Wikipedia:WikiProject Chemistry/IRC discussions/12 Feb 2008
From Wikipedia, the free encyclopedia
--- Log opened Tue Feb 12 10:35:19 EST 2008
10:38 -!- itub [n=tubert@lalo.chemie.unibas.ch] has joined #wikichem
10:38 -!- mode/#wikichem [+v itub] by ChanServ
11:02 -!- walkerma [n=chatzill@admin-151-108.potsdam.edu] has joined #wikichem
11:02 -!- Rifleman_82 [n=blahblah@wikipedia/Rifleman-82] has joined #wikichem
11:02 -!- mode/#wikichem [+v Rifleman_82] by ChanServ
11:02 <+Rifleman_82> hi all
11:02 <+Rifleman_82> sorry i'm late, just got home!
11:02 <+Rifleman_82> have you guys started?
11:02 <walkerma> Hello! You're not late
11:03 <+Rifleman_82> sorry about last week....
11:03 <+Rifleman_82> was out buying new year flowers... nurseries open 24 hours!
11:04 <+itub> hi
11:04 <walkerma> I was hoping PC would be here- I just emailed him
11:04 <walkerma> The agenda he suggested last week was: Choice and indexing of identifiers
11:05 <walkerma> Can we talk about this anyway? I think it's a fairly general topic that we need to keep working on.
11:06 <+Rifleman_82> sure
11:06 <walkerma> Or is there something you guys were talking about before I got here?
11:06 <+itub> nope
11:06 <walkerma> That needs finishing off?
11:07 <walkerma> OK: The first on PCs list was:
11:07 <walkerma> Which identifiers (InChI, CAS, etc) are the most important for us (already discussed to some extent)?
11:08 <walkerma> I would put that as: Which should we try and have in all Chemboxes?
11:08 <walkerma> And which should be optional?
11:08 <+itub> inchi and smiles should definitely be optional
11:08 <walkerma> And which should be hidden, and which should be in view?
11:08 <+itub> some compounds don't have a structure that can be handled by them
11:09 <+itub> inorganics and such
11:10 <walkerma> Yes, definitely, though I think IUPAC is working on that
11:10 <walkerma> I think we should make them required fields for organics, but perhaps hide them
11:11 <+Rifleman_82> i would disagree with hiding any fields
11:12 <+Rifleman_82> if the field exists it should be shown
11:12 <+Rifleman_82> if it's too cumbersome, we should move it to the data page
11:12 <+Rifleman_82> but whether something should be in the main chembox or on the data page, we should decide on
11:12 <+Rifleman_82> might be arbitrary, but we should be consistent
11:13 <+Rifleman_82> if there's something that notable such that it should be in the chembox, instead of the data page against our across the board consensus, it should be discussed in-text
11:14 <+Rifleman_82> what do you guys think?
11:14 <walkerma> The reason for hiding is not the issue of notability, it's the issue of (a) size and (b) use
11:14 <+Beetstra> Well, some things don't show nicely .. but need to be in the main-page, otherwise it does not get google-indexed
11:15 <+Beetstra> (a.o.)
11:15 <+Rifleman_82> a.o. ?
11:15 <walkerma> Beetstra: Right!
11:15 <walkerma> http://en.wikipedia.org/w/index.php?title=Quassin&oldid=188784759
11:15 <+Beetstra> amongst other things ..
11:15 <+Rifleman_82> ah thenotorious quassin
11:15 <+Beetstra> (google, yahoo, alexa, ..., name them)
11:16 <+Rifleman_82> the problem with hidden fields is that it is hidden to potential contributors -
11:16 <+Beetstra> There is a nice dilemma there, indeed
11:16 <+Beetstra> And I don't know if something can be made invisible, while it is still there in the html-output of the wikipage
11:16 <walkerma> If we limit hidden fields to being ONLY machine-readable ones, it's not a problem because
11:17 <+Rifleman_82> cut and pasting? i do it quite a bit
11:17 <+Rifleman_82> for searches
11:17 <walkerma> These can be generated by a machine - so passing contributors only need supply another form of input
11:17 <walkerma> Such as a structure or IUPAC name?
11:18 <+Rifleman_82> iupac name can be generated by machine too
11:18 -!- PC62|away is now known as Physchim62
11:18 <+Rifleman_82> and if smiles/inchi is there already, the structure can be generated too
11:18 <+Physchim62> HI? SORRY i4M LQTE
11:18 <+Rifleman_82> (circular problem?)
11:18 <+Rifleman_82> hi pc
11:18 <+Rifleman_82> we just started
11:19 * Beetstra hands Physchim62 an 'A' ..
11:19 <+Beetstra> (or two)
11:19 <walkerma> Hi, we're just discussing "To hide or not to hide"
11:19 <walkerma> Rifleman82: Harder to make a NICE structure from InChI/SMILES
11:20 <+Rifleman_82> surprisingly, it works well enough on chemsketch most of the time
11:20 <walkerma> Yes, ChemSketch is not too bad
11:20 <+Rifleman_82> as in, i copy smiles from pubchem into chemsketch and generate the structure to generate the image to uplaod
11:20 <+Rifleman_82> (jmol will solve the problem? :) )
11:21 <walkerma> As a reminder, the feedback from the listserve makes very good reading on this topic:
11:21 <walkerma> http://en.wikipedia.org/wiki/User:Walkerma/Sandbox5
11:21 <+Rifleman_82> pc sending you log of today
11:21 -!- mode/#wikichem [+o Rifleman_82] by ChanServ
11:22 -!- mode/#wikichem [+v walkerma] by Rifleman_82
11:22 -!- Rifleman_82 changed the topic of #wikichem to: *Next channel meeting: 19 Feb 2008; 1600h UTC* Welcome to the Wikipedia Chemistry IRC channel. Queries to User:Rifleman_82 or User:Beetstra.
11:22 <+Physchim62> Thnaks I've jusr read through my screen base
11:22 -!- mode/#wikichem [-o Rifleman_82] by Rifleman_82
11:22 <+Rifleman_82> oops forgot :)
11:22 <+Physchim62> no probs.
11:23 <+walkerma> Here is an interesting response to the question, Do you ever copy/paste such identifiers FROM Wikipedia into Google, etc, in order to do a search?
11:23 <+Rifleman_82> martin i promised to check on making text wrap arbitrarily, such as every 25 chars. tried and searched and i can't figure it out. sorry about that
11:23 <+walkerma> "This could be very useful, too. It doesn't matter if it's visible or not, a link "copy SMILES" would be enough. Thanks for asking."
11:23 <+Physchim62> Beetstra, "hidden" content still appears in HTML output (there is a lot that is hidden in HTML)
11:24 <+itub> the one I copy most often is CAS, to search in scifinder
11:24 <+Beetstra> Yes, it would be not too hard to do, actually
11:24 <+walkerma> Rifleman82: (Thanks, that's a shame it's so hard to do)
11:24 <+Rifleman_82> the possible solutions would require some developer support i think...
11:24 <+Rifleman_82> there are many other workarounds
11:24 <+Beetstra> But there are things that get lost if it does not get used .. I don't think shows up in the final html
11:24 <+Rifleman_82> but nothing easily usable
11:24 <+Rifleman_82> ') - diff - (-347)- summary: /* Side effects */
12:38 <+itub> the molar mass doesn't depend on the isomer, but it can vary if you consider related forms such as hydrochlorides (especially common for drug-like molecules)
12:38 <+Rifleman_82> we'll skip the .HCl for the moment?
12:38 <+itub> sure
12:39 <walkerma_> Rifleman82: Yes, that's next week
12:39 <+Rifleman_82> hazards, solubility - we can keep it in the main box; for most isomers they shouldn't differ too far from each other
12:39 <+Rifleman_82> where they are significantly different, discuss in text/
12:39 <+Physchim62> walkerma_, you are assuming that people want to use WP to go from InChI to structure. I'm sorry to be uncivil, but that is ridiculous. We cannot give them that, nor do we pretend to. However there are several freeware packages which will do such a conversion
12:40 <+itub> I just noticed that http://en.wikipedia.org/wiki/Tartaric_acid already has a table lising the CAS numbers and other identifiers for each isomer!
12:40 <+Physchim62> people want to use WP to go from name to another identifier, or possibly from structure to name
12:41 <walkerma_> Not if they found the page initially from a Google search
12:41 <walkerma_> of the InChI or InChIKey
12:41 <+Physchim62> you hypothesis is that they searched for an InChI and then found the WP page! so they already know the InChI they want, we do not have to inform them of it
12:42 <walkerma_> But they need to know which structure goes with which InChI
12:42 <walkerma_> Here are three responses to my survey:
12:42 <+Physchim62> if they want a structure from an InChI then sorry, MediaWiki is not the best software solution to do this relatively simple transformation
12:42 <walkerma_> # I search multiple internet sources (e.g. ChemSpider, Wikipedia, search engines, online catalogs, etc) using various chemical identifiers (common names, IUPAC names, CAS number, SMILES, INCHI, etc). Since I didn't see your original posting, I don't have the full context for your questions.
12:42 <walkerma_> # YES
12:43 <walkerma_> # Yes and I would use it more if I knew that I would come up with more useful data, including Wikipedia entries. I copy SMILES or InChI strings from Chemdraw and paste them in internet searches.
12:43 <+itub> yes, whenever there is an identifier, it has to be clear what it means
12:43 <+itub> in ambiguous cases, an ambigous identifier should be used (for example, tartaric acid has a SMILES with no stereochemistry)
12:43 <+Physchim62> OK, so we eliminate all InChIs for possible ambiguity, is that what you want?
12:44 <walkerma_> I don't see us competing with ChemSpider - it's more a case that they are looking at a structure and they want to copy/paste the RIGHT InChI
12:44 <+itub> when detail is wanted, an extra table can be added, again as in tartaric acid
12:45 <+itub> what I wouldn't want is to have an article called tartaric acid with just one inchi which hapens to be the one for a randomly chosen isomer
12:45 <walkerma_> Tartaric acid does this fine, as far as it goes
12:45 <walkerma_> itub: Yes
12:46 <walkerma_> itub: This is unfortunately what we have in many cases
12:46 <walkerma_> Many of the problems Antony found were of this sort
12:46 <walkerma_> So which do we define as right - the Structure or the InChI? Or the IUPAC name?
12:46 <walkerma_> I would choose the structure, and derive everything from that
12:49 <+itub> we need to start from the title and use chemical sense... :)
12:50 <+itub> if the title is tartaric acid, one expects an article about a set of isomers
12:50 <+itub> if the title is DL-tartaric acid, one expects an article about a specific compound
12:52 <+itub> a more obvious example would be http://en.wikipedia.org/wiki/Xylene
12:52 <+itub> which again deals with an unspecified mixture of isomers, with its very own CAS number but no SMILES
12:53 <+itub> so, the first thing one needs to ask is "what is this ARTICLE about?"
12:54 <walkerma_> That sounds like a good starting point for next week's discussion
12:56 <walkerma_> Should we call it a day/night?
12:56 <+Rifleman_82> yeah sure
12:56 <+itub> sure
12:56 <+Rifleman_82> i won't be around next week, travelling
--- Log closed Wed Feb 13 12:56:23 EST 2008
