Chemical Journal Publishing in an Online World. Jason Wilde, Publisher Physical Sciences Nature Publishing Group ACS Spring Meeting 2009

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1 Chemical Journal Publishing in an Online World Jason Wilde, Publisher Physical Sciences Nature Publishing Group ACS Spring Meeting

2 Overview Chemists and chemistry NPG and chemistry Nature Chemistry features Back office production Future developments Chemistry interlinking 2

3 Chemists and chemistry Chemistry is a visual science The challenge for publishers is to move research from a 2D representation into an online world 3

4 Chemists and chemistry Very little has changed in how we publish chemistry research: There are new tools to draw structures but little has changed in how they are represented in publications (journals/books etc ) The introduction of machine readable identifiers have given us (publishers) the Nature June 1874 Nature Jan 2009 opportunity to lift the 2D structure from the page and make it work in an online world JACS June 1879 JACS Feb

5 NPG and chemistry Across the portfolio of titles (Nature and nonnature branded) we published a significant amount of chemistry Nature Chemical Biology was our first journal in mainstream chemistry launched in June 2005 Nature Chemistry has allowed us to re-invent the way we publish chemistry 5

6 NPG and chemistry In launching Nature Chemistry our aim was: build on, and then improve, the functionality created for Nature Chemical Biology look at the offerings from databases and other publishers to determine what we would like to add talk to the chemistry community to understand: what features they need in a journal what extra information they want from an article 6

7 Nature Chemistry features Firstly, behind the scenes, we have improved our production and editorial systems enabling us to continue to: Create compound pages for all bold numbers linked from both the HTML and PDF version of articles Produce CML, CDX and 3D files for all bold numbered compounds Deposit all structures in PubChem (and extend this to other databases) Deliver graphical abstracts in TOCs and RSS feeds 117

8 Nature Chemistry features Secondly we have enhanced the online user experience References can now be looked-up from the text of the article Bold compounds numbers pop-up the structure Clicking on bold numbers takes you to enhanced compound pages 8

9 Nature Chemistry features Enhanced compound pages offer: Chemdraw file CML file View structure in 3D Synonyms Chemical formula Molecular Weight Elemental Analysis InChI and InChIKey SMILES string Links to external databases 9

10 Nature Chemistry features Finally we are annotating our articles so users can link out to other information resources 10

11 Nature Chemistry features 11

12 Back office production Adding this functionality into our manuscripts created challenges, behind the scenes, to gather and encode new data The first stage was to encourage authors to provide additional information The second stage was to generate (automatically) the additional data The final stage was to develop tools to annotate the published manuscripts 12

13 Back office production CDX GIF/PNG 3D CML + PubChem Author file Compound data ChemSpider 13

14 Back office production All bold numbers within a manuscript highlight compounds key to the paper These compounds are, where needed, redrawn to be machine readable The InChIs are then generated and are in the manuscript XML. They will soon be in the HTML metadata 14

15 Back office production We will be making our HTML more semantic to provide machine readable information for compounds: <p><spanclass="b">inchikey:</ span>qgxlvxzrprrcrp-imcbxcbxbl</p> <dl class="meta"> <dt>inchi</dt> <dd class="inchi">inchi=1/c10h14n5o7p.2na/ c ( )15(3-14-5)</dd> </dl> This should happen before the next issue 15

16 Back office production Annotation adds value and functionality to the article: MOL file Tris(4-pyridyl)triazine 1,4-pryazine 4,4 -bipyridine InChI generated monophosphate Thymidylyl-(3-5 )-2 -deoxyadenosl Links fed back Into ms text hydrogen adenine thymine monophosphate External Database links 16

17 Future developments Allow readers to comment on articles published in Nature Chemistry Expanding the annotation of journal articles from Nature Chemistry to Nature Chemical Biology and then to all NPG journals Creating a central NPG database of compounds and related journal articles efficient for the production process allows us to link all papers with common compounds forms the basis for structure based searching 17

18 Future developments Integration of supplementary data into compound pages PDF/graphic files, videos etc relating to a compound will be available from the compound page Provide links to raw data i.e. CIF, JCAMP files etc... on the compound page Investigate potential collaboration with other publishers/databases to interlink content based on compounds 18

19 Chemistry interlinking Interlinking chemical content is a key next step in making chemical research discoverable Creating links between publishers and journals allows scientists to track research by compounds Adding additional links (or information) for chemical vendors patent information ensures that articles becomes the hub of research information 19