Archive for July, 2013

The ACS Indianapolis is going to be a very busy week for the RSC as evidenced by the long list of presentations we will be delivering at the conference….come along and see what we are up to…

SUNDAY

1. PRESENTER: Antony Williams

PAPER ID: 11394 PAPER TITLE: Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry SESSION: Chemistry on Tablet Computers DAY & TIME OF PRESENTATION: September 08, 2013 from 8:10 am to 8:40 am LOCATION: Indiana Convention Center, Room: 141

2. PRESENTER: Simon Coles (University of Southampton)

PAPER ID: 13 PAPER TITLE: Tablets in the lab: Enabling the flow of chemical synthesis data into a chemistry repository. SESSION: Chemistry on Tablet Computers DAY & TIME OF PRESENTATION: September 08, 2013 from 10:55 am to 11:25 am LOCATION: Indiana Convention Center, Room: 141

3. PRESENTER: Antony Williams

PAPER ID: 12750 PAPER TITLE: Accessing chemical health and safety data online using Royal Society of Chemistry resources SESSION: New Horizons in Chemical Health and Safety DAY & TIME OF PRESENTATION: September 08, 2013 from 5:35 pm to 5:55 pm LOCATION: Indiana Convention Center, Room: 115

MONDAY

4. PRESENTER: Antony Williams

PAPER ID: 12406 PAPER TITLE: @ChemConnector and my personal experiences in participating in the expanding social networks for science SESSION: Role and Value of Social Networking in Advancing the Chemical Sciences DAY & TIME OF PRESENTATION: September 09, 2013 from 8:20 am to 8:45 am LOCATION: Indiana Convention Center, Room: 141

5. PRESENTER: Bibi Campos-Seijo

PAPER ID: 52 PAPER TITLE: Exploiting the digital landscape to advance the chemical sciences

SESSION: Role and Value of Social Networking in Advancing the Chemical Sciences DAY & TIME OF PRESENTATION: September 09, 2013 from 1:00 pm to 1:25 pm LOCATION: Indiana Convention Center, Room: 141

6. PRESENTER: Valery Tkachenko

PAPER ID:  57 PAPER TITLE: Building support for the semantic web for chemistry at the Royal Society of Chemistry SESSION: Joint CINF-CSA Trust Symposium: Semantic Technologies in Translational Medicine and Drug Discovery DAY & TIME OF PRESENTATION: September 09, 2013 from 1:35 pm to 2:05 pm LOCATION: Indiana Convention Center, Room: 142

7. PRESENTER: Antony Williams

PAPER ID: 14637 PAPER TITLE: Practical semantics in the pharmaceutical industry: The Open PHACTS project SESSION: Joint CINF-CSA Trust Symposium: Semantic Technologies in Translational Medicine and Drug Discovery DAY & TIME OF PRESENTATION: September 09, 2013 from 3:20 pm to 3:50 pm LOCATION: Indiana Convention Center, Room: 142

WEDNESDAY

8. PRESENTER: Antony Williams

PAPER ID: 10738 PAPER TITLE: Social profile of a chemist online: The potential profits of participation SESSION: Before and After Lab: Instructing Students in ‘Non-Chemical’ Research Skills DAY & TIME OF PRESENTATION: September 11, 2013 from 1:35 pm to 2:05 pm LOCATION: Indiana Convention Center, Room: 141

9. PRESENTER: Antony Williams

PAPER ID: 11513 PAPER TITLE: Digitizing documents to provide a public spectroscopy database SESSION: Back to the Future: Print Resources in a Digital World DAY & TIME OF PRESENTATION: September 11, 2013 from 3:15 pm to 3:45 pm LOCATION: Indiana Convention Center, Room: 141

 

THURSDAY

10. PRESENTER: Antony Williams

PAPER ID: 11519 PAPER TITLE: Importance of standards for data exchange and interchange on the Royal Society of Chemistry eScience platforms SESSION: Exchangeable Molecular and Analytical Data Formats and their Importance in Facilitating Data Exchange DAY & TIME OF PRESENTATION: September 12, 2013 from 9:10 am to 9:40 am LOCATION: Indiana Convention Center, Room: 140

11. PRESENTER: Jean-Claude Bradley

PAPER ID:  114 PAPER TITLE: Practical open data exchange formats for open organic chemistry projects SESSION: Exchangeable Molecular and Analytical Data Formats and their Importance in Facilitating Data Exchange DAY & TIME OF PRESENTATION: September 12, 2013 from 10:55 am to 11:25 am LOCATION: Indiana Convention Center, Room: 140

 

 

The RSC eScience Team has always been keen to get more links to literature references and we are currently engaged in work to extract much more information from the wealth of articles that are published in our journals (keep your eyes peeled for more information on this in the future).

The RSC now encourages authors for several of our journals to supply extra information, structures and spectra in their original file formats – which are attached to the article as supplementary information. Already we’ve seen several submissions of data that we have incorporated into ChemSpider records, both enriching the ChemSpider database and also showcasing the research of these authors through their publications. In this way, the RSC hopes to encourage the addition of reusable data files to the research paper as the start of its efforts to promote increased data sharing within chemical science research.

In a few short weeks we’ve received a number of submissions from authors that include key chemical structures as mol files and in some cases extra data including 1H and 13C NMR spectra as well as UV and IR spectra.

We’ve selected a few examples that show how this data not only enriches ChemSpider but, we hope, has benefits to researchers as authors and as consumers of chemical data.

Below are 4 articles for which we received additional supplementary files – the first 2 entries are from submissions where mol files were provided, which allowed us to deposit the structures and associate the article references with the ChemSpider records. The 3rd and 4th entries are examples of submissions where spectra were also provided

10.1039/c3ob40642c  - 26 structures – 4  new to ChemSpider (eg. CSID 28945604)

10.1039/C3OB40745D  – 26 structures – 24 new to ChemSpider (eg. CSID 28941464)

10.1039/C3CC43488E - 9 structures – 7 new to ChemSpider (eg. CSID 16462787CSID 28605621 - both of which have 1H and 13C NMR spectra)

10.1039/C3CC42396D  – 5 new ChemSpider records (eg. CSID 28945607 - Has 1H 13C  NMR and also IR and Raman spectra)

 

A closer look at the data

Taking this last example, let us investigate some of the benefits of supplying these files along with the submission:

1. With the mol file that was supplied we were able to create a new ChemSpider record (CSID 28945607) and then use the DOI of the article to insert the literature reference of the source article.

Feringa-Browne_reference

2. With the spectra files that were supplied we were able to add them to the ChemSpider record as interactve components; we hope that making the spectra interactive makes them easier to use. Lets compare the PDF version of the 1H NMR spectrum with the ChemSpider version – the screenshots below are taken as they appeared on my screen (then scaled to 80% to fit in the blog post). At first glance, they seem similar but. . .

1H NMR Spectrum

1H NMR Spectrum from Supplementary Information PDF

 

Feringa-Browne spectrum in ChemSpider record

1H NMR Spectrum from CSID 28945607


In the ChemSpider record you can use your cursor to easily select an area of interest and instantly see the peaks’ fine structure.

Feringa-Browne_CS_zoom_spectrum

The authors have supplied a very high quality PDF  - so you can zoom in on the PDF to get a better view of the splitting of the peaks, but there are always limitations. In the final image (below) we can see a comparison of the peak centred at 4.23 ppm. In embedded spectrum on ChemSpider you can clearly distinguish the splitting – but looking at the same peak from the PDF we reach the limit of the resolution (this shot was taken when the pdf was scaled to 1200% in the viewer)

Feringa-Browne_Zoom_comp_spectrum

Comparison of the peak centred at 4.23 ppm in ChemSpider and the PDF

 

So by supplying their NMR data as supplementary information it has become easier to discover and use.

3. We can provide links to relevant sources and a comment that can contain extra information above any spectra or CIF files that are displayed in ChemSpider. In this way, rather than your article pointing others to useful data within it, you are using your data to showcase and point back to your article.

 

How can you get involved?

If you are already publishing in the RSC  journals ChemComm, OBC, MedChemComm and Toxicology Research - when you receive the Author Revision email it will contain details about how you can supply extra Supplementary Information. If you have already had your article published (either with the RSC or another publisher) you can email us at chemspider-at-rsc.org and we can add data for you, or alternatively you can register for a ChemSpider account and add your own data at your leisure.

If you have any questions please do leave a comment (or email us directly). We look forwards to hearing from you!