Wikipedia:WikiProject Chemistry/IRC discussions/2009

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/13 January 2009

Can we meet at 1600h UTC (11am US Eastern Time, 1700h Central European Time) to discuss the following?

  • How the CAS # upload/validation/matching and database work is going.
  • How we might use Magnus' tool for citing CAS nos. (see this discussion)?
  • How should we associate an image with the validated data, so that we don't have validated content but a vandalized structure?

ChemSpiderMan is out of the country right now, and may not be available, but if some of us could chat on IRC it would be useful, I think. Walkerma (talk) 15:34, 9 January 2009 (UTC)[reply]

A further point to discuss:

  • How should we display validated CASRN's in the chembox (as per my message to the mailing list, and the objections being raised about out current use of green text)?

Physchim62 (talk) 09:52, 10 January 2009 (UTC)[reply]

Summary of discussion

  1. We will continue to use the colour system and the {{cascite}} template, because when I checked, it is in compliance with policy and it is accessible for colour-blind people as it is.
  2. We agreed to start using the Excel file (the latest version is also attached) for validation rather than the "first 500" file that we had used. Ultimately everything from the master SDF will have been uploaded to WP, just in a different order. The inorganics will continue to be handled by Physchim62.
  3. We still need to find a good way to explain the system to ordinary users of WP.
  4. We are still unsure about how to use the new tool developed by Magnus - should we link direct to the new CAS web pages for the compounds, or to a page on the toolserver for that CAS#?
  5. We will discuss validation of image files next week.

/20 January 2009

Can we meet at 1600h UTC (11am US Eastern Time, 1700h Central European Time) to discuss the following?

  • How should we associate an image with the validated data, so that we don't have validated content but a vandalized structure?
  • How can we best communicate the system to ordinary users?

/27 January 2009

Can we meet at 1600h UTC (11am US Eastern Time, 1700h Central European Time) to discuss the following?

  • Continued discussion on validation of structure images.
  • Update on how the validation work is going.
  • How can we best communicate the system to ordinary users?
  • I've invited the folks from WP:PHARM, and if we get some pharmacology people showing up we should discuss use of cascite and CheMoBot for drugboxes. Walkerma (talk) 05:38, 26 January 2009 (UTC)[reply]


/3 February 2009

We didn't have some key people around last week, so could we meet at 1600h UTC (11am US Eastern Time, 1700h Central European Time) to discuss the following?

  • Continued discussion on validation of structure images.
  • Update on how the validation work is going.
  • How can we best communicate the system to ordinary users?

Thanks, Walkerma (talk) 16:23, 2 February 2009 (UTC)[reply]

/10 February 2009

I don't think we need to have a formal meeting this week - there has been no news from CAS, and only routine work going on. If Beetstra has an update on the bot, please let us know! Walkerma (talk) 17:25, 9 February 2009 (UTC)[reply]

Agreed, but the IRC channel is open for "routine" discussions! Physchim62 (talk) 15:30, 10 February 2009 (UTC)[reply]

/17 February 2009

If people are around, I'd like to meet at 1600h UTC to discuss progress, issues regarding the SDF files, and where we go next. If Beetstra is around to update us on bot progress, that would be useful as well. Walkerma (talk) 21:24, 16 February 2009 (UTC)[reply]

Bring candles and birthday cake ;) and fire extinguisher :( Physchim62 (talk) 21:29, 16 February 2009 (UTC)[reply]
I got a a seminar this week. Someone can have my slice of cake. DMacks (talk) 14:37, 17 February 2009 (UTC)[reply]

/24 February 2009

No one has proposed a formal meeting this week. I won't be around in person until about 1800 UTC, but I will set the channel to log. At some point we need to discuss wider questions of article assessment, as a result of developments elsewhere in Wikipedia. I can try to answer questions after 1800 UTC if people are interested, but we will have to wait for a talk page discussion to refine the possibilities. Physchim62 (talk) 11:08, 24 February 2009 (UTC)[reply]

I'll check in at 1600h TUC, and again at 1800h UTC. Walkerma (talk) 14:34, 24 February 2009 (UTC)[reply]
Whoops, sorry everyone: I can be around a little after 1700 UTC (1800 CET). I'm currently logging, so if anyone wants to complain about awful coordination when walkerma isn't around, they are welcome to do so! Physchim62 (talk) 15:10, 24 February 2009 (UTC)[reply]

/3 March 2009

At last week's IRC, we agreed to try to ratify the use of

official style guide. In the meantime, all of use should look at the draft, discuss, comment and edit. Walkerma (talk) 02:34, 28 February 2009 (UTC)[reply
]

  • Time:1600h UTC (11am US ET, 1700h CET, and probably the middle of the night in Singapore).
  • Agenda: Ratifying
    Wikipedia:Manual_of_Style_(chemistry)/draft

Cheers, Walkerma (talk) 02:34, 28 February 2009 (UTC)[reply]

/10 March 2009

No one's asked for a formal IRC meeting this week, but the channel will be logged from 1600 UTC onwards if anyone has any spontaneous points to raise. type chemobot silent to get quiet discussion. I will be around from about 1700 UTC onwards. Physchim62 (talk) 14:09, 10 March 2009 (UTC)[reply]

Reminder - for people in the US, the "non-meeting" is now at noon, Eastern Daylight Time, because of our time change. I expect to be there, but I don't think we have/need a formal agenda. Walkerma (talk) 14:12, 10 March 2009 (UTC)[reply]
I would welcome any comments editors may have on our current "safety" sections for chemical compounds, either on IRC for discussion or on my talk page or by email. Physchim62 (talk) 14:40, 10 March 2009 (UTC)[reply]

/17 March 2009

I think we should meet informally at least, at 1600 h UTC (noon US EST). I can see three things that need discussing, in no particular order:

  1. What we want to ask CAS, and say to them, at the Salt Lake City ACS meeting. This can include where we are now, and where we should take things next. Both myself and ChemSpiderMan will be there, and I will almost certainly get to talk face-to-face with one of our CAS contacts.
  2. The A-Class review started by Physchim62.
  3. The ongoing work on the Manual of Style.

Walkerma (talk) 16:32, 16 March 2009 (UTC)[reply]

Fine by me. This week I am able to be around at 1700 CET (1600 UTC, 1200 EST, 2400
SST so spare a thought ;) Physchim62 (talk) 16:50, 16 March 2009 (UTC)[reply
]
I'll try to drop by, but midnight my time will be increasingly difficult due to my daytime commitments I told you about previously. Any chance we could move it up an hour in future? --Rifleman 82 (talk) 02:27, 17 March 2009 (UTC)[reply]

/7 April 2009

Let's meet and talk about the [CAS Common Chemistry] website, which now has an alpha version officially up (they announced it at the Salt Lake City ACS meeting), and the beta should be going up very soon. Also see ChemSpiderman's blog on this.

Regarding the time, both Europeans and North Americans are on "summer time", so 1600h UTC is noon US EST, and 18h00 Central European Summer Time. I think Rifleman82 would prefer if we met an hour earlier, at 1500h UTC, 11am US EST, 17h00 CST. Would this be acceptable to people? I can do either time, as long as I know in advance. Walkerma (talk) 16:12, 6 April 2009 (UTC)[reply]

Summary of main conclusions

Collaboration with CAS
  • The CAS website is now up and running in a beta-test version here. Editors are invited to test the search algorithm and report any problems to Walkerma. The basic structure of the pages will probably not change much before the site is officially announced.
  • We will make an announcement in
    Wikipedia Signpost
    when CAS are happy with their search algorithm.
  • We will deep link to the CAS site from our validated CAS numbers, not all CAS numbers as Beetstra's quick fix led to. The links will be in light blue as for other external links, and in bold so they show up as verified.
Time of meetings
  • The meeting to be brought forward to 1530 UTC from next Tuesday
Other chembox stuff
  • GHS
    classifications of chemical hazards: no plans to do a mass change yet, although the current EU classifications will be obsolete from 1 December 2010.
  • Rifleman 82 asked about including a Organic Syntheses id in the chembox.
  • Walkerma spoke of the dangers of "table creep"; it was agreed that the chembox needs a "spring clean", and on-wiki discussion should be started on the subject.
ChemSpider news
  • InChI
    , hashed InChI (InChI key) and a systematic name in a format suitable for pasting directly into the chembox. Comments are welcome.

Action

Physchim62
Any editor
  • visit http://www.commonchemistry.org and report any problems with the search algorithm
  • start discussion about "spring-cleaning" the chembox
  • continue chembox validation

/14 April 2009

TIME CHANGE: The meeting will start at 1530 UTC (1030 CDT, 1130 EDT, 1630 BST, 1730 CEST, 2330 SST).

  • I won't be around for the first half-hour or so, but I'll keep IRC open and logging as usual. Physchim62 (talk) 17:59, 8 April 2009 (UTC)[reply]

Agenda

How about a discussion on the new Chembox generator that ChemSpiderman developed? Walkerma (talk) 18:31, 13 April 2009 (UTC)[reply]

/21 April 2009

I suggest we have an informal meeting at 1530 UTC (1030 CDT, 1130 EDT, 1630 BST, 1730 CEST, 2330 SST) - is that OK? Walkerma (talk) 01:30, 21 April 2009 (UTC)[reply]

  • OK by me (I can make it to the start this week). If we need a topic for discussion, I suggest "which data should we include in the chembox?" Physchim62 (talk) 02:02, 21 April 2009 (UTC)[reply]

/5 May 2009

Meeting starting at 1500 UTC. We should discuss the offer from ChemAxon for some chemistry software. They are interested even in adapting some of their software to meet our needs. See my email for details. However, they can only meet BEFORE 1530 UTC, so I'm suggesting we start the meeting at 1500 UTC (11am US EDT, 17h00 CEST). After that meeting is over, I'd like to resolve the issue of how we link to the CAS website - CAS themselves are asking about this. Any other agenda items? Walkerma (talk) 20:22, 4 May 2009 (UTC)[reply]

/12 May 2009

I can't make the usual time on May 12th, because I'm giving a final exam at that time. Feel free to meet if you wish - just be sure to delete any rude remarks about me from the log. Walkerma (talk) 01:42, 12 May 2009 (UTC)[reply]

Once I'd removed all the rude comments, the log was blank… Well, OK, it was blank to start with! Physchim62 (talk) 05:37, 13 May 2009 (UTC)[reply]

/19 May 2009

I'm around this week. Do we have anything that needs discussing? We are getting some nice feedback from the CAS announcement… Physchim62 (talk) 14:03, 19 May 2009 (UTC)[reply]

Nothing that really seems to need reporting from our little chat about the CAS announcement. Physchim62 (talk) 07:25, 26 May 2009 (UTC)[reply]

/26 May 2009

Again, I'm around this week (I think, the log will be open anyway). I suggest we talk about chemboxes, specifically the questions of referencing and parameters (box-creep). Physchim62 (talk) 07:25, 26 May 2009 (UTC)[reply]

I can be around for a bit, but the demolition squad are smashing up my lab at 7am tomorrow morning so I'm desperately trying to clear out samples + glassware. Walkerma (talk) 14:22, 26 May 2009 (UTC)[reply]
I though you had grad students to destroy your lab for you… Physchim62 (talk) 14:49, 26 May 2009 (UTC)[reply]

/9 June 2009

I think we should meet at 1600h UTC (noon US EDT, 1700h British Summer Time, 1800h in Spain) to agree on implementing {{Chembox_CASNo/Sandbox}} as the new "official" Sandbox (see discussion on 7 April meeting). Currently Chembox generates a link to the Common Chemistry website, even if there is no corresponding page; this change will allow us to link ONLY to those pages that exist, so we don't have dead links. Beetstra has indicated that he will try to make it; I will have to leave by 1650h UTC at the latest. Walkerma (talk) 03:41, 9 June 2009 (UTC)[reply]

/15 June 2009

I propose starting at 1530 UTC (1130 EDT, 1630 BST, 1730 CEST): I will be around earlier if anyone wants to transmit comments. Two points of discussion come to mind:

  • The interview in this week's
    Wikipedia Signpost
    : myself and Martin gave our personal opinions, but are there any things which we said which people don't agree with?
  • RSC ontologies: this is a bit of a kite-flyer, as I'm still exploring them, but they may well have implications for who we organise information at Wikipedia. They are a set of defined terms (a bit like the Gold Book, but smaller), but machine-readable and with semantic links between them.

All PoVs welcome! Physchim62 (talk) 22:29, 15 June 2009 (UTC)[reply]

OK, I'll be there. Sounds like a good discussion. Walkerma (talk) 03:53, 16 June 2009 (UTC)[reply]

Apologies in advance but I cannot attend, have a good one. Ambix (talk) 08:49, 16 June 2009 (UTC)[reply]

Not sure, may be lurking there. I surely invite everyone to have a look at the beginnings of the new User:CheMoBot, implementing colours for clarity, and more. --Dirk Beetstra T C 09:14, 16 June 2009 (UTC)[reply]


/23 June 2009

1530 UTC (1130 EDT, 1630 BST, 1730 CEST)

/30 June 2009

I'm around if anyone has any questions. We have some news on the RSC ontologies, we've also just changed the assessment scheme. As ever, all comments welcome. Physchim62 (talk) 14:08, 30 June 2009 (UTC)[reply]

/7 July 2009

I'll be away this Tuesday - so please can you email me any logs? Cheers, Walkerma (talk) 15:13, 4 July 2009 (UTC)[reply]

I might not be able to make it either, with an imminent death in the family and a huge pile of RL work to do. I'll keep the IRC client open to get a log. Physchim62 (talk) 12:55, 7 July 2009 (UTC)[reply]

/14 July 2009

Is anyone around on Tuesday 14th? I will log in at 1600h UTC (or earlier if someone emails me to do so). FYI:The RSC chap can't talk with us about reaction ontologies until July 28th or August 4th. Walkerma (talk) 06:20, 14 July 2009 (UTC)[reply]

/28 July 2009

I'm suggesting we meet at 1530h UTC (1630h British Summer Time, 1130am US Eastern Daylight Time, 17h30 Central European Summer Time) Meeting with Colin Batchelor from RSC to discuss reaction ontologies - how should we best use these within WP, and what direction future work should take? Please join us! Walkerma (talk) 15:50, 27 July 2009 (UTC)[reply]

/11 August 2009

Can you send me a log? Sorry I'm swamped with work right now, but I'll look into this more after the weekend. Cheers, Walkerma (talk) 20:57, 11 August 2009 (UTC)[reply]
Well, we did not have a meeting, so I am postponing that to next week. There was some talk with an international guest, maybe worth to put it here, so I make the placeholder. --Dirk Beetstra T C 21:13, 11 August 2009 (UTC)[reply]

/18 August 2009

  • Heh. Well. I'll try to be here, but I'd like people to have a look at Wikipedia:Bots/Requests for approval/CheMoBot 2, so we can discuss it one of these days (this week, or the next). I have started to write the request, but I am not sure if it is finished. We may want to have some discussion before I really transclude the request (i.e., really make the request official), and maybe some others can try to screw the bot (yes, all of you, please, test it, edit User:Beetstra/Propane, don't worry, you can't break anything. And if you manage to break it, then that is exactly what I want, that is the only way to find out if I missed things. Do it .. DO CLICK HERE). --Dirk Beetstra T C 19:35, 3 August 2009 (UTC)[reply]
  • The bot request has in the meantime been transcluded after some testing. --Dirk Beetstra T C 12:10, 9 August 2009 (UTC)[reply]
  • Pff .. I had a productive day. I was thinking, that I could do some 'automated checking' if a page was available on CommonChemistry. Part of the bot that does the above checking, now does that automatically. It finds the CASNo, loads the page from CommonChemistry.org, and sees if the pagename is one of the synonyms in the list. If so, it auto-updates the appropriate index to add the last revid of the page. It adds a comment to show where it got the data (example: diff,it stores them off-wiki, so I can copy them onto a wikipage for checking. They still need checking, but it might speed up the process as these are the ones that get edited on-wiki, and this sorts out the ones which are not on CC, which may be fine, and which may be problematic. If the auto-revid is wrong (it can't check the images), then please make sure to remove the entry from the index ánd remove the CASNo from the infobox (if the latter is not done, the bot will keep re-adding it!). --Dirk Beetstra T C 21:24, 3 August 2009 (UTC)[reply]
I'm at the ACS national meeting at the moment, with very sporadic internet access. I also have an important meeting happening at 16:30 UTC, so it'll be hard to get on IRC. ChemSpiderman (and maybe others?) are also here at the ACS conference. Next week I'll be arriving in Buenos Aires for Wikimania - who knows if I'll be able to get internet! So go ahead and by all means meet without me - but please let me know what you decide. Meanwhile - my grant is in, Version 0.7 is completed, so I should be back on WP again soon. Cheers, Walkerma (talk) 06:07, 18 August 2009 (UTC)[reply]

/1 September 2009

I can give a Wikimania report on IRC (I'll write something up, too), and perhaps Dirk can update us on the bot? How about meeting at 1530h UTC? Walkerma (talk) 16:08, 31 August 2009 (UTC)[reply]

  • Sounds fine. Looking forward to hear about Wikimania. I have something to do late this afternoon, but this should be late enough. Ping me! --Dirk Beetstra T C 08:42, 1 September 2009 (UTC)[reply]
    Would suggest that people have a look at Wikipedia:Bots/Requests for approval/CheMoBot 2, which gives a pretty good explanation of what the bot will do from now (approval pending ..), tests can be performed on User:Beetstra/Propane (yes, try it!). --Dirk Beetstra T C 08:57, 1 September 2009 (UTC)[reply]
  • Yep, I would love to hear about Wikimania. If there's time, I'll update on current validation efforts, which Beetstra and I have been working on over the summer (honest!). 1530 UTC = 1730 CEST. Physchim62 (talk) 12:15, 1 September 2009 (UTC)[reply]

/8 September 2009

When should we meet? Do you want to meet at 1530h UTC, or 1600h? I can do either time, just let me know what is better. Walkerma (talk) 20:15, 7 September 2009 (UTC)[reply]

(Beetstra) Proposing some points:

Hope to see you all there! --Dirk Beetstra T C 06:23, 3 September 2009 (UTC)[reply]

  • Since Friday morning (UTC), the bot is editing in mainspace, tagging articles (for mainspace edits see list of mainspace contribs). Until now 2 quirks which needed some re-programming, and it also spotted the first page with a problem. --Dirk Beetstra T C 20:39, 5 September 2009 (UTC)[reply]
  • For my part, I've been going through the "SAA" list, that is "sugars and amino acids", which pose many of the most serious problems. It's only about 300 entries long, but it's fairly slow work: I'm about halfway through C6 at the minute, it will take me at least another week to finish it.
  • I can prepare a list of "missing WP articles" once Beetstra has completed his run through the drugboxes. My list won't be 100% complete — for technical reasons that I can explain if anyone is interested – but my guess is that it would have 2–3 thousand entries on it all the same… Physchim62 (talk) 23:32, 7 September 2009 (UTC)[reply]


/22 September 2009

I'd like for us to resolve the problem articles listed at

User:Beetstra/CASFoundCorrect
. I've looked at some entries, and in many cases I'm not sure how best to proceed. I'd really like to hear Physchim62's conclusions on the amino acids and carbohydrates, which would resolve many but not all problems. Some representative examples of other problems:

  • But-1-yne)? There are others like this such as Benzoin
    , where it's unclear to me why it's a problem. Or did I miss something?
  • Malonyl-CoA: It looks as if CASCC botched the drawing of the malonyl group. I'd suggest that if two of us agree there is a problem with the CASCC entry, we compile a list of these to send to CAS.
  • Toxaphene is a mixture of all sorts of things. Can we validate a structure which - though quite generic - only represents a subsection of the mixture?
  • Citronellal: We have one enantiomer, presumably the natural form of this. CAS gives the racemate. On the Excel files we'd have just listed it as a 1 or a 2, and left it unvalidated. Should we continue to do the same?
  • Dioctyl_adipate vs. Bis(2-ethylhexyl) adipate (DEHA): - our article indicates that "DEHA is sometimes incorrectly called dioctyl adipate." CASCC includes dioctyl adipate as a synonym for DEHA - it's a bad, misleading one, but it's there anyway.

I'm going to be busy till noon USEDT, so I'd like to propose we start at 1600h UTC. Walkerma (talk) 05:53, 20 September 2009 (UTC)[reply]

Summary

Beetstra's validation work is going on rapidly, and soon all of the nonproblematic compounds should have been validated and listed. Physchim62 proposed a policy for handling "SAAs" (sugars and amino acids) which is straightforward, and this was approved by those present on IRC. This policy will be written up for our manual of style, and will be used to guide the validation work on at least some of the problem compounds listed. For mixtures such as heparin, many things remain unresolved, though it was agreed that if a representative Markush or other structure is believed correct but unvalidatable (is that a word?), we move it from the Chembox into the text body to allow the validation to be done - at least until we have a workable system for validating some chembox parameters and leaving others unvalidated. Some of the other problem types (listed above) still need to be addressed, at another meeting.

/6 October 2009

I suggest 1600h start. User:ChemSpiderMan will be around, so I propose we discuss our ongoing collaboration with ChemSpider. Agenda items should include (please add any others you consider important):

  1. The Chembox generation tool on ChemSpider
  2. How best to use ChemSpider to assist us in our validation work - and can WP help ChemSpider content to be validated?

Talk to you on Tuesday, Walkerma (talk) 05:01, 4 October 2009 (UTC)[reply]

/3 November 2009

I'm planning on being around on November 3rd at 1600h UTC, though I have been horribly inactive on WP of late. Will anyone else be around? Walkerma (talk) 06:06, 3 November 2009 (UTC)[reply]

/17 November 2009

Could we have a chat on November 17th at 1600h UTC, just to find out where we are? Let us know here if you think a later time is better for you. Cheers, Walkerma (talk) 21:39, 16 November 2009 (UTC)[reply]

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