Blogotrivia

Posted on May 6, 2007 by pm286

A few points for readers and contributors.

  • SPAM. I get a few hundred a day. Akismet does a superb job of precision/recall but occasionally a few genuines get false spam. If so, repots and mail me and I’ll see if I can find it
  • Puzzles. The answer to last year’s puzzle was ordinary sulfur,  S8. Everyone who has every come across it would recognise it. I have had only one reply to my current problem – the most incorrectly submitted molecule in publications – so I may not continue issuing puzzles.
  • Spellchecker occasionally goes wonky so forgive the typos
  • Please send in comments – without them I haven’t a clue what people think. I know I have readers – but they just lurk. If you are a bid timorous, mail me and I’ll post the comment anonymously.
Posted in Uncategorized | 6 Comments

Christoph CUBIC

Posted on May 6, 2007 by pm286

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Christoph writes:
Christoph Steinbeck: Move to Tuebingen
17:01 06/05/2007, Planet Blue Obelisk
After the shutdown of CUBIC, I’ve moved to Tuebingen to the Lehrstuhl of Andreas Zell as a guest lecturer.During the summer semester of 2007 I’m teaching the “Basics of Chemoinformatics”. In addition to that, the Zell group is a great place to learn something about evolutionary algorithms and machine learning. For the last years, this had been the research group where Joerg Wegener of JOELIB fame had been pursuing his PhD work.
This is great news Christoph. I have been very saddened by the shutdown of CUBIC – the five or so years there have done an enormous amount to catalyse and advance Open chemoinformatics. I had hesitated to blog about it in case I fouled up some political process. But I reiterate how important it has been. It’s worth pointing out how few chemoinformatics centres there are and especially how few that pick up on the explosion of Web 2.0. Yes, we have social computing, and yes you can do it from anywhere, but there needs to be some real-world glue. CDK doesn’t get built jsut by randomly distributed volunteers – it gets build by people who at leas don’t need to worry where their next day’s pay is coming from (I’ve been there and know what it feels like).
So does this allow you to continue things?
I note that several of the staff at Tuebingen including are called “Thomas Template”. Quite a coincidence 🙂
Posted in blueobelisk, chemistry | Leave a comment

"Open Access" and "low fat"

Posted on May 6, 2007 by pm286

In an earlier post Open Access and Fuzzy Access I challenged the position of “Molbank” as a collection of Open Molecules. The position is that Molbank is “Open Access” but copyrights the articles and imposes special conditions on their re-use – i.e. “not for commercial use with permission”. I have argued that this is not compliant with the BOAI declaration in that material is not reusable Openly.
There is confusion in that “Molbank” started out as “Molecules” and then split. IIRC Molecules was supported by a grant from the Soros foundation to develop Open Access publishing. Here I argue that botj Molecules and Molbank try to keep to the letter of some of the words in the declaration rather than the spirit. I shall repeat the material – allow readers (if there are actually any readers interested in Open Data) to make their own assessments – and invite discussion.
=== Molbank ===

  1. Dietrich Rordorf Says:
    May 5th, 2007 at 4:40 pm eThanks for the comments.Firstly, “MolBank” and “Molecules” have been separated since 2001, and are published as separate journals.Secondly, the copyright notice for MDPI journals has been “(c) 200x by MDPI (http://www.mdpi.org/). Reproduction is permitted for noncommercial purposes.” since 2000, excepted for the MolBank journal. Actually we forgot to change the copyright statement for this journal, and it is only changed this year (see http://www.mdpi.org/molbank/molbank2007/m522.htm for an example).
    Thirdly, regarding BOAI, the statement says “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.” “Should” is not the same as “must”. Therefore, we believe to adhere to the BOAI.
  2. Dietrich Rordorf Says:
    May 5th, 2007 at 4:45 pm eIn reply to Jean-Claude Bradley:You may read the “Instructions for Authors” of the MolBank journal at http://www.mdpi.org/molbank/publguid.htm:“Copyright of published papers: We will typically insert the following note at the end of the paper: © 200… by MDPI (http://www.mdpi.org). Reproduction is permitted for noncommercial purposes. For ALTERNATE ARRANGEMENTS concerning copyright, please CONTACT THE PUBLISHER.”

=== PMR ===
“Should” is not the same as “must”. Therefore, we believe to adhere to the BOAI.
These are weasel words. (Yes, there is a distinction between SHOULD, MUST and MAY in computer science, but here it is very clear that SHOULD does not mean OPTIONAL). This is of that same standard as the food industry claiming that it is “low fat” because it has persuaded the governments that anything not 100% fat is low fat. Here “Open Access” is being used to sell journals which in fact have a high degree of closedness to them.
(I have suggested several times that the words “Open Access” should be qualified in a more rigorous manner than Green and Gold which confuse people I suggest something like Creative commons:
OA – copyright author; all re-use permitted;
as opposed to the weaker:
OA: copyright publisher; visible on publishers website when they feel like it; mountable on personal website; commercial re-use at whim of publisher.
Personally I do not regard the latter as OA. Unfortunately for me many members of the Open Access movement do.
=== Molecules ===
Molecules says:

Open Access: free for readers, with low publishing fees paid by authors or their institutions.
I quote from this completely (the statement is, of course copyright MDPI but I am claiming fair use):

Open Access (free subscription for readers) Advantages

  • Much higher citation impact: Open Access papers are much more frequently cited [1]. They have higher publicity because they are free to read and the full text is searchable on the Internet and they are more quickly and easily added into many indexing databases.
  • Much less costly: Open Access publishing is supported by authors and their institutes and is much less costly. Open Access publication fees we collect are only 800 CHF (approximately 500 EUR) per paper (compare to much higher fees of other nonprofit publishing organization such as PLoS [2,3] or to Springer’s Open Access publishing fees of 3000 USD [4,5]) regardless of the length of the paper, because we wish to encourage publication of long papers with complete results and full experimental or computational details [6]. The instructions for transfer of donated funds are at the http://www.mdpi.org/transfer.htm website.
  • Open Access papers are typically published online more rapidly [7].
  • Waiver of publication fees: In order to encourage publication of high quality papers, we will continue to waive publication fees with Open Access for those papers of high quality recommended by referees or editors and for papers from those who have published high impact factor papers in our journals [8].
Links and Notes
  1. Open Access citation impact advantage: http://en.wikipedia.org/wiki/Open_access#Authors_and_researchers. For example, a very ordinary research paper “Molecules 1998, 3, 100-106” has been cited 49 times, the highest number of citation among all the papers published up to 2006 by the same author.
  2. According to a recent report (Rovner, S. Evolving Access. Chem. Eng. News 3 July 2006, 84 (27), 8) the nonprofit Open Access publishing organization PLoS has just increased its author fees from $1500 USD per article to 2000−2500 USD to better reflect the cost of publication, in addition to other revenue (grants, institutional memberships, and advertisement).
  3. MDPI also plans to increase the amount of Open Access publishing fees to an adequate level in 1 April 2007.
  4. See: http://www.springeronline.com/openchoice
  5. The traditional subscription-based publishing are even more expensive. The scientific journal subscription has a standard price of 1 USD per page (see the subscription price for journals published by Elsevier or Springer). For example, if a journal has a worldwide circulation of 5000 copies, for a article of 10 pages, the other parties (readers, libraries, etc.) pay the publishing company 50000 USD. That is why a single journal e.g., Tetrahedron or Tetrahedron Letters of Elsevier, can bring tens of millions of USD revenue for the publishing house. Elsevier and Springer both started to provide author paid immediate Open Access and the cost of 3000 USD per paper has been charged to authors [2]. This amount looks very high, yet this Open Access service should be encouraged because Open Access publishing is much less costly for other parties to pay the publishing service.
  6. Recently a research paper of 23 pages has been published: http://www.mdpi.org/molecules/papers/11110867.pdf.
  7. Well written papers have been peer reviewed and published in less than two weeks from manuscript submission, see the example: http://www.mdpi.org/molecules/papers/11040212.pdf.
  8. The choice of Non-Open Access (Editorial: “Open Access and Author’s Open Choice“) or Delayed Open Access publishing (Editorial: “Delayed Open Access or Permanent Non-Open Access“) is not recommended since September 2006 as we decided to make all MDPI journals fully Open Access again.
Dr. Shu-Kun Lin
Publisher of MDPI journals

Last change: 6 March 2007, Webmaster: lin@mdpi.org
© 2007 by Molecular Diversity Preservation International (MDPI), Basel, Switzerland

They have also completely confused the issue in that many of the papers they have published are not Open Access at all, see their CDROM stuff.

The fees 80 CHF* per paper can be easily paid afterwards by credit card through Paypal or directly through Paypal. Note: 5% of the bank fees should be added. For example, you need to send 84 CHF (80 + 80×5%) so that MDPI can receive 80 CHF.

Personaly I do not find paying 80CHF for a 1-2 page paper “easy”. Nor do I have any confidence in the guardianship of the scholarly record. (But most of my readers don’t seem to care about that…)
So the message is clear. The publishers are running rings round us with clever marketing campaigns. Springer et al are far worse. How many of you have seen a Springer Open Choice paper in chemistry? Or for that matter any other subject? What percentage of papers are published in this way? It allows publishers to say

“we are an Open Access publisher. We have Open Access journals. We are trying get authors to publish Open Access. But it’s very hard – they don’t seem to be interested”.

I know the publishers read this blog. I wonder if any of the “low fat Open Access” publishers can convince us that it’s anything more than a marketing gimmick.
My main concern is that Open Data doesn’t become “low fat”. For data there are no weasel words – no halfway houses – no “Open Choice Data”. For data it is very simple. It belongs to the scientific commons, not the publishers.
Do you care enough to do something about it?

Posted in chemistry, open issues | 4 Comments

Open Data At WWW 2007

Posted on May 6, 2007 by pm286

polemic level AMBER
I am in Canada – can get internet but have some difficulty in sending email.
This post is quite a good way of letting everyone in the world know where I am…
I shall be talking on a panel here about Open Data. It is a very serious potential problem – I have blogged about it before. If you don’t do something about it you will wake up one morning and find that the publishers own your data as well as your free text. And that when you are reviewed for tenure, research assessment, etc.; and when this assessment also includes your data sources then you will be required to deposit your data in closed data repositories and choose those with the highest “impact factor”. Then the publishers will start to have control of the scientific process and will move on to the next phase.
But – it seems – few people are particularly worried about this. The sessions where I am talking about Open Data have a wide variety of motives – maps, personal data and science will come low on the agenda unitl scientists, librarians and provosts speak out.

Posted in data, open issues, www2007 | 2 Comments

Curating data on ChemSpider…should it be supported by the community?

Posted on May 5, 2007 by pm286
I’m replying to a reference from Chemspider to my blog. It’s titled:

Curating data on ChemSpider…should it be supported by the community?

Posted by: Antony Williams in Quality and Content
I extract some of the material below, but the simple answer is –
only if the community has time on its hands and wants to donate significant goods to commercial organisation(s) who will then own and control the content.
(People already do this, of course – they are called scientists and as authors they donate their goods to commercial publishers. )
Put simply Chemspider is Web 1.0; The chemical blogosphere, Pubchem, Blue Obelisk, CrystalEye is Web 2.0.Chemspider’s business model was fine for the early web. No public content, significant effort to extract it, few alternative sites. Chemspider looks extremely similar to Chemfinder which started about 2000 (I can’t remember when). It’s model was similar – aggregate compound supplier information, add some searchable properties, encourage the community to contribute, offer unlimited free access. Then, for whatever business reason it stopped giving free access.I see very little difference between Chemfinder and Chemspider. They are both closed, proprietary, do not expose data, or metadata, or algorithms; have closed code, do not allow downloads or re-use. They lose metadata in their aggregation process. I have nothing personal against Chemspider (or, if they are associated, ACDLabs) – I just think the Web 1.0 model is out of date for chemistry.
99% of Chemspider’s data appears to come from Pubchem. If so, surely it is better to curate Pubchem directly. There are mechanisms for this and as Pubchem is effectively the normalised source it gives less problems for maintenance. And if any site is creating a more acceptable name-structure linkage, then this is better done by a standoff markup rather than aggregate-and-possess. Web 1.0 denormalises and confuses data; Web 2.0 looks to normalise and mashup. Egon has shown how Pubchem can be annotated with standoff community involvement – surely a more scalable model.
Selected from the Chemspider blog:

ChemSpider has been online since March 24th 2007, about 6 weeks. We opened the ability to curate the data one month later.
Is there a need to curate the data? ChemSpider is built up of a series of databases. The list of contributors continues to increase
and there will be some very exciting announcements made in the next few days about new contributors.
…
One of the largest components is the PubChem database. Peter Murray-Rust recently blogged about the quality of the name-structure pairs inside the PubChem database. He used as an example methane… I point you to the original blog for his comments. For my purposes I will use water. Here is the list of names, synonyms and registry numbers posted for Water at PubChem. Certainly a number of these have carried over to ChemSpider. Out of interest it is worth comparing the results of the searches for the word “water” at both PubChem and ChemSpider. Search Pubchem for water title=”Water on PubChem”>here and ChemSpider for water title=”Water on ChemSPider”>here. 228 hits versus 1. Looking at ChemSpider we get the following list of names, synonyms and registry numbers. The hyperlinks below are those links to wikipedia.
“water; Water vapor; Dihydrogen oxide; Distilled water; Purified water; Water, purified; hydrogen oxide; Deionized water; Oxygen atom; dihydridooxygen; ether; ethers; hydroxide; oxidane; Monooxygen;
[… other (wrong) synonyms deleted]
NOT what I would call a quality set of names. These will be curated, some will be done with appropriate robots and some manually.
This is an extreme. Let’s look at other examples already identified by curators. Below is an example of curation in process.
Some examples of curated data
Returning to Peter’s blog…an excerpt states “Pubchem faithfully reflects the broken nature of chemical infomation. It cannot mend
it – there are only ca. 20 people – and anyway the commercial chemical information world prefers to work with a broken system. But
could social computing change it? Like Wikipedia has? [..] I think chemistry is different. And I think we could do it almost effortlessly
– rather like the Internet Movie Database. Here every participant can vote for popularity or tomatos. A greasemonkey-like system could allow us to flag “unuseful names” or to vote for the preferred names and structures. And this doesn’t have to be done on PubChem – it could be a standoff site [..].” I happen to agree. I believe social computing can change it. That is the purpose of the curating process on ChemSpider. When we set up the system we were not sure that people would care or help in curating the data. Why? Here’s why people might NOT want to help us curate the data:

  1. ChemSpider is not PubChem. The data cannot be downloaded.
  2. ChemSpider is a business…why should people help a business increase the quality of the data they host?
  3. ChemSpider is new. Who says that the efforts made to curate data will be of value to others? How long will ChemSpider be around to allow peoples work to benefit others?

All valid questions. And they likely ARE deterrents to people helping improve the quality of data on ChemSpider. So, what are the
answers to these questions.. are they enough to convince ChemSpider users to assist in curating the database? Our responses to the
questions above are as follows:

  1. We do not have permission from all depositors to ChemSpider to allow their data to be downloaded, only viewed. However, we WILL redeposit all curated data originally sourced from PubChem back to PubChem. In an email exchange this past week with Steve Bryant from PubChem commented that they would willingly accept curated data back to their database. We will also make available a downloadable database of all curated data originally sourced from public sources. We will also provide feedback to other depositors when we find errors.
  2. I have done my utmost to explain this in a previous post here.
  3. ChemSpider has traction. It is getting lots of use. Based on interest we believe that our initial efforts have already provided enough response to have us continue this work. We have challenges as discussed previously but we are busily addressing these now. We believe that every effort made to improve the quality of data on the ChemSpider database will benefit all users and the community in general with our giveaway to PubChem and other database providers of the curated data.

I have outlined only a small number of possible concerns above. There may be more. I welcome any other questions you may have about our intentions.

I interpret this to mean that Chemspider is curating a name-structure map. Fine. They are doing it with robots and humans. I can see how to use both – I have no idea what the percentage recall and precision is. They will own the results and the results will not be made Openly available but served through their gateway. You are invited to contribute.
The Web 2.0 community will use a different mechanism.
Posted in chemistry | 4 Comments

Open Access and Fuzzy Access

Posted on May 5, 2007 by pm286

In reply to my request for lists of Open Molecules

  • Dietrich Rordorf Says:
    May 4th, 2007 at 10:52 am eHave a look at MolBank: http://www.mdpi.org/molbank/
    Molbank (ISSN 1422-8599, CODEN: MOLBAI) is fully open-access and publishes one-compound-per-paper short notes and communications on synthetic compounds and natural products. A MDL Mol file is available for each compound. The journal is fully HTML and downloadable with WGET over http.
    Dietrich

This is a useful start. Yes, there is a MOL file for each compound. And the MOL file format is so primitive that there is no space to add a copyright notice, so we can reasonably regard this as factual data and therefore Open.
However the journal, which describes itself as Open Access includes the statement on each paper:

© 2006 MDPI. All rights reserved.

This is incompatible with the BOAI declaration of Open Access, which states:

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.

The fact that Molecules has required the author to transfer copyright to the journal makes it incompatible with the declaration. I queried this more than once with the editor of Molecules but did not receive a reply. Perhaps Dietrich can help?
On a more technical note. It is actually not easy to download all the molecules from Molecules. AFAICS you have to write a spider which traverses the idiosyncratic HTML for the TOC and then scrape every mol file in every paper. This is a limitation of many sites which think that humans are the only readers than matter.
If Molecules provide:

  • an index of the molecules
  • an agreement that we can download every paper and scrape chemistry from it
  • and reuse the results

then I shall be delighted and I shall publicly praise their endeavour.

Posted in open issues | 5 Comments

Chemical phraseology

Posted on May 3, 2007 by pm286

From the ChemBlog…

Writing the intro for papers is silly

May 03rd 2007 Posted to Sciency politics
I’m starting to write my second paper for JOC, fresh off the heals of my recent JACs submission* (fingers crossed) and I’ve sort of grown tired of the formulaic way the introduction of papers are written. I can basically boil it down with the Mad Lib here, so you can write your own paper in the future:The obligatory first sentences (Pick two, mix with proper punctuation to create an opening statement):
  1. (insert the germane specialty) has become of considerable interest recently.
  2. Efforts to develop an effective (means/method to do something) have emerged recently but currently there exists very few instances in the literature which (insert limitations they have that your novel crap doesn’t have)
  3. The (your family of chemical compound or compound class) has become the focus of research efforts based upon emerging applications in (list at least 3 things. I.E. nanofilms, antitumor agents, biowarefare detection shit)
  4. (Some chemical transformation which the world needs) has been challenging and often requires (list of awful conditions culled from carefully chosen literature).
  5. Here we present a method to (your method) using (some awesome feature, I.E. greater yields, higher e.e., lower temperatures, without the use of explosive peroxides/azides, autofellatio)

Now that the beginning is done, the rest of the article almost writes itself and you can fill it with data and facts and pictures.
Here is an example of a filled out Mad Lib using the above methods I made:
Crapping out awful introductions for papers has become of considerable interest recently. Efforts to develop an effective means to open a paper have emerged recently but currently there exists very few instances in the literature which don’t make me want to shoot myself in the face. Here we present a method to mock the fuck out of people that use these cliche openers using only a withered sarcastic spirit and little prospect for trying to write my JOC article anymore today.

I agree completely – and thanks to ChemBlog for raising this.
However it has one unexpected benefit – it makes it easier for machines to read it. So in our Sciborg project (see Peter Corbett’s blog) we are analysing chemical language for these types of phrases. We then use them to work out the motivation for writing the paper. For example:
“In previous work we have shown that foobarium iodide provides a facile and novel method of oxidising aldehydes[1], ketones[2], alkanes[3]. Now we show that it oxidises cycloakanes…”
is an immediate pointer to the machine that unless its owner is passionate about foobarium iodide (or is dependent on the goodwill of the authors for their next grant) it can inform the human reader that the paper is boring and can be skipped. There are many other stock phrases conveying motivation.
Even worse are the recipes and the stilted language:
“To 3 g of (1) dissolved in toluene were added 2 g of (2)”.
This is equivalent to “to my dog was given a bone by me” instead of “I gave my dog a bone”. Even better would be to encode it in CMLReact so the machine could read it and work out the quantities, mole fractions, etc. It’s easy to do – so let’s start doing it. It would make it much easier to check all those yields in the literature.
But first we’re liberating crystallography
Then spectra
Then reactions
BTW Many chemical syntheses are primarily competitive sporting events so the real motivation should read:
“we chose something to synthesise that was harder than previous work and put an army of grad students onto it” .
Posted in chemistry | 2 Comments

ICD-10 – past and present

Posted on May 3, 2007 by pm286

I am really excited and pleased by Peter Suber’s latest post. WHO converts a disease database to a wiki.
WHO adopts Wikipedia approach for key update, CBC News, May 2, 2007. Excerpt:

If the collaborative wiki process works for compiling an encyclopedia, couldn’t the same approach work for classifying all the diseases and injuries that afflict humankind? The World Health Organization thinks it can.
It is embarking on one of its periodic updates of a system of medical coding called the International Classification of Diseases, or ICD, and it wants the world’s help doing it.
While work on previous versions has been the domain of hand-picked experts, this time the Geneva-based global health agency is throwing open its portal to anyone who wants to weigh in on the revision….
The new, more open approach to updating the disease classifications won’t be entirely wiki-esque. That process, with its anyone-can-edit approach, builds a degree of vulnerability into the end product, with some contributors deliberately planting false information for the fun of it.
With the ICD, people can propose changes and argue for them on a WHO-sponsored blog. But groups of subject matter experts will weigh and synthesize the suggestions, said [Robert Jakob, the WHO medical officer responsible for the ICD]….

OK, the WHO is a good thing and I’m very keen on Open collaborative science and medicine but there is a special aspect. For several years I worked on ICD-10 to convert it to XML – before most people had ever heard of it. ICD-10 has thousands of diseases in a hierarchical classification and a code for each. Nowadays it would pprobably be called an ontology.
Lesley West and I created a DTD to hold the ICD-10 and other dictionaries – we called our approach the “Virtual Hyperglossary”. We created a company to produce information products for the pharmaceutical industry and the regulatory process in which ICD-10 and other terminologies were important.
How naive our efforts look now! We used a DTD rather than a schema. We didn’t have language processing tools to make the translation of the scanned material better structured.We used ISO-12620 as the basis – and I spent time on the ISO meetings. Pace was often slow. But at the time it was ahead of its time.
Most things in the brave new world don’t make it – the VHG was one such. There are lots of others. I’ve moved a long way since then. But some of what we are doing now will make it and change the face of scholarship. We have only just started.

Posted in XML | Leave a comment

Turning a PDF into a cow

Posted on May 3, 2007 by pm286

cimg1171_s.JPG
I have frequently quoted the maxim that turning PDF into XML is like turning a hamburger into a cow. But here is a printed PDF turned into a cow (in Denver airport). It’s called “Rhapsody in Moo” – you can guess what is the content of the PDF. (I have no idea whether I have broken copyright in posting this, but I’ll take the chance)

Posted in Uncategorized | Leave a comment

Tagging molecules

Posted on May 3, 2007 by pm286

Another of last night’s ideas that I have been beaten to – that’s the power of the blogosphere! Nick Day and I are trying to find a social mechanism for commenting on data – specifically his CrystalEye collection of 60 000 crystal structures. And can we do this without writing any software. So I’ll first propose my idea, then comment on Egon’s.
The problem is to annotate molecules on someone else’s site. We don’t care about being Open – in fact we want everything to be public. So my model is to use a public tagging system like del.icio.us – the only barrier is that to use it you have to register with del.icio.us. But most young people have already done that months ago. So when you find a molecule in Nick’s knowledge base that you want to comment on you simply tag its HTML page. It’s probably useful to have a small tag vocabulary like “serious error”, “wrong space group” and then comment in free text. The comments would accumulate on del.icio.us pages and Nick’s robot could scrape them from time to time and add them to the relevant entries.
In practice I would like to use Connotea as it’s been developed specifically for scientists, because it’s Open Source and most importantly we have had a great collaboration with the folks at Nature Publishing Group (New technologies). I don’t know whether Connotea has been used for data tagging – if not we might have ideas that we’d like to see incorporated. I’m sure Timo, Ben, Tony will pick up this post!
The only downside is that we have to scrape the Connotea site at regular intervals.
Egon has a different model…

Cb comments for InChI’s

About a year ago Pedro wrote a Greasemonkey script to add comments from PostGenomic.com to table of contents of scientific journals. Noel extended it with support for Chemical blogspace (see also this earlier item). Now, the later website is maintained by me, and I extended the aggregator software with molecule support, for example to show hot molecules on the frontpage (at some point my patches will be backported into mainstream. Euan, why not invite me to London HQ in, say, June?).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 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 InChI‘s, 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):

The downside of this is that users have to install the greasemonkey to use this, but that’s not too much of a problem since I predict that soon Blue Obelisk Greasemonkey will be widely distributed. The data have to be accumulated somewhere, and that requires maintenance. The Greasemonkey group have already done that – at Koeln, I think.
Perhaps they could be combined? The greasemonkey could save the comments at Connotea. That’s an almost maintenance-free system. It would also start to create an implicit mashup – data from different sources would be linked through the Connotea site.

Posted in chemistry, semanticWeb | 3 Comments