Wikipedia:WikiProject Chemistry/IRC discussions/11 Mar 2008
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--- Log opened Tue Mar 11 11:58:03 EDT 2008
11:58 <+walkerma> Mark, I should mention, I did announce a different topic for the agenda when I didn't hear back from you, but I know you've been ill. We can be flexible about that, and maybe start to cover the other topic too.
11:58 <+walkerma> Hi Beetstra!
11:58 <+markleach> no worries
11:58 <+Rifleman_82> hiya dirk
12:00 <+walkerma> ChemSpiderman is going to be driving home at this time, he won't be able to join us until 12:45 or so
12:01 <+Rifleman_82> is it 12 EDT now?
12:02 <+dmacks> yes
12:02 <+walkerma> I think we should start, is that OK?
12:02 <+dmacks> sure
12:02 <+Rifleman_82> ok, that's convenient... 12 hours from my time
12:02 <+Rifleman_82> yes please start
12:03 <+walkerma> I should start by mentioning the news from my discussions with Chemical Abstracts yesterday
12:03 <+walkerma> This is still not official - I'm still waiting for the confirmation email - but the people I spoke with there were very positive
12:03 <+walkerma> They would like to work with us
12:04 <+dmacks> yay!
12:04 <+walkerma> They will validate our complete collection of CAS nos for us, free of charge
12:04 <+Rifleman_82> in future?
12:04 <+Rifleman_82> or one-off?
12:05 <+walkerma> Please don't breathe a word of this until it's official - dmacks, can you hold off on posting any log, or perhaps just delete this section?
12:05 <+dmacks> Okay, I'll wipe the log. Please tell me when to start actually logging again.
12:05 <+walkerma> They agreed to the one-off help, but with the expectation of an ongoing (occasional) collaboration
12:06 <+walkerma> In return, I said we would be wanting to link from our CAS number entry in each Chembox to a (yet to be written) public page for each compound
12:07 <+Rifleman_82> they will publish this public page?
12:07 <+Rifleman_82> so it'll be their page on D2O for example?
12:07 <+walkerma> You find it in WP, you click on the CAS no, and you can (if you want to pay) then do a CAS search on that compound - that is the view
12:07 <+walkerma> Yes, it's still a notional idea at the moment, but it seems they are thinking along the same lines anyway
12:07 <+Rifleman_82> that'll be complementary to our project
12:08 <+walkerma> Exactly
12:08 <+Rifleman_82> :)
12:08 <+Rifleman_82> just a note
12:08 <+Beetstra> Hmm .. that might violate our external links guideline .. and I don't see the use of linking to a searchpage which is not free ..
12:08 <+walkerma> And I'd much prefer a link to CAS than to emolecules
12:08 <+Rifleman_82> louisBB is trying to join us
12:08 <+Rifleman_82> he's having difficulties getting onto IRC
12:08 <+Rifleman_82> at the moment
12:08 <+walkerma> Do you know who louisBB is?
12:09 <+Rifleman_82> no, but he seemed like an aspiring wikichemist
12:09 <+walkerma> Beetstra: It would be free, that's the intent
12:09 <+Beetstra> OK
12:09 <+walkerma> It would be like a Pubchem page, I think
12:09 <+Rifleman_82> perhaps we'll adjourn this conversation to the next time when he comes?
12:09 <+walkerma> Only more reliable :)
12:09 <+Rifleman_82> beetstra: i think no COI; they're the official source so it's not as bad as linking out to emolecules
12:09 <+Beetstra> I think it should be free, and contain info that helps people get further ..
12:09 <+markleach> most public databases are very organic. CAS is org and inorg
12:10 <+Beetstra> edit conflict .. like pubchem would be great
12:10 <+Beetstra> Though hopefully better
12:10 <+walkerma> OK, let's introduce Mark Leach, who runs the chemthes site
12:10 <+Beetstra> COI is not necesserily bad .. as long as it is acknowledged (on wiki), preferably by members of a wikiproject
12:10 <+markleach> Hi all
12:10 <+Beetstra> Hi Mark
12:11 <+walkerma> I should mention, Mark has been ill, and almost didn't make it
12:11 <+dmacks> hi mark!
12:11 <+Beetstra> This meeting .. or ..
12:11 <+walkerma> Yes, just for this meeting! Sorry! So I had prepared an alt agenda in case, but while we have him here I'd like him to talk about his work
12:11 <+walkerma> Can you tell us about your site, Mark?
12:12 <+markleach> I have a chemical reaction database set up on MySQL
12:13 <+markleach> http://www.chemthes.com/
12:13 <+markleach> It is full relational and at the WP level of knowledge
12:14 <+markleach> It deals with organic, inorganic & main group chemistry
12:15 <+markleach> I have been working on this project for many years, and I am looking to move it on in someway.
12:16 <+markleach> The tata
12:17 <+markleach> The ChemThes database is link rich but text poor... WP is the other way round...
12:17 <+Rifleman_82> are you looking to find a home for your data? and retire? or will you continue to maintain it?
12:17 <+Rifleman_82> just wondering
12:17 <+markleach> OK. I would join you guys
12:18 <+Beetstra> In principle, you could link every compound back to wiki, and reactions in wiki could link to the database ..
12:18 <+markleach> yup!
12:18 <+Beetstra> A link on every compounds page .. I don't know .. there are so many databases to link to ..
12:18 <+markleach> something like: http://www.chemthes.com/xenon_test.php
12:19 <+markleach> This page is a lash up!
12:20 <+markleach> Or benzene: http://www.chemthes.com/benzene_test.php
12:21 <+dmacks> Quick question about how this data is generated: "42 reactions utilise: Benzene".
12:21 <+Beetstra> Mark, two questions: 1) how is your database checked and 2) how complete are you by now?
12:22 <+dmacks> Does that mean specific reactions that specifically use C6H6, or is benzene aromatic, and therefore all reactions that have "aromatic starting material" are included?
12:22 <+markleach> "42 reactions utilise: Benzene": these are held relationally. Add another reaction and everything is _automatically_ updated.
12:24 <+markleach> 1) how is your database checked: i use text book knowledge
12:24 <+markleach> 2) how complete are you by now?: exactly...
12:24 <+dmacks> Right. I meant how is "everything" linked together? When that next reaction is added, is it identified as "benzene is the starting material"?
12:24 <+Rifleman_82> org/inorg synth?
12:25 <+markleach> org/inorg synth? Yes, there are both included. Lots of industrial and process chemistry
12:26 <+Beetstra> the thing is, which is a bit similar to sites like emolecules, it is not your data, the data is external. None of it is complete, and either subject to changes or to typo's .. linking a CAS number to CAS is directly related .. it is their number what they issue (and already there, we don't link to them atm because we can't, but also because it is incomplete or wrong ..)
12:27 <+Beetstra> So I do see the mutual benefits of linking .. but also the problems ..
12:27 <+Rifleman_82> that's great, mark
12:28 <+Beetstra> I mean .. it is great to be able to find 'all' reactions that create benzene .. but ..
12:28 <+markleach> ChemThes is not CAS. It links chemical entities together, and classifies them.
12:30 <+Rifleman_82> poor man's scifinder?
12:30 <+dmacks> Beetstra: I think you're getting at same issue I was pondering.
12:31 <+markleach> scifinder does not give the info that ChemThes does. It is unique.
12:32 <+dmacks> Are there really "11 reactions that form *benzene*" or are there 11 reactions that form classes of molecules to which benzene belongs?
12:32 <+Rifleman_82> tony is joining us in a while
12:32 <+Rifleman_82> he's setting up his mirc
12:32 <+markleach> Can I suggest that people look/play with this stuff at their leisure? No discissions have to be made now! Hove been working on this for years...
12:32 <+Beetstra> I mean, if we link, it should be good (complete, reviewed, and/or the official source)
12:33 <+walkerma> markleach - do you want WP links to an external site, or do you want to add this content into WP itself in some way?
12:33 <+Beetstra> CAS -> CAS .. pubchem -> pubchem ..
12:33 <+dmacks> markleach: I've used the site often. It's quite useful! (not sure if you get positive feedback often enough)
12:34 <+markleach> walkerma- open to discussion. I am currently adding WP links from ChemThes
12:35 <+walkerma> How would you see it working from within Wikipedia?
12:36 <+markleach> Rather like to the XeF6 page. With links back to other WP pages. The reactions pages would be WP branded. Or put in frames?
12:37 <+walkerma> Where would the database portion reside? Or do you need us to help work that part out?
12:37 <+markleach> Where would the database portion reside? One for the techies.
12:38 <+dmacks> WP doesn't have the ability to embed content from external sites, so either the actual data would have to be on WP, or else a bot would have to update the pages when an external database is updated.
12:39 <+markleach> And there is no rush, as the first thing is for me to add links from my pages to the WP pages, which I want to do anyway! (I started this morning.)
12:39 <+dmacks> There's the *idea* of framing, but only within/among other Wikipeida-site content.
12:39 -!- ChemSpiderman [n=tony@c-68-33-211-217.hsd1.md.comcast.net] has joined #wikichem
12:40 <+walkerma> Hi Antony! I understand from PC that the Persondata template works through something like a database, could we use that? (I'm not a techie, so I may be completely wrong)
12:40 <+Rifleman_82> hiya antony!
12:40 <ChemSpiderman> whoa...just showed up. What are we talking about?
12:41 <+Rifleman_82> mark leach is introducing his website, www.chemthes.com
12:41 -!- mode/#wikichem [+v ChemSpiderman] by ChanServ
12:42 <+walkerma> I'm sending you a rough log of so far
12:42 * Beetstra has to leave .. see you all later/next week!
12:43 <+ChemSpiderman> Sorry for the delay...had to arrive, fight wireless issues then install mIRC and fight with that...
12:43 <+Rifleman_82> cya dirk
12:43 <+walkerma> Bye Dirk
12:44 <+walkerma> Rifleman 82: Could we use the persondata approach? PC's {{InChI}} template works like that
12:45 -!- Beetstra [n=djbeetst@Wikimedia/Beetstra] has quit ["Bye Bye"]
12:45 <+Rifleman_82> persondata = ?
12:45 <+Rifleman_82> sorry
12:45 <+Rifleman_82> are you talking about the idea we were discussing?
12:45 <+Rifleman_82> where in each reaction diagram, be it an image or text
12:45 <+Rifleman_82> we tag each reactant/solvent/catalyst/product
12:46 <+Rifleman_82> and we have a search site which searches for "benzene" in "all roles", or refine it to solvent
12:47 <+Rifleman_82> or do you mean something else?
12:48 <+walkerma> http://en.wikipedia.org/wiki/Wikipedia:Persondata
12:49 <+Rifleman_82> hmmm
12:50 <+Rifleman_82> i see some tools which can extract the data
12:50 <+Rifleman_82> i am not qualified to say if it can or cannot be done
12:50 <+Rifleman_82> but having data a bot can read and extract will be very useful
12:51 <+Rifleman_82> and i suppose given time and effort we can do something similar to persondata
12:51 <+markleach> We would need MySQL & php servers running within WP
12:51 <+Rifleman_82> the next step of course, will be to add it to the few thousand articles
12:51 <+Rifleman_82> wikipedia has a toolserver
12:51 <+Rifleman_82> http://en.wikipedia.org/wiki/Wikipedia:Toolserver
12:52 <+walkerma> (I have students in here right now, please keep things moving!)
12:52 <+walkerma> Back soon
12:53 * dmacks has to run, will read the logs tonite.
12:53 -!- dmacks [n=dmacks@pdpc/supporter/active/dmacks] has quit ["leaving"]
12:53 <+Rifleman_82> mark: dirk's the expert with templates
12:53 <+Rifleman_82> he can help you best
12:53 <+Rifleman_82> physchim is the 2nd best guy to ask
12:54 <+Rifleman_82> i've been around and i know a bit of what we have and can do, but i know nothing of the nuts and bolts
12:54 <+markleach> As I said: there is no rush. I am just starting a first dialog.
12:54 <+Rifleman_82> yup
12:54 <+Rifleman_82> what else can we talk aboutnow?
12:55 <+Rifleman_82> there's you, me and antony at the moment
12:55 <+Rifleman_82> have you any thoughts of my approach?
12:55 <+Rifleman_82> where a template will transclude a little tag
12:55 <+Rifleman_82> and a search page
12:55 <+Rifleman_82> something like
12:55 <+ChemSpiderman> I can't comment yet....need to read the log and get a context for the discussion
12:55 <+Rifleman_82> http://en.wikipedia.org/wiki/Special:Whatlinkshere/Frankfurt_Airport
12:55 <+Rifleman_82> will show you a search page of all linking to this article
12:56 <+Rifleman_82> since our chair is not around
12:56 <+Rifleman_82> perhaps i can help answer whatever questions you have of WP/WPchem?
12:56 <+walkerma> OK, the other main thing I want to get on the table is: We still need to build a collection of the inorganics
12:56 <+walkerma> (I'm back now)
12:57 <+walkerma> ChemSpiderman has got us a database of around 5000 organics
12:57 <+walkerma> But we have about 2000 more not in his list
13:04 <+ChemSpiderman> Yes..that's my estimate..inorganics and organometallics
13:04 <+walkerma> If CAS can come through for us, we'd like to get them to validate those 2000
13:04 <+ChemSpiderman> you'll have to do it by names I think...provide the list of names rather than connection tables
13:04 <+ChemSpiderman> (By the way, I will follow up with mark offline regarding potential to hook his site into ChemSpider)
13:04 <+walkerma> What should we do to compile that list? Currently any list from {{chemicals}} is woefully incomplete
13:04 <+walkerma> We do have Emmanuel's list from last April
13:04 <+markleach> ChemThes is comprehensive with respect to all flhories,
13:04 <+markleach> fluorides, chlorides, bromides, iodides and oxides
13:04 <+Rifleman_82> tony: all the better for chemists... a true web of interconnected databases and info sources
13:04 <+walkerma> Sorry, I mean a list of WP articles to send to CAS for validation
13:04 <+markleach> When I have the WP links, I will be able to tell you which ones you do not have
13:04 <+Rifleman_82> how about a list of all articles transcluding {{chembox new}}?
13:04 <+walkerma> Combined with a complete list from http://en.wikipedia.org/wiki/Category:Chemical_compounds_by_element
13:04 <+markleach> not very complete!
13:04 <+Rifleman_82> the problem if you will, is that not all chemical articles are started by wikichemists
13:04 <+markleach> No, it is not so bad... (on looking further)
13:04 <+Rifleman_82> those which we start or stumble on, we fix
13:04 <+Rifleman_82> but!
13:07 <+walkerma> Rifleman_82: Can you put a list together through AWB?
13:07 <+Rifleman_82> i can try
13:08 <+Rifleman_82> i've sent you one copy but you mentioned it's incomplete
13:08 <+Rifleman_82> i've not received your list from emmanuel
13:08 <+Rifleman_82> if he gives me his search criteria i might be able to tweak the process further
13:10 <+walkerma> It's an old list, he used some German tool from the Toolserver that searches subcategories of subcategories of, well you get the idea. I couldn't get it to work myself. I'll resend copies of that list to anyone who wants it, it's about 25,000 articles on chemistry-related topics
13:11 <+Rifleman_82> walkerma: i'll contact him and try to figure out how he did it
13:11 <+walkerma> Does anyone have any better ideas regarding the inorganics & organometallics?
13:11 <+Rifleman_82> i'll try to wrap it up before i reach you
13:12 <+walkerma> Rifleman 82: I'll dig out the old email and send it to you, it tells how he did it
13:12 <+Rifleman_82> ok thanks
13:12 <+ChemSpiderman> Nothing from me...there were some listed in the original file you sent me but I did a lot of manual curation
13:12 <+ChemSpiderman> I want to focus on organics before I bite off anything on inorganics I'm afraid
13:13 <+walkerma> I'll also try contacting Axiosaurus and Smokefoot, also PC knows the inorganics pretty well, see if they have any ideas.
13:13 <+walkerma> Should we close the meeting now, then?
13:14 <+ChemSpiderman> works for me. Sorry I was late
13:14 <+walkerma> I hoping that we'll have plenty to discuss next week - I left the agenda wide open this week for a variety of reasons, sorry I had to do that!
13:14 <+Rifleman_82> any comments about the mos so far?
13:15 <+ChemSpiderman> mos?
13:15 <+Rifleman_82> http://en.wikipedia.org/wiki/WP:MOSCHEM
13:15 <+Rifleman_82> manual of style
13:15 <+ChemSpiderman> ah-ha
13:15 <+Rifleman_82> oops
13:15 <+Rifleman_82> the draft!
13:15 <+Rifleman_82> http://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style_%28chemistry%29/draft
13:16 <+walkerma> Rifleman 82, I'll get back to you today with my comments - thanks for working on that. I know it's a lot of work!
13:16 <+Rifleman_82> sure, my pleasure
13:16 <+Rifleman_82> i know i haven't written the subpages yet
13:16 <+Rifleman_82> but i was hoping the skeleton is okay first
13:16 <+Rifleman_82> there are a few blanks, which i'll need to fill out too
13:16 <+walkerma> OK,I need to go now, I have another meeting ! I'll stay logged on though
13:16 <+Rifleman_82> sure
13:17 <+Rifleman_82> i've nothing else for th emeeting
13:17 <+ChemSpiderman> bye all
13:17 <+Rifleman_82> so... action: i'll figure out how to plumb the categories for our articles
13:17 <+Rifleman_82> and i'll continue writing the mOS
13:17 <+Rifleman_82> yup
13:17 <+Rifleman_82> that's all for me
13:17 -!- ChemSpiderman [n=tony@c-68-33-211-217.hsd1.md.comcast.net] has quit []
13:18 <+Rifleman_82> thanks for coming, mark
13:19 <+walkerma> Yes, thanks a lot, Mark!
--- Log closed Wed Mar 12 13:19:29 2008
