Last modified: 2012-07-26 15:20:47 UTC
I would like to request the addition of the two extensions in the directory Chemical (spec. ChemFunctions.php, SpecialChemicalsources.php and the additional language file ChemFunctions.i18n.php) to the wikipedia server (the files reside in http://svn.wikimedia.org/viewvc/mediawiki/trunk/extensions/Chemistry/). Could these extensions be applied in the test wikipedia, and later (if they behave correcly) on the wikipedia? The programme has been reviewed by Jimmy Collins, and he helped me to remove some errors in my programming. Why do we want this patch: Within the Wikiproject:Chemicals (and the higher Wikiproject:Chemistry) one of the issues has for long been the addition of external links to the pages about specific chemical substances. The extension SpecialChemicalsources adds a special page which loads a special-page like the special:booksources, but then for chemical identifiers. The extension in ChemFunctions adds the functionality of a tag for the chemical formulae (which are now a hassle to put into a document), and additionally links this to the special:Chemicalsources. The addition of the Specialpage should enable us to remove many (biased) external links, especially those to commercial suppliers. Installation: copy the three files to the extensions folder, and add lines to localsettings.php: require_once( "$IP/extensions/ChemFunctions.php" ); require_once( "$IP/extensions/SpecialChemicalsources.php" ); (removing these two lines should disable the functionality again). Thank you! Dirk Beetstra
Is there any user's guide for that extension? Or a demo installation?
A user's guide has been written on meta.wikipedia.org (http://meta.wikimedia.org/wiki/Chemistry), but that is still quite rudimentary. I do not have a demo-installation, can't open my computer for outside access. Still looking for a publically accessable wiki to test things on (I have a question posted in the en.wikipedia.org on the chemicals portal (http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemicals) to see if there is somewhere a wiki for that).
(In reply to comment #0) Hi. I did not review the complete code. I just fixed some PHP errors.
Demo of the extensions is running on http://chemistry.poolspares.com (thanks Nickj)
I would say it is very important that the template supports InChI too. I looked up the caffeine example on poolspares.com, but could not find the InChI for caffeine. Is there such support, or otherwise, would you be open to having such support? see: iupac.org/inchi/
Something else... I worked on some semantic markup for SMILES, CAS number etc [1]. Are you open for a patch for support for that? It basically works like this: <span class="chem:casnumber">50-00-00</span>, <span class="chem:inchi">InChI=1/...</span> and <span class="chem:smiles">CCCOC</span>. It is available as microformat and RDFa. I wrote a Greasemonkey script [2] which uses it, and I set up Chemical blogspace [3] that picks up the semantics too; The last focuses on blogs, but shows the acceptance. I also wrote a JavaScript for the server to use these semantics to automatically make links to PubChem, eMolecules and Google [4], similarly to the Greasemonkey script. 1.http://chem-bla-ics.blogspot.com/2006/12/including-smiles-cml-and-inchi-in.html 2.http://chem-bla-ics.blogspot.com/2006/12/chemistry-in-html-greasemonkey-again.html 3.http://wiki.cubic.uni-koeln.de/cb/ 4.http://chem-bla-ics.blogspot.com/2007/01/chemistry-in-html-javascript-from.html
I also think that this is an excellent proposed new feature. Regards, proclus http://www.gnu-darwin.org/
I completely agree on the relevance of external searches *and* interal explicit (more or less unique) molecule identifiers like InChI. Why? First, help to avoid the 'deep web' problem, so we need explicite 'unique' molecule identifiers on pages and links to external search pages. http://en.wikipedia.org/wiki/Deep_web Second, how to find a molecule I can draw, but I do not know the name? E.g. InChI=1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 In other words, we need substructure searches, not just cross-links for ID-numbers Joerg
I agree with the inclusion of SMILES code and and InChI for Wikipedia, especially since two recent papers have shown that the SMILES code can be used as a similarity indices showing comparable (or better) power than the widely used Tanimoto indices (Hirst etal 2007) and SMILES codes have been used to directly develop interpretable rules for chemical structure activity relationships (Karwath and DeRaedt 2006) Ronald Cook
What is the status of this request?
(In reply to comment #10) > What is the status of this request? > I imagine code review is needed.
Bug has been dead for the past 3 years. Extension has not been reviewed for deployment on Wikimedia sites and there is no apparent consensus for this extension to be enabled on enwiki. RESOLVED INVALID.
(In reply to comment #12) > Bug has been dead for the past 3 years. Extension has not been reviewed > for deployment on Wikimedia sites and there is no apparent consensus for this > extension to be enabled on enwiki. RESOLVED INVALID. Of those 3 reasons, only the last one is a reason to resolve a bug INVALID.
So WONTFIX instead then?
INVALID is fine I guess, I'm not trying to bikeshed. My main point was that we don't close bugs just for being 3 years old, and we don't close bugs just because the requisite review hasn't happened yet.
