Archive for the Chemspider Journal Category

I have been at the German Conference for Cheminformatics for the past three days. The conference is in Goslar. I twittered the conference using #goslarcheminf and it appears that there was little interest in twittering here…seems like it’s an “American” thing to do. I gave a presentation entitled “ChemSpider – Building a Foundation for the Semantic Web by Hosting a Crowd Sourced Databasing Platform for Chemistry” and have put it on SlideShare here. The abstract for the talk is below as well as the embedded Slideshare widget for the talk. This talk was a lot less rushed than usual…not just 20 minutes and I personally enjoyed giving this talk to the audience. Commonly I feel that the talks I give are very rished and I only get to scratch the surface of what we are up to with ChemSpider. It’s amazing how an additional 15 minutes allowed me to expand on the issues and the work. The presentation drew a lot of questions and attention after the session and I’m hoping that many of the discussions regarding collaboration and depositions of new data come to fruition.

Abstract

There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge.

There are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them.  Despite the fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.

ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry.

This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.

nature-chemistryNature have released their Nature Chemistry journal and in their press release they commented on some of the resources they are linking out to.

“…Nature Chemistry articles are annotated to identify all of the chemical compounds mentioned throughout the text. Users can choose to view the article with all of the compounds highlighted, and find out more about those compounds by linking out to other information resources including PubChem and ChemSpider.”

It’s great to be seen as a database of value to be linked to! Neil Withers highlighted it in his blogpost too.

Egon has already given a good overview of the markup and semantic nature of the articles so I won’t repeat that. Egon did comment in his post: “Like many other chemistry journals, Nature Chemistry does not consider properties of the molecule interesting, and NMR spectra are hidden in the Supplementary Information. This paper in particular, disregards a lot of machine readable facts by putting all experimental section bits in a PDF document. So, the next challenge for Nature Chemistry will be to get the authors of papers contribute the original spectra (JCAMP-DX, CMLSpect, etc) in the supplementary information section. Better, have the raw data or even the NMR peak-atom annotations deposited in public repositories such ”

We have done this on the ChemSPider Journal of Chemistry already for this example.

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Issue 2 of the ChemSpider Journal of Chemistry (CJOC) is released and this month’s articles are being deposited over the next few days.

Yesterday I received an article entitled “Applications of Computer-Aided Methods of Structure Elucidation to the  Revision of Chemical Structures. I. Structure Revision of Lamellarin g.

This manuscript was deposited, marked up, inked up to structures and published via the ChemSpider Journal of Chemistry in less than an hour. It is available here. (I knew a bit about it as I was a co-author but the final manuscript came from my colleague Mikhail Elyashberg.

Overnight the first peer reviewer had commented and the comments were made public. Check the manuscript for details. We’ve now added another  RSS feed for comments made on the CJOC articles and it is available here: http://www.chemmantis.com/rss.ashx?c=comments.

Not every publication is so “easy” to publish…another 70 “page” manuscript was published today “Computer-assisted methods for molecular structure elucidation: Realizing a spectroscopist’s dream. ” and is a marked up version of our manuscript recently published on Journal of Cheminformatics. When the HTML version of the article is available on the journal we will replace our version with theirs and markup their version.

Issue 2 of the ChemSpider Journal of Chemistry starts to populate today. The first article is by Dr Martin Walker of Potsdam University. This report provides a selection from the organic methodology literature, taken from articles published in January 2009.

It’s a colorful beasty of an article with colored highlights all over the article showing chemical names, groups, families, reactions etc.  If it’s TOO colorful be sure to use the Hide All button to remove all markups or selectively remove the various classes one by one. Enjoy!

chemmantis2

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The Journal of Cheminformatics is now officially online, just in time for the ACS meeting,  with the first three articles. One of them is an article about Computer Assisted Structure Elucidation written in collaboration with my friends (and ex-colleagues) at ACD/Labs.

In the Editorial Comment David Wild writes about “Grand challenges for cheminformatics” and comments:

“We have seen huge leaps forward in the provision of freely accessible chemical databases such as PubChem [3] and ChemSpider [4]. A wealth
of information is buried in these databases as well as many other related sources.”

To be listed with alongside PubChem is very humbling. PubChem is an incredible contribution to the community and we wish to deliver similar, though additional contributions.

One of the papers is a commentary

Chemistry publication – making the revolution
Steven M Bachrach
Journal of Cheminformatics 2009, 1:2

Steven touches my heart with his two references to our works

ChemSpider “Publishers should welcome the additional supporting materials and make then available under the Open Data principle. Furthermore, publishers should encourage the mining of these supporting materials, like the CrystalEye [42] and ChemSpider [43] projects.”

ChemMantis “There are two fledgling experiments that attempt to put into place some of these enhanced-publication/datument ideas: Project Prospect [51] from the Royal Chemical Society and ChemMantis from the ChemSpider [43] group.”

And he states… “We need to encourage these projects and the development of more tools. We need to encourage our colleagues to adopt a new model for publication. We can revolutionize how we perform our science. This is the real hope of the internet for scientists.”

Amen Steve…Amen.

The only articles I print nowadays are my own articles for the purpose of reading at the proofing stage and something “chunky” that I want to read on a flight. As a result i was not aware of the fact that there are pretty significant formatting problems when printing the articles but ONLY if you use the File>Print method of printing. For a perfectly formatted printed article simply right click on the article and select Print from that menu. All will be well.

We will add a more obvious way to print in a future build.


We have continued to extend the capabilities of document markup on ChemMantis. For the floating Article Markup widget, where it is possible to switch various entities on and off in the display, there is a new tab entitled “entities”. In this tab we gather together all extracted entities under the specific entity family and display them as a list for fast review.

Where could we go from here? Some potential ideas….

1) provide the ability to switch on/off each individual entity in the paper.

2) select a name and highlight it across the paper

3) export the list(s) to text files

4) Link each of the names out to ChemSpider/Wikipedi/others

What else…we welcome your suggestions.

The ChemSpider Journal of Chemistry is formally released this evening with eight articles. These articles are all marked up using ChemZoo’s ChemMantis technology. The articles are sourced, with permission, from two Open Access journals – MDPI’s Molbank and Chemistry Central. We also have original articles sourced from a number of contributors.

The eight articles are provided at www.chemmantis.com or at the alternative redirect from www.chemspider.com/journal.

We welcome your feedback. The authors of the articles welcome your feedback. At the bottom of each article is a “post new comment” button. Please do so provide us with your thoughts.

This is a short post. It’s been a long few days getting the ChemSpider Journal of Chemistry online. There have been family emergencies, technical challenges and the general distractions of ChemSpider’s growing attention. But, the journal has been rolled out with its first collection of marked up articles.

Markup has been performed using our ChemMantis markup platform. ChemMantis stands for Chemical Markup And Nomenclature Integrated System. Markup is fully automated and then manual curation of the markup is performed. In general markup is taking less than 60 seconds and curation of course depends on the complexity of the content.

Over the next few days I will provide more detail about the platform and we will rollout a stack of articles. For now there is a teaser article here. This article is taken from Chemistry Central, with their permission, and my thanks to Jan Kuras for his support. This article is of the “Christmas tree Light” type of markup where we have chemical names, species, elements, chemical reactions, chemical groups, hardware vendors and software vendors all highlighted!!! Whoa…TOO colorful you say???? Simply switch off the “offending” entity classes using the checkboxes as shown in the image below (Click on the Thumbnail to see the full effect please)!

We are continuing to welcome submissions for the ChemSpider Journal of Chemistry. Please contact us at infoATchemspiderDOTcom if you want to submit an article to the journal.

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I am happy to announce early members of the editorial board for the ChemSpider Journal of Chemistry. To date four people have stepped up to serve the ChemSpider community. These are:

Sean Ekins (Focus: Medicinal Chemistry and Computational ADME/Tox)

Jean-Claude Bradley (Focus: Organic Chemistry and Open Science)

Rajarshi Guha (Focus: Cheminformatics and Open Science)

Alex Tropsha (Focus: Computational Chemistry and Molecular Modeling)

The editorial board will likely grow in the next few days but I am fortunate that people I trust, respect and care about the development of a comunity for chemistry have chosen to help us with the journal.

Things are coming together for the release of ChemSpider Journal of Chemistry by the end of 2008. We are presently developing an editorial board and invitations have been sent out to those who support what we have been trying to deliver in terms of ChemSpider as a resource for chemists, those who have a passion for sharing chemistry with the community and specifically people who are willing to actively participate.

One of the discussions that we hope to have completed before we go live is the “peer-review process”. The journal is going to be a mixture of content including interesting posts from the blogosphere, other Open Access content, reviews and original research articles. Our intention is that every research article will go online as a “preprint” for feedback from the community. If any issues are seen with the initial submission (missing figures, missing sections etc) then feedback will be given immediately to the submitter. When the “preprint” is put online then up to four people will be invited to provide feedback. This will be public feedback. In parallel the entire community is invited to participate in the feedback process.

Based on the feedback the submitter(s) will edit their article and respond to the community, if they wish, and, after a certain embargo period, may reissue their article. Feedback may then continue.

This journal format represents the shifts occuring in the reporting of science today. While today some scientists report via their blogs and wikis this is a very small community. With the ChemSpider Journal of Chemistry we are offering an environment where, in theory, the traffic exposure of a scientists work will be much higher than on a blog or wiki, a peer review process will be operating and, if the journal gains the intended credibility, will be appropriate for listing on a CV (not that blogs and wikis are inappropriate!).

This is a process in development…

The ChemSpider Journal of Chemistry is an experiment. We intend to demonstrate how modern web technologies can be used to dramatically enhance the type of information that can be communicated using web-based tools over standard online publishing approaches. There are some publishers who are working in delivering additional value to their readers by providing enhanced HTML articles and adding information to their articles such as InChIs to allow structure-based queries online. These publishers include the Royal Society of Chemistry with their Project Prospect and the Nature Publishing Group with their Nature Chemical Biology papers. The majority of articles presented by the commercial publishers are not of a “just-in-time” nature and are delayed by the “processes of publishing”. They are generally fairly lengthy documents and report successful results. They are commonly peer-reviewed and have endured a significant timeline from initial writing to submission, publishers processing, review and publication. Science is however being reported in near real-time under Open Notebook Science (ONS) initiatives. We believe that an online journal can co-exist between the immediate nature of blogging and wiki tools hosting ONS efforts and the more standard processes of the scientific publishers. Some publishers are already allowing online and open peer-review whereby readers provide their feedback to the author in a public forum. Papers can enter a period of online peer review and commentary during which readers provide feedback to the author(s). As a result of this process the authors can engage in public discourse with the commentators and issue a final form of the manuscript. We will offer similar facilities.

We invite manuscripts from anybody interested in exposing their work in the field of chemistry and intersecting fields. In general we expect these communications to be 1500-3000 words in length but there is no limit. We encourage submissions relating to chemistry, biochemistry and chemical biology; regarding synthesis, the analytical sciences and computational chemistry; as research, as commentaries and as questions to the community. Provided the submission relates to the domain of the chemical sciences we will find a place for it within the ChemSpider Journal of Chemistry. We encourage submissions from academia and industry, from students and senior scientists, from individuals and teams, for successful research or failed experiments. We encourage submitters to challenge us to host your manuscripts in a manner which most clearly communicates your science. This may include hosting various forms of data made available to the public as Open Data, providing visualization tools for the display of molecules, spectra, images and videos. We intend to not be constrained and to make full use of web-based tools available today and coming online tomorrow.

All articles will be Open Access articles. We will abide by the Budapest Open Access Initiative which declares “By ‘open access’ to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.” Authors must agree to allow unrestricted reading, downloading, distribution, printing, searching and linking to the published work.

Over the past 2 years we believe we have demonstrated our passion for public science, our willingness to serve the community, and integrity in our actions. We hope that the ChemSpider Journal of Chemistry will provide a vehicle to all scientists operating within the domain of the chemical sciences to expose their work and interests to the community. We intend to deliver a facile process of submission and superior tools for delivery. We welcome your support and look forward to expanding the communication of chemistry.

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