the one on Wikipedia.
Either way…from release to Wikipedia same day and nine authors in two days. Now that’s community collaboration!
The story of Olympicene, and our intention to try and get it synthesized and analyzed, was first reported in August 2011 here. The original conversation was between Prof Graham Richards and I over a drink in Belgium at the RSC Editors Symposium in March 2010. The concept of having someone synthesize a small organic molecule that would be a molecular representation of a famous symbol of sport was a fascinating challenge. And, always one for a challenge, it was one that was pursued with great gusto!
Since we had started the ChemSpider SyntheticPages (CSSP) platform recently I thought it was appropriate to kick off a grand vision discussion with Peter Scott, one of the editors of CSSP. My original idea that I bounced off of Peter was a big one…an international competition exposed to the chemistry community. Encourage chemistry labs around the world to submit their step-by-step syntheses to CSSP. We would be able to collect and expose all of this work to the entire chemistry community. We would set up a voting scheme for the community to give their input on what was the most elegant synthesis, the greenest, what had the best analytical data, what had the best write up. Not all categories were detailed at that time and would come later but the concept of bronze, silver and gold medal winners in an international chemistry competition made sense. We were really excited by the possibilities but for many reasons (read that as many distractions) we rolled the announcement out as a smaller announcement and encouraged participation as best as we could with a small engagement profile via this blog. It did seem to garner a lot of attention but as is common with such projects the participation was not as high as we expected. Nevertheless one lab did step up to participate in the project, the lab of David Fox Group at the University of Warwick. David is a colleague of Peter Scott’s…small world…
David had one of his students pursue the synthesis, not only because the olympicene molecule might be an elegant piece of synthetic work, but also because some of the envisaged properties could well be of value (more on that later!). Anish started publishing his syntheses to CSSP in November of last year as listed here. You can see the Olympicene compound coming together step by step and yes, the final step is not yet reported! Once the compound was made then the possibilities of having it analyzed seemed rather interesting, especially having seen the work reported by IBM in 2009 regarding the single molecule imaging of pentacene. Also, I had followed the work of Marcel Jaspars, who I had known during my time working at ACD/Labs when I was working on Computer-Assisted Structure Elucidation [1,2]. Marcel had recently worked on an NMR and microscopy imaging project to confirm a chemical compound structure. Again, small world. I asked Marcel for an intro to the researchers at IBM and we started a dialogue. Researchers at University of Warwick had already applied Scanning Tunnelling Microscopy (Dr Giovanni Costantini and Ben Moreton at Warwick) and they then connected with Leo Gross with the idea of using the noncontact atomic force microscopy approach.
Within a fairly short period of time IBM had performed the very elegant work of imaging olympicene…just one of the images is shown below but there are others shown on the Flickr account.
A single olympicene molecule is just 1.2 nanometres in width, about 100,000 times thinner than a human hair. This is beautiful! For whatever reason it looks like a molecule with a smile at the success of the work too!
The story of the work is described in this video below.
The work is not over yet! There is a research paper to come from the University of Warwick and IBM Research labs as there is definitely unique science that has come out of this work and definitely needs to be reported. That molecule, as it were, is “NOT just a pretty face”. We will submit all the appropriate images and available analytical data onto ChemSpider and CSSP as time allows.
For now I simply smile at the story of a concept discussion between Graham and I that was taken into the hands of superb scientists and brought to fruition. Congratulations to ALL of those who worked on the project in David Fox’s and Leo Gross’s labs. Thanks to the marketing people at IBM, RSC and Warwick for bringing together all of the materials in a tight time frame to tell the story. My thanks to my colleagues at RSC who believed in the potential of this project and especially to Peter Scott for seeing the potential and willingly participating! This project is a great example of international collaboration and pushing science to its extremes. It was a pleasure to be involved if only at a concept level and HOPEFULLY I will get to meet the scientists who did the work sometime!
I think the Google Scholar Citations resource is excellent. I was one of the fortunate ones that managed to get onto the system early and I signed on immediately and used it to aggregate my papers very easily and quickly as represented here. One of my favorite aspects of the system is how it keeps me informed, by emails direct to my inbox, that other papers are referencing papers for which I am an author. Today the email that hit me listed four such papers. A free service, regular updates and, as best as I can tell, working as advertised for me at least.
Scholar Alert: New citations to my articles
MJ Simpson… – Journal of Chemical Ecology, 2012
Abstract Soil organic matter (OM) contains vast stores of carbon, and directly supports
microbial, plant, and animal life by retaining essential nutrients and water in the soil. Soil OM
plays important roles in biological, chemical, and physical processes within the soil, and …
JL Lahti, GW Tang, E Capriotti, T Liu… – Journal of The Royal Society …, 2012
Abstract Marketed drugs frequently perform worse in clinical practice than in the clinical trials on which their approval is based. Many therapeutic compounds are ineffective for a large subpopulation of patients to whom they are prescribed; worse, a significant fraction of …
LA Gribov… – Journal of Analytical Chemistry, 2012
Abstract The authors discuss the methodology of quantitative analysis of pure substances
and mixtures by optical spectra (IR, Raman, UV, etc.) without using samples of standard
composition (standardless molecular spectral analysis). An algorithm of quantitative …
M Hilbig… – Journal of Cheminformatics, 2012
Chemists working in biomolecular application projects are usually looking at many related
molecules (eg results of a virtual screening run, lead series development or library design).
For a convenient visual analysis of this data it is essential that differences between …
This Google Scholar Alert is brought to you by Google.
I get interviewed quite regularly regarding ChemSpider, my views on Open Data and data quality on the internet, as well as general comments about the chemistry data explosion online. So, when I was interviewed recently for the online article “Chemistry’s web of data expands” I was more than happy to give my thoughts regarding patent data coming online, data quality and the need for standards for handling chemistry data.
One of the parts of the conversation was regarding the work put in to clean up chemistry data on Wikipedia. What seems like an eternity ago I did “Dedicate Christmas Time to the Cause of Curating Chemistry on Wikipedia” and initiated a project to check every chemical compound on Wikipedia, bond by bond, atom by atom. However, I very quickly connected with Walkerma who then introduced me to a number of other Wikipedia Chemistry people. I started participating in IRC Chats with this group and we started exchanging comments about how we could move the project along. It was a pleasure to work with the team and while I did continue to participate it was nowhere near the level that I had contributed in the early days of the project. The project was a collaborative effort for sure, one of the best I have been involved with over the past few years.
When the original article on Nature.Com was published it stated “In fact, notes Williams, Wikipedia proved the most reliable source of structure information in that experiment – largely because he had led an effort to clean up the site’s 13,000 structures.” I definitely didn’t want that statement in the article and had specifically requested that I was represented as being part of a collaborative effort. I did not lead the project…I was a part of it only. So, with a couple of email exchanges with the author of the article, Richard van Noorden, the language was changed to “In fact, notes Williams, Wikipedia proved the most reliable online source of structure information in that experiment – largely because of an effort to clean up the site’s 13,000 pages about drugs and chemicals”. It’s a subtle edit but I definitely did not want to carry the responsibility for leading a project that was an ideal representation of crowdsourcing, collaboration and caring for chemistry on Wikipedia. And, to clarify…I know for a fact that all pages are not fully curated and validated yet…it’s a long process!!!
This is one of my presentations at the ACS meeting today in San Diego regarding how to use social networking tools to expose yourself as a scientist
Social networking tools as public representations of a scientist
The web has revolutionized the manner by which we can represent ourselves online by providing us the ability to exposure our data, experiences and skills online via blogs, wikis and other crowdsourcing venues. As a result it is possible to contribute to the community while developing a social profile as a scientist. At present many scientists are still measured by their contributions using the classical method of citation statistics and a number of freely available online tools are now available for scientists to manage their profile. This presentation will provide an overview of tools including Google Scholar Citations and Microsoft Academic Search and will discuss how these are and other tools, when integrated with the ORCID identifier, may more fully recognize the collective contributions to science. I will also discuss how an increasingly public view of us as scientists online will likely contribute to our reputation above and beyond citations.
It’s going to be a busy meeting at the ACS Spring Meeting in San Diego. I am presenting five of my own talks and am co-author on 5 more. It’s going to be fun to get them all done! Read that as a challenge…and unfortunately despite my best intentions I NEVER get them written before I leave and am writing/tweaking them the night before. Such it is….
If you happen to be coming to the ACS and are interested in ChemSpider and how RSC informatics contributes to the world of chemistry please do find time to come and visit the RSC booth and, if you have time, let’s sit over a computer and a coffee and chat!
PAPER ID: 15442 PAPER TITLE: “ChemSpider as a chemical term resolver” (final paper number: 131) DAY & TIME OF PRESENTATION: March 29, 2012 from 10:00 am to 10:20 am LOCATION: San Diego Convention Center , Room: Room 27A
PAPER ID: 10915 PAPER TITLE: “Great promise of navigating the internet using InChIs” (final paper number: 101) DAY & TIME OF PRESENTATION: March 28, 2012 from 9:05 am to 9:35 am LOCATION: San Diego Convention Center , Room: Room 27A
PAPER ID: 10902 PAPER TITLE: “Chemistry made mobile – the expanding world of chemistry in the hand” (final paper number: 68) DAY & TIME OF PRESENTATION: March 26, 2012 from 2:45 pm to 3:20 pm LOCATION: San Diego Convention Center , Room: Room 25C
PAPER ID: 11299 PAPER TITLE: “Social networking tools as public representations of a scientist” (final paper number: 123) DAY & TIME OF PRESENTATION: March 28, 2012 from 2:25 pm to 2:50 pm LOCATION: San Diego Convention Center , Room: Room 25C
PAPER ID: 10893 PAPER TITLE: “Teaching NMR spectroscopy using online resources from the Royal Society of Chemistry” (final paper number: 61) DAY & TIME OF PRESENTATION: March 25, 2012 from 2:50 pm to 3:10 pm LOCATION: Westin San Diego , Room: Diamond II
There are many social networking tools for scientists that can be used to share information, engage the social network and move information about activities across the web. This presentation provides an overview of some of the tools available and how they can be used by scientists to expose their activities, manage their profile publicly and participate in the network.
I’m a BIG Wikipedia fan. It is one of my favorite sites, our 9 year old twins have spent many hours on the site with me, and I have personally spent a lot of time, including Christmas, curating chemistry on Wikipedia. I like what Wikipedia has achieved, have willingly contributed articles, but also enjoy a good laugh at Wikipedia’s expense when appropriate. In the past 24 hours I’ve giggled at the latest XKCD cartoon as well as this blog post about Jimmy Wales.
Despite my affection for Wikipedia this week I am annoyed about what’s going on for me on Wikipedia. I’ve read The Wikipedia Revolution and understand the editorial activities and I’ve had many discussions about how authors of Wikipedia articles have been “beaten up” in a friendly way. I’ve been warned about Conflict of Interest policies and yet, because I think it’s important, have tried to navigate the complexities of contributing articles. At present however my contributions on Wikipedia regarding scientists and projects I know about have all been flagged, either for deletion or for “notability”.
I’ve written the bulk of these articles: Gerhard Ecker, Sean Ekins and Gary Martin. Some of the flags on the articles include “It may have been edited by a contributor who has a close connection with its subject. Tagged since November 2011.”
Gary Martin and Sean Ekins are personal friends so YES, I have close connections with the subject. And I believe I can objectively write a good article about them. Just like I wrote about the village I grew up in…Afonwen. I only spent 12 years of my life there….so have a close connection with that too. I have known Gerhard Ecker for about three years, and know about his work from reading his articles and hearing him speak, and feel its valid to contribute an article as I JUDGE he’s a notable scientist. Gary Martin has almost 300 publications, and an h-index of 27. In the domain of NMR anyone who is doing small molecule structure elucidation is almost certainly using technology he has contributed too. He is notable. Sean Ekins is also notable, in my opinion. And surely Wikipedia is about collective opinions.
I have tried to follow notability guidelines for academics but have clearly failed so encourage anyone reading this post to help clean up the articles. If any of you out there happen to know Gerhard, Gary or Sean DON’T contribute though…you might get flagged as being a contributor who has a close connection. It’s much better to write about people you don’t know. Clearly I understand the possible bias …
If I look at the number of chemists on Wikipedia I find the following list of about 480 chemists. That article is a list of world-famous chemists. There is also a smaller list of Russian Chemists. The end of the list looks like this:
These are likely all NOTABLE chemists as I couldn’t find a single article in the list with a challenge on it…but I confess to not looking at each one one at a time. But that’s what we have for chemists….a list of world-famous chemists, biochemists and Russian chemists.
Many of us have heard about how “open” Wikipedia is including many of the exchanges regarding pornography on Wikipedia. In many cases I have to simply caution “welcome to the internet”. We all know its out there…how could we not. There is material on Wikipedia that is shocking, but at the same time educational. But where I take issue, just for comparison purposes, is that top-notch scientists, in my opinion (and I judge that of many others) can be flagged as not notable, yet pages like those listed below for pornstars can exist without question, without flagging but, I have to assume, are both encyclopedic and notable.
Similar to the list of chemists a search on pornstars gives a full article here but then these incredibly long lists!
- Category:Pornographic film actors
- Category:Lists of pornographic film actors
- List of British pornographic actors
- List of Asian pornographic actors
- List of African-American pornographic actors
- List of pornographic actors who appeared in mainstream films
- List of pornographic actresses by decade
The last one is quite a list! I guess its appropriate to list pornstars by decade but scientists tend to perform better over the longer term and can have 40-50 year careers whereas I don’t even want to imagine that for the other career! I struggle to see why the list of references for Ron Jeremy is any more notable/appropriate than the list of references for Gary Martin.
What’s ridiculous is that there is even an article about pornstar pets. What??? This has more of a place on Wikipedia than some of our worlds most published scientists? Is there something wrong with this picture?
While I may not fully understand what is deemed to be appropriate in terms of notability for a scientist, and I do understand the judgment that I might be too close to the scientists to be objective (but I challenge that!) I definitely challenge the status that ponstars deserve more exposure, pardon the pun, than the worlds chemists.
Despite my rants I understand the challenges that will likely show up as comments on this blogpost. I understand that I will be pointed to WP:COI and WP:Notability. I do not get to set the rules, I need to follow them as I am a small part of a very important community of crowdsourced improvement. But, overall, I remain surprised at how there appears to be so much diligence looking at the articles of scientists rather than those of pornstars. I think scientists are generally involved in very notable activities that generally distinguish them from the bulk of the population. I think pornstars are involved in activities that are not particularly notable as the bulk of the population will do them at some point in their life….well, not ALL activities that pornstars do I’m sure…..
I believe we need a change in policy. I believe that scientists deserve more notability than pornstars and that diligence, while appropriate, should be used in a more tempered manner.
There is an alternative solution…