Following on from my post regarding copy-paste of “structure-based” blog entries Joerg Wegner has asked some very good questions.

First of all my thanks to him for enhancing what I copied and pasted. He linked to some Wikipedia articles and to some ChemSpider compounds. He is likely familiar with the user of the Wikipedia editor since no manual exists yet for the editor we implemented but he did just fine using it.

Joerg then asked a couple of questions:

1) Is there a version history, or what happens, if someone is messing-up or spamming a certain entry?
2) Can I put pages on my watchlist seeing when others change them?

The answers are as follows:
1) Yes, there is a version history. At present we can revert to the previous version (but for now it is a manual operation for us..but will not be shortly..work is underway). The version history is presently visible to the curators only as we finish the development of this work. However, the screenshot below shows we know who you are …if someone spams us..and they have done…we issue a warning and ask them to cease and desist and if they don’t we cut off them ability to curate. (Click on the thumbnail to see.


2) There is no record view watcher in place yet but it is of course on our list. We are more keen to do this when we get more people adopting molecules and taking care of them etc. See this previous blog post if you wish to adopt a molecule…by adopt we mean tend to and nurture – keep it updated with new articles, interesting info etc. I have three of my own.

Joerg also asked “Finally, is Paul’s blog now sub-structure searchable? Well, it links back via ChemSpider, but how does Paul now link to ChemSpider? Only via the comments? If there would be a version history, and he would have added this entry, then people could see it in his ChemSpider profile, like they can for Wikipedia edits.”

It is not possible to search Paul’s blog by substructure directly at totallysynthetic.com. Paul used to mark up his articles with InChIs but I think the process was problematic so he’s stopped. What would be excellent is to work with paul to have him submit all of his structures as CDX files, or an SDF file, with his URL and Blog Post title to us as a deposition. We would then be able to deposit all of his molecules onto ChemSpider if they don’t exist and make the link to his blogpost automatically. We could then setup totallysynthetic.chemspider.com and as his collection grows people would be able to search all of his blogposts (all structures, not just the title structure). We could of course turn ChemSpider into a “structure-based blogging environment for chemists” by adding the ability to add comments (oh..we did that already). Hmmm…let me think about this..for Paul’s basic style of “structure centric blogging” we already have the ability to host his structures, deposit and link all structures in his articles back to the central blog post, that blog post could be hosted on ChemSpider and people could comment on it. Probably we would need to lock down the initial blog post so that other people could not change it but already we see the value of other people editing it so should we?

Would anybody like to host a structure centric blog on ChemSpider? Let us know and we’ll help you. We already put links to Molecule of the Day hosted over on ScienceBlogs and have motd.chemspider.com

Back to Joerg’s questions…
“Well, it links back via ChemSpider, but how does Paul now link to ChemSpider? Only via the comments?
If there would be a version history, and he would have added this entry, then people could see it in his ChemSpider profile, like they can for Wikipedia edits.”
Paul doesn’t link to ChemSpider to the best of my knowledge. Would be good if he did. Paul could embed links directly to ChemSpider in his article but would need to search for the matching molecules etc. If he worked with us to set up the deposition process then we could return a list of ChemSpider IDs and he could simply publish them.
Yes to the suggestion regarding having his postings in his ChemSpider profile. All in the plan but not there yet.

Stumble it!

2 Responses to “Rich Text Formatting and Substructure Searchable Blogs”

  1. Joerg Kurt Wegenr says:

    Two more comments on this
    1. I think InChIKey’s are ways better than InChI itself, because the special characters and non-word or non-sentence like lookalike.
    See Rich’s post on this
    http://depth-first.com/articles/2007/03/05/why-the-web-isnt-ready-for-chemistry

    2. For a chemical aware blog, I would refer to Egon’s concept used on the chemical blogspace aggregation as well.
    http://chem-bla-ics.blogspot.com/2006/12/including-smiles-cml-and-inchi-in.html
    This is basically just checking blog feeds for the RDF entries and puts them as molecules into the aggregation system. See it here in action (being more exact post-processing action)
    http://cb.openmolecules.net/inchis.php

    In other words, beside the active hosting of content, I highly appreciate, the blog content of blogs could get indexed fairly easy, if bloggers would follow some rules.

    @Egon, Rich, Noel: Any more comments on this?

  2. Joerg Kurt Wegenr says:

    Thanks for the flowers, but rich text editing is like any other office tool, means very easy to use. And the versioning on the entries is marvellous news, especially when facing silly spammers entering additional viagra links, suspicious company links, or a few (almost invisible) xxx words into long texts.

    And for the Tekki’s reading this, it is really ‘rich’ text editing with a lot of extra parameters for people getting fancy about formatting and layout.

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