Data Rich Publishing

Peter had a detailed blog about why he joined the editorial board:

I take this position with some trepidation as I have grave reservations about the current practice of cheminformatics. It suffers from closed data, closed source and closed standards, and thereby generally poor experimental design, poor metrics and almost always irreproducible results and conclusions which are based on subjective opinions.

I strongly agree with this observation, and have discussed my view on this in my thesis (send me an email if you want a copy).

So, what has the journal to say about this (see Instructions to the Author, emphasis mine):

Journal of Cheminformatics recommends, but does not require, that the source code of the software should be made available under a suitable open-source license that will entitle other researchers to further develop and extend the software if they wish to do so.

Regarding data, they even less revolutionary; recommended figures formats (EPS, PDF, PNG) focus on nice graphics instead of reuse of data. I also note that I cannot upload data in the Open Document Format, or, hey, let’s really push things, in RDF. Well, not according to the Instructions. And surely, I can put the [O|R]DF in the supplementary information, anyway. It would also be nice if I could use Jmol as an applet to enrich the graphics, and improve data reusability of the paper, like the RSC recently started to allow .

Regarding the supplementary information, there is a section on additional files, which, unconveniently are capped at 20MB size. No mention of chemical formats at all, neither any recommendation on semantic formats like CML (I wonder when this was discussed with the Editorial Board, and where Peter was at the time). How am I going to put online my 500 molecular structure CML file now? (Though it’s good to know it is virus scanned ;)

So, why do I vent my concerns about these limitations? I had not blogged about the launch of the journal earlier, because I have not made up my mind about it. On one side, I am happy to see a journal that promotes (scientific) use of papers, and a journal that allows me to keep copyright on the material. However, on the other side, what the current Instructions suggest, the data I could use from the papers is available only in an old-fashion way. That’s a lost opportunity and could have killed competition for sure. Instead, the unique selling point is now restricted to using an open access license. Nature Chemistry, on the other hand, chose data rich publishing as a selling point (though in competition with things done at the RSC).

The other thing I want to mention about the journal is the following. Rajarshi blogged about Bachrach’s paper on Chemistry publication - making the revolution (DOI:10.1186/1758-2946-1-2). Firstly, by adding a link like that for the DOI I just gave, Chemical blogspace can pick it up; we need this later. Secondly, the paper actually suggests that “[b]y publishing lots of data, available for ready re-use by all scientists, we can radically change the way science is communicated and ultimately performed”; this is in strong contrast to what I have seen in the Instructions so far.

Starting the Scientific Communication

Rich replied to Rajarshi about the requirement to log in before someone could make a comment, which he did not like. He suggested alternative ways to prevent SPAM and sorts. The choice for this commenting approach may also originate from having an Open discussion, where everyone takes responsibility for what he says. The use of OpenID, as Rich suggests would only partially address that; on the other hand, setting up a fake email address is quite common in the blogosphere too.

If Rajarshi would have used the DOI to link to the Steven’s paper, as said, Chemical blogspace would have recognized it. Instead, he chose to link directly to the PDF. This is a typical case of hamburgers in action. However, others did when they discussed the first research paper in the journal (DOI:10.1186/1758-2946-1-3). These blogs were picked up by Cb and are listed on this page.

Now, I only need to remind you of Userscripts for the Life Sciences (DOI:10.1186/1471-2105-8-487) that we have the methods to link these comments back to the journal website. The Quotes from Chemical Blogspace and Postgenomic script in particular, does the hard work (needs GreaseMonkey, the script can be downloaded here; see also Noel’s original post). This way, we can read the comments when we visit the papers homepage:

Now, the script has not yet been updated for the new journal (Noel, can you please upload the revision?), so you need to edit the source right now and add http://*.jcheminf.com/* to the list of website the script acts on:

Userscripts

The paper on userscripts describes how Greasemonkey scripts can be used to combine different information sources (DOI:10.1186/1471-2105-8-487). A trailer:

Background
The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This pens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources.

Peter et al. have been using this technology for CrystalEye too, but the paper was in a finalizing state when the userscript was announced , unfortunately.

Bioclipse 1.2.0

The other present is the Bioclipse 1.2.0 release, for which the QSAR feature is a great new feature addition (see my blog the other day with an overview of blog items detailing my participation in that feature ). Ola et al. have done a great job with the plot functionality, which is very nice to scatter plot calculated descriptors. This release is likely going to be the last one in the Bioclipse 1 series, except for bug fix releases, so, this release also means I can start contributing to the Bioclipse 2 series. Recent items in the Bioclipse blog show a bright future, with project based resource handling, better scripting (R, ruby, JavaScript, BeanShell?).

BTW, we never have presents under the tree; we have Sinterklaas.

• wrote a Greasemonkey script to automatically link to webservices ,
• explained how that script can be used on the server , and
• adapted a Greasemonkey script to show blog items related to molecules .

All using the new semantic markup.

Of the two, I think RDFa has the best future. Then I discovered Operator , written by Mike. While the Greasemonkey scripts already allow me to link to, for example, PubChem and eMolecules, the Operator Firefox Addon allowed me to open vCards incorporated in HTML pages directly to my address book client. Thus, I could open chemistry directly in Bioclipse too!

That was the idea, at least. I contacted Mike, and he asked me to wait until the first 0.8 releases, which he announced earlier this month. This version allows user scripts to be written, which define how RDFa should be handled. And with his patience and help, this was the result:

The HTML is almost as explained before , and looks like:

<html xmlns="http://www.w3.org/2002/06/xhtml2/">

<h1>Chemical RDFa with Operator</h1>

<div about="#chem_123" xmlns:chem="http://www.blueobelisk.org/chemistryblogs/">
  Methane has the following identifier: <span property="chem:inchi">InChI=1/CH4/h1H4</span>
</div>

</html>

It is important here to wrap the statement in a <div> element and to add the @about attribute to it, defining the Subject. Moreover, you need to use the @property attributes instead of @class. The content of this attribute defined the Predicate, and the content of the <span> element is the Object, completing the RDF triple.

Operator detects these RDFa statements from the HTML, and creates a new menu item Search in Pubchem using this piece of code:

var pubchem_inchi = {
  description: "Search in PubChem",
  short: "PubChem",
  scope: {
    semantic: {
      "RDFa" :  {
        property : "http://www.blueobelisk.org/chemistryblogs/inchi",
        defaultNS : "http://www.blueobelisk.org/chemistryblogs/"
      }
    }
  },
  doAction: function(semanticObject, semanticObjectType) {
    if (semanticObjectType == "RDFa") {
      return "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=%22" + semanticObject.inchi + "%22[InChI]";
    }
  }
};

SemanticActions.add("pubchem_inchi", pubchem_inchi);

You can reproduce this by installing Operator 0.8a in Firefox, saving the script to a file in your home directory, and reading it via the Operator “Options” dialog. Make sure to also set the Display Style in the General tab of the dialog to Data formats. Only then will the RDFa magic kick in.

Adding support for eMolecules, ChemSpider and whatever else we like is easy now. What I still need to explore (or ask Mike), is how I can trigger the Open With/Save As dialog of Firefox.

So, when we can show comments from blogosphere for journal articles, why can’t we do that for molecules too? Sure we can. Just needs some hacking. Right, and done that today. The scripts works for PubChem:

Works for any <a href> element with an URL to PubChem like http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=%22InChI=1/CH4/h1H4%22[InChI]. BTW, while the URL is not very readable, this might actually be a good way to hide InChIs , though I am sure Google will not index this InChI either.

And it also works for semantically marked up InChI’s (using either microformats or RDFa) :

You’ll notice here that it is friendly with my Sechemtic script to make links to Google and PubChem .

The tools to make this happen involves a new Greasemonkey script (based on Noels code), and a few patches to the Postgenomic.com software. The user script can be downloaded here. An entry on the Blue Obelisk userscript page will follow; check that page for more goodies.

sechemtic.js

Consider this (X)HTML:

<html xmlns="http://www.w3.org/1999/xhtml"
      xmlns:chem="http://www.blueobelisk.org/chemistryblogs/">

<head>
 <title>m1</title>
 <script type="text/javascript" src="sechemtic.js" />
</head>

<body onload="addGoogleAndPubChemLinks(1,1)">
  <h1>The Output</h1>
  <p>This article is about <span class="chem:compound">m1</span> 
  (SMILES:<span class="chem:smiles">CCCOC</span>).</p>

</body>

</html>

I think the above example shows the simple setup of the Sechemtic Web script (please forgive me my habit to use bad linguistic mashups ;). Just load the script in the HTML <head>, and add in the onload="addGoogleAndPubChemLinks(1,1)" attribute to the <body> element. With blogs these bits would be part of the template, and, therefore, need to be installed once. From then on, just use the semantic markup as explained earlier . Both the microformat and the RDFa method are supported. In case of the latter, I recommend to define the chem namespace in the template of webpages too, instead of in the <span> elements.

Currently, the Sechemtic Web script only has one functionality: to add links to PubChem and Google, with the addGoogleAndPubChemLinks(int, int) method. The first parameter determines (0 or 1) if links to Google should be made, and the second parameter does the same for links to PubChem.

Download

For now, the script can be downloaded here. It is licensed with the GPL version 2.0.

Microformats

Here’s the same example using microformats instead of RDFa:

<html>

<head>
 <title>m1</title>
 <script type="text/javascript" src="sechemtic.js" />
</head>

<body onload="addGoogleAndPubChemLinks(1,1)">
  <h1>The Output</h1>
  <p>This article is about <span class="compound">m1</span> 
  (SMILES:<span class="smiles">CCCOC</span>).</p>

</body>

</html>

This new version also supports chem:compound, for any chemical. For example:

• isopropyl alcohol

Remember that it only works for properly marked up content, as described in Including SMILES, CML and InChI in blogs . The HTML source code of the above example looks like (in RDFa):

<ul><li>
<span xmlns:chem="http://www.blueobelisk.org/chemistryblogs/"
      class="chem:compound">isopropyl alcohol</span>
</li></ul>

The current script only adds search links to PubChem and Google, but the possibilities are endless, and potentially very powerfull. Here are some future ideas.

A link to predict NMR spectra using NMRShiftDB.org:

Making a link to the NMRShiftDB.org website to predict ¹³C or ¹H NMR from a SMILES, and InChI likely too, is easy, if the website provides a URL to do this. (I will discuss this with Stefan.)

A popup window with the 3D structure in Jmol:

This would involve some more work, but this most certainly possible too, given that we actually have a website around which allows downloading 3D coordinates given a SMILES or InChI. While a simple approach would be to make a popup with Jmol that takes the URL to that 3D coordinate website, it could be extended using Ajax to query the 3D structure first, and depending on success, show Jmol or a message “Could not find 3D coordinates”.

Summarize molecular details hidden in CML:

This is likely the most exiting possibility. I blogged about CMLRSS many times now (check the AVI, the article, etc), and combining these two technologies will take the semantic, chemistry internet to the next level. CMLRSS describes how CML can be embedded in blog items (e.g. Blogging chemistry on blogspot.com ), but really works for any XHTML.

Consider this mockup: add CML content to your blog item, containing molecular properties, such as its NMR peaks, elemental analysis, etc. This will not show up in your blog item, so that the user is not bothered with implementation details. Now, a userscript will now about the CML content, as it has access to the whole content of the page. The visible text will mention the molecule for which CML contains experimental or other details. Using the <span class="chem:compound"/> technology shown above, it is possible to link that compound to this CML bit (details to follow in this blog in January 2007). The userscript will then on the fly create a popup for the compound name in the visible text to show those experimental details.

How about that? Comments and other ideas are more than welcome!

Server side scripts:

Greasemonkey allows users to decide which scripts to run on a website, and which not. If you, as blogger or XHTML editor, want to force a script like the above to be run, that should be possible too. Greasemonkey scripts are written in JavaScript, so including them on the server side should be possible too. I might explore this option soon too.

So, how does this relate to my blog of last week? Well, would it not be nice that if your blog uses the markup as suggested in that blog , that you automatically get links to PubChem and Google? That is now possible with a small GPL-ed Greasemonkey script called blogchemistry.user.js.

The Greasemonkey plugin requires Firefox to be installed. If ready, install the script by cli·cking this link earlier, and the Greasemonkey will ask you if you want to install the script. After, check the output for this RDFa markup content:

• a SMILES: CCO
• a CAS registry number: 50-00-0
• and an InChI: InChI=1/CH4/h1H4

It should look like the output for this blog item:

Note the superscript PubChem and Google links.