Wikipedia:WikiProject Chemistry/IRC discussions/11 Mar 2008

--- Log opened Tue Mar 11 11:58:03 EDT 2008

11:58 &lt;+walkerma&gt; 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 &lt;+walkerma&gt; Hi Beetstra!

11:58 &lt;+markleach&gt; no worries

11:58 &lt;+Rifleman_82&gt; hiya dirk

12:00 &lt;+walkerma&gt; 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 &lt;+Rifleman_82&gt; is it 12 EDT now?

12:02 &lt;+dmacks&gt; yes

12:02 &lt;+walkerma&gt; I think we should start, is that OK?

12:02 &lt;+dmacks&gt; sure

12:02 &lt;+Rifleman_82&gt; ok, that's convenient... 12 hours from my time

12:02 &lt;+Rifleman_82&gt; yes please start

12:03 &lt;+walkerma&gt; I should start by mentioning the news from my discussions with Chemical Abstracts yesterday

12:03 &lt;+walkerma&gt; 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 &lt;+walkerma&gt; They would like to work with us

12:04 &lt;+dmacks&gt; yay!

12:04 &lt;+walkerma&gt; They will validate our complete collection of CAS nos for us, free of charge

12:04 &lt;+Rifleman_82&gt; in future?

12:04 &lt;+Rifleman_82&gt; or one-off?

12:05 &lt;+walkerma&gt; 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 &lt;+dmacks&gt; Okay, I'll wipe the log. Please tell me when to start actually logging again.

12:05 &lt;+walkerma&gt; They agreed to the one-off help, but with the expectation of an ongoing (occasional) collaboration

12:06 &lt;+walkerma&gt; 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 &lt;+Rifleman_82&gt; they will publish this public page?

12:07 &lt;+Rifleman_82&gt; so it'll be their page on D2O for example?

12:07 &lt;+walkerma&gt; 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 &lt;+walkerma&gt; Yes, it's still a notional idea at the moment, but it seems they are thinking along the same lines anyway

12:07 &lt;+Rifleman_82&gt; that'll be complementary to our project

12:08 &lt;+walkerma&gt; Exactly

12:08 &lt;+Rifleman_82&gt; :)

12:08 &lt;+Rifleman_82&gt; just a note

12:08 &lt;+Beetstra&gt; 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 &lt;+walkerma&gt; And I'd much prefer a link to CAS than to emolecules

12:08 &lt;+Rifleman_82&gt; louisBB is trying to join us

12:08 &lt;+Rifleman_82&gt; he's having difficulties getting onto IRC

12:08 &lt;+Rifleman_82&gt; at the moment

12:08 &lt;+walkerma&gt; Do you know who louisBB is?

12:09 &lt;+Rifleman_82&gt; no, but he seemed like an aspiring wikichemist

12:09 &lt;+walkerma&gt; Beetstra: It would be free, that's the intent

12:09 &lt;+Beetstra&gt; OK

12:09 &lt;+walkerma&gt; It would be like a Pubchem page, I think

12:09 &lt;+Rifleman_82&gt; perhaps we'll adjourn this conversation to the next time when he comes?

12:09 &lt;+walkerma&gt; Only more reliable :)

12:09 &lt;+Rifleman_82&gt; beetstra: i think no COI; they're the official source so it's not as bad as linking out to emolecules

12:09 &lt;+Beetstra&gt; I think it should be free, and contain info that helps people get further ..

12:09 &lt;+markleach&gt; most public databases are very organic. CAS is org and inorg

12:10 &lt;+Beetstra&gt; edit conflict .. like pubchem would be great

12:10 &lt;+Beetstra&gt; Though hopefully better

12:10 &lt;+walkerma&gt; OK, let's introduce Mark Leach, who runs the chemthes site

12:10 &lt;+Beetstra&gt; COI is not necesserily bad .. as long as it is acknowledged (on wiki), preferably by members of a wikiproject

12:10 &lt;+markleach&gt; Hi all

12:10 &lt;+Beetstra&gt; Hi Mark

12:11 &lt;+walkerma&gt; I should mention, Mark has been ill, and almost didn't make it

12:11 &lt;+dmacks&gt; hi mark!

12:11 &lt;+Beetstra&gt; This meeting .. or ..

12:11 &lt;+walkerma&gt; 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 &lt;+walkerma&gt; Can you tell us about your site, Mark?

12:12 &lt;+markleach&gt; I have a chemical reaction database set up on MySQL

12:13 &lt;+markleach&gt; http://www.chemthes.com/

12:13 &lt;+markleach&gt; It is full relational and at the WP level of knowledge

12:14 &lt;+markleach&gt; It deals with organic, inorganic & main group chemistry

12:15 &lt;+markleach&gt; I have been working on this project for many years, and I am looking to move it on in someway.

12:16 &lt;+markleach&gt; The tata

12:17 &lt;+markleach&gt; The ChemThes database is link rich but text poor... WP is the other way round...

12:17 &lt;+Rifleman_82&gt; are you looking to find a home for your data? and retire? or will you continue to maintain it?

12:17 &lt;+Rifleman_82&gt; just wondering

12:17 &lt;+markleach&gt; OK. I would join you guys

12:18 &lt;+Beetstra&gt; In principle, you could link every compound back to wiki, and reactions in wiki could link to the database ..

12:18 &lt;+markleach&gt; yup!

12:18 &lt;+Beetstra&gt; A link on every compounds page .. I don't know .. there are so many databases to link to ..

12:18 &lt;+markleach&gt; something like: http://www.chemthes.com/xenon_test.php

12:19 &lt;+markleach&gt; This page is a lash up!

12:20 &lt;+markleach&gt; Or benzene: http://www.chemthes.com/benzene_test.php

12:21 &lt;+dmacks&gt; Quick question about how this data is generated: "42 reactions utilise: Benzene".

12:21 &lt;+Beetstra&gt; Mark, two questions: 1) how is your database checked and 2) how complete are you by now?

12:22 &lt;+dmacks&gt; 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 &lt;+markleach&gt; "42 reactions utilise: Benzene": these are held relationally. Add another reaction and everything is _automatically_ updated.

12:24 &lt;+markleach&gt; 1) how is your database checked: i use text book knowledge

12:24 &lt;+markleach&gt; 2) how complete are you by now?: exactly...

12:24 &lt;+dmacks&gt; 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 &lt;+Rifleman_82&gt; org/inorg synth?

12:25 &lt;+markleach&gt; org/inorg synth? Yes, there are both included. Lots of industrial and process chemistry

12:26 &lt;+Beetstra&gt; 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 &lt;+Beetstra&gt; So I do see the mutual benefits of linking .. but also the problems ..

12:27 &lt;+Rifleman_82&gt; that's great, mark

12:28 &lt;+Beetstra&gt; I mean .. it is great to be able to find 'all' reactions that create benzene .. but ..

12:28 &lt;+markleach&gt; ChemThes is not CAS. It links chemical entities together, and classifies them.

12:30 &lt;+Rifleman_82&gt; poor man's scifinder?

12:30 &lt;+dmacks&gt; Beetstra: I think you're getting at same issue I was pondering.

12:31 &lt;+markleach&gt; scifinder does not give the info that ChemThes does. It is unique.

12:32 &lt;+dmacks&gt; Are there really "11 reactions that form *benzene*" or are there 11 reactions that form classes of molecules to which benzene belongs?

12:32 &lt;+Rifleman_82&gt; tony is joining us in a while

12:32 &lt;+Rifleman_82&gt; he's setting up his mirc

12:32 &lt;+markleach&gt; 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 &lt;+Beetstra&gt; I mean, if we link, it should be good (complete, reviewed, and/or the official source)

12:33 &lt;+walkerma&gt; 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 &lt;+Beetstra&gt; CAS -> CAS .. pubchem -> pubchem ..

12:33 &lt;+dmacks&gt; markleach: I've used the site often. It's quite useful! (not sure if you get positive feedback often enough)

12:34 &lt;+markleach&gt; walkerma- open to discussion. I am currently adding WP links from ChemThes

12:35 &lt;+walkerma&gt; How would you see it working from within Wikipedia?

12:36 &lt;+markleach&gt; 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 &lt;+walkerma&gt; Where would the database portion reside? Or do you need us to help work that part out?

12:37 &lt;+markleach&gt; Where would the database portion reside? One for the techies.

12:38 &lt;+dmacks&gt; 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 &lt;+markleach&gt; 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 &lt;+dmacks&gt; 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 &lt;+walkerma&gt; 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 &lt;+Rifleman_82&gt; hiya antony!

12:40 &lt;ChemSpiderman&gt; whoa...just showed up. What are we talking about?

12:41 &lt;+Rifleman_82&gt; mark leach is introducing his website, www.chemthes.com

12:41 -!- mode/#wikichem [+v ChemSpiderman] by ChanServ

12:42 &lt;+walkerma&gt; I'm sending you a rough log of so far

12:42 * Beetstra has to leave .. see you all later/next week!

12:43 &lt;+ChemSpiderman&gt; Sorry for the delay...had to arrive, fight wireless issues then install mIRC and fight with that...

12:43 &lt;+Rifleman_82&gt; cya dirk

12:43 &lt;+walkerma&gt; Bye Dirk

12:44 &lt;+walkerma&gt; 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 &lt;+Rifleman_82&gt; persondata = ?

12:45 &lt;+Rifleman_82&gt; sorry

12:45 &lt;+Rifleman_82&gt; are you talking about the idea we were discussing?

12:45 &lt;+Rifleman_82&gt; where in each reaction diagram, be it an image or text

12:45 &lt;+Rifleman_82&gt; we tag each reactant/solvent/catalyst/product

12:46 &lt;+Rifleman_82&gt; and we have a search site which searches for "benzene" in "all roles", or refine it to solvent

12:47 &lt;+Rifleman_82&gt; or do you mean something else?

12:48 &lt;+walkerma&gt; http://en.wikipedia.org/wiki/Wikipedia:Persondata

12:49 &lt;+Rifleman_82&gt; hmmm

12:50 &lt;+Rifleman_82&gt; i see some tools which can extract the data

12:50 &lt;+Rifleman_82&gt; i am not qualified to say if it can or cannot be done

12:50 &lt;+Rifleman_82&gt; but having data a bot can read and extract will be very useful

12:51 &lt;+Rifleman_82&gt; and i suppose given time and effort we can do something similar to persondata

12:51 &lt;+markleach&gt; We would need MySQL & php servers running within WP

12:51 &lt;+Rifleman_82&gt; the next step of course, will be to add it to the few thousand articles

12:51 &lt;+Rifleman_82&gt; wikipedia has a toolserver

12:51 &lt;+Rifleman_82&gt; http://en.wikipedia.org/wiki/Wikipedia:Toolserver

12:52 &lt;+walkerma&gt; (I have students in here right now, please keep things moving!)

12:52 &lt;+walkerma&gt; 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 &lt;+Rifleman_82&gt; mark: dirk's the expert with templates

12:53 &lt;+Rifleman_82&gt; he can help you best

12:53 &lt;+Rifleman_82&gt; physchim is the 2nd best guy to ask

12:54 &lt;+Rifleman_82&gt; 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 &lt;+markleach&gt; As I said: there is no rush. I am just starting a first dialog.

12:54 &lt;+Rifleman_82&gt; yup

12:54 &lt;+Rifleman_82&gt; what else can we talk aboutnow?

12:55 &lt;+Rifleman_82&gt; there's you, me and antony at the moment

12:55 &lt;+Rifleman_82&gt; have you any thoughts of my approach?

12:55 &lt;+Rifleman_82&gt; where a template will transclude a little tag

12:55 &lt;+Rifleman_82&gt; and a search page

12:55 &lt;+Rifleman_82&gt; something like

12:55 &lt;+ChemSpiderman&gt; I can't comment yet....need to read the log and get a context for the discussion

12:55 &lt;+Rifleman_82&gt; http://en.wikipedia.org/wiki/Special:Whatlinkshere/Frankfurt_Airport

12:55 &lt;+Rifleman_82&gt; will show you a search page of all linking to this article

12:56 &lt;+Rifleman_82&gt; since our chair is not around

12:56 &lt;+Rifleman_82&gt; perhaps i can help answer whatever questions you have of WP/WPchem?

12:56 &lt;+walkerma&gt; 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 &lt;+walkerma&gt; (I'm back now)

12:57 &lt;+walkerma&gt; ChemSpiderman has got us a database of around 5000 organics

12:57 &lt;+walkerma&gt; But we have about 2000 more not in his list

13:04 &lt;+ChemSpiderman&gt; Yes..that's my estimate..inorganics and organometallics

13:04 &lt;+walkerma&gt; If CAS can come through for us, we'd like to get them to validate those 2000

13:04 &lt;+ChemSpiderman&gt; you'll have to do it by names I think...provide the list of names rather than connection tables

13:04 &lt;+ChemSpiderman&gt; (By the way, I will follow up with mark offline regarding potential to hook his site into ChemSpider)

13:04 &lt;+walkerma&gt; What should we do to compile that list? Currently any list from chemicals is woefully incomplete

13:04 &lt;+walkerma&gt; We do have Emmanuel's list from last April

13:04 &lt;+markleach&gt; ChemThes is comprehensive with respect to all flhories,

13:04 &lt;+markleach&gt; fluorides, chlorides, bromides, iodides and oxides

13:04 &lt;+Rifleman_82&gt; tony: all the better for chemists... a true web of interconnected databases and info sources

13:04 &lt;+walkerma&gt; Sorry, I mean a list of WP articles to send to CAS for validation

13:04 &lt;+markleach&gt; When I have the WP links, I will be able to tell you which ones you do not have

13:04 &lt;+Rifleman_82&gt; how about a list of all articles transcluding chembox new?

13:04 &lt;+walkerma&gt; Combined with a complete list from http://en.wikipedia.org/wiki/Category:Chemical_compounds_by_element

13:04 &lt;+markleach&gt; not very complete!

13:04 &lt;+Rifleman_82&gt; the problem if you will, is that not all chemical articles are started by wikichemists

13:04 &lt;+markleach&gt; No, it is not so bad... (on looking further)

13:04 &lt;+Rifleman_82&gt; those which we start or stumble on, we fix

13:04 &lt;+Rifleman_82&gt; but!

13:07 &lt;+walkerma&gt; Rifleman_82: Can you put a list together through AWB?

13:07 &lt;+Rifleman_82&gt; i can try

13:08 &lt;+Rifleman_82&gt; i've sent you one copy but you mentioned it's incomplete

13:08 &lt;+Rifleman_82&gt; i've not received your list from emmanuel

13:08 &lt;+Rifleman_82&gt; if he gives me his search criteria i might be able to tweak the process further

13:10 &lt;+walkerma&gt; 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 &lt;+Rifleman_82&gt; walkerma: i'll contact him and try to figure out how he did it

13:11 &lt;+walkerma&gt; Does anyone have any better ideas regarding the inorganics & organometallics?

13:11 &lt;+Rifleman_82&gt; i'll try to wrap it up before i reach you

13:12 &lt;+walkerma&gt; Rifleman 82: I'll dig out the old email and send it to you, it tells how he did it

13:12 &lt;+Rifleman_82&gt; ok thanks

13:12 &lt;+ChemSpiderman&gt; Nothing from me...there were some listed in the original file you sent me but I did a lot of manual curation

13:12 &lt;+ChemSpiderman&gt; I want to focus on organics before I bite off anything on inorganics I'm afraid

13:13 &lt;+walkerma&gt; I'll also try contacting Axiosaurus and Smokefoot, also PC knows the inorganics pretty well, see if they have any ideas.

13:13 &lt;+walkerma&gt; Should we close the meeting now, then?

13:14 &lt;+ChemSpiderman&gt; works for me. Sorry I was late

13:14 &lt;+walkerma&gt; 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 &lt;+Rifleman_82&gt; any comments about the mos so far?

13:15 &lt;+ChemSpiderman&gt; mos?

13:15 &lt;+Rifleman_82&gt; http://en.wikipedia.org/wiki/WP:MOSCHEM

13:15 &lt;+Rifleman_82&gt; manual of style

13:15 &lt;+ChemSpiderman&gt; ah-ha

13:15 &lt;+Rifleman_82&gt; oops

13:15 &lt;+Rifleman_82&gt; the draft!

13:15 &lt;+Rifleman_82&gt; http://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style_%28chemistry%29/draft

13:16 &lt;+walkerma&gt; 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 &lt;+Rifleman_82&gt; sure, my pleasure

13:16 &lt;+Rifleman_82&gt; i know i haven't written the subpages yet

13:16 &lt;+Rifleman_82&gt; but i was hoping the skeleton is okay first

13:16 &lt;+Rifleman_82&gt; there are a few blanks, which i'll need to fill out too

13:16 &lt;+walkerma&gt; OK,I need to go now, I have another meeting ! I'll stay logged on though

13:16 &lt;+Rifleman_82&gt; sure

13:17 &lt;+Rifleman_82&gt; i've nothing else for th emeeting

13:17 &lt;+ChemSpiderman&gt; bye all

13:17 &lt;+Rifleman_82&gt; so... action: i'll figure out how to plumb the categories for our articles

13:17 &lt;+Rifleman_82&gt; and i'll continue writing the mOS

13:17 &lt;+Rifleman_82&gt; yup

13:17 &lt;+Rifleman_82&gt; that's all for me

13:17 -!- ChemSpiderman [n=tony@c-68-33-211-217.hsd1.md.comcast.net] has quit []

13:18 &lt;+Rifleman_82&gt; thanks for coming, mark

13:19 &lt;+walkerma&gt; Yes, thanks a lot, Mark!

--- Log closed Wed Mar 12 13:19:29 2008