Last modified: 2012-07-26 15:20:47 UTC

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Bug 7514 - Review (and install?) Extension:Chemistry on en.wikipedia
Review (and install?) Extension:Chemistry on en.wikipedia
Status: RESOLVED INVALID
Product: Wikimedia
Classification: Unclassified
Extension setup (Other open bugs)
unspecified
All All
: Low enhancement with 8 votes (vote)
: ---
Assigned To: Nobody - You can work on this!
http://meta.wikimedia.org/wiki/Chemistry
:
Depends on:
Blocks: 17598
  Show dependency treegraph
 
Reported: 2006-10-07 17:37 UTC by Dirk Beetstra
Modified: 2012-07-26 15:20 UTC (History)
6 users (show)

See Also:
Web browser: ---
Mobile Platform: ---
Assignee Huggle Beta Tester: ---


Attachments

Description Dirk Beetstra 2006-10-07 17:37:44 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
Comment 1 JeLuF 2006-10-09 17:17:45 UTC
Is there any user's guide for that extension?
Or a demo installation?
Comment 2 Dirk Beetstra 2006-10-09 17:24:46 UTC
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).
Comment 3 Jimmy Collins 2006-10-10 18:39:21 UTC
(In reply to comment #0)
Hi. I did not review the complete code. I just fixed some PHP errors.

Comment 4 Dirk Beetstra 2006-10-26 14:55:03 UTC
Demo of the extensions is running on http://chemistry.poolspares.com (thanks Nickj)
Comment 5 Egon Willighagen 2007-01-31 08:26:34 UTC
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/
Comment 6 Egon Willighagen 2007-01-31 08:40:58 UTC
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
Comment 7 proclus realm 2007-01-31 14:42:31 UTC
I also think that this is an excellent proposed new feature.

Regards,
proclus
http://www.gnu-darwin.org/
Comment 8 Joerg Kurt Wegner 2007-01-31 20:28:32 UTC
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
Comment 9 Ronald Cook 2007-01-31 21:26:43 UTC
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
Comment 10 Joerg Kurt Wegner 2007-08-07 23:03:36 UTC
What is the status of this request?
Comment 11 Mike.lifeguard 2009-02-21 16:04:25 UTC
(In reply to comment #10)
> What is the status of this request?
> 

I imagine code review is needed.
Comment 12 Alex Monk 2012-07-26 01:27:53 UTC
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.
Comment 13 Chad H. 2012-07-26 14:54:24 UTC
(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.
Comment 14 Alex Monk 2012-07-26 14:58:31 UTC
So WONTFIX instead then?
Comment 15 Chad H. 2012-07-26 15:20:47 UTC
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.

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