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- 1 Serogroup
- 2 Category:Wikipedian chemist
- 3 Image copyright problem with Image:2bix.jpg
- 4 Let me know, if you need help
- 5 Suppliers 'dispute'
- 6 Chemical publishing
- 7 special:chemicalsources
- 8 Re: thanks for references
- 9 Open Science
- 10 Your article
- 11 Hello after MKM
- 12 CSA Trust
- 13 CrystalEye
- 14 Workshop
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Hi. This article doesn't really say anything. Are you planning on expanding it with information on exactly what 'Serogroup' is? Otherwise it might be deleted.
This was done as part of a class activity. We found many references to 'serogroup' in Wikipedia and elsewhere but no explanation. I couldn't even find it in a dictionary on the Web. So this stub is really a call for help from anyone who can give even a semi-authoritative description.
Petermr 13:16, 25 February 2006 (UTC)
Hi Peter, on the WikiProject page you have linked yourself to User:Peter Murray-Rust, not Petermr. As for the Category, I am not convinced we need it. We do not have a userbox that puts people into this category, so I doubt it will catch on. I think you should have discussed this on the talk page of the WikiProject before creating it. Regards, Brian Duke 12:12, 2 April 2006 (UTC)
Peter, lets keep the discussion here in one place. Your talk page is now on my watch list (suggestion - change your preferences so everything you edit automatically goes on your watchlist). Being the other side of the world, my message to you last night was the last thing I did before going to bed. I think the place to discuss the category is Wikipedia talk:WikiProject Chemistry. I suppose some people might want it as there are several sub-projects and it would list everybody. WP is trying to move from lists to categories, but some people do not like the Wikipedian categories - not central to writing an encyclpedia.
Take a look at Wikipedia:Using Jmol to display molecular models. That is right up your street. It is my current project but I am having to rely on others who have root access to various wikis. Progress is slow. Nico, who is running the new Jmol wiki, got it working in a fashion on the Folding@Home wiki, but I have tried to repeat this in the CompChem wiki with no success. The last I heard from Nico, he was going to develop his approach further yesterday on the Jmol wiki. I hope he is successfull. WP needs Jmol on the chemicals pages. Brian, --Bduke 21:33, 2 April 2006 (UTC)
Image copyright problem with Image:2bix.jpg
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Let me know, if you need help
Peter, good to have you here, too. Let me know if you need any help with Wikipedia since I have already edited some things;-) Best, Joerg JKW 22:51, 9 May 2006 (UTC)
- O.k. and do not forget to sign you messages with the four tildes;-) I am pretty sure you can work the copyright thing out. Otherwise ask just students if they can create some new images or use talk pages on a higher level. JKW 23:04, 9 May 2006 (UTC)
Dear Peter, I still have the 'dispute' about the chemical suppliers in the back of my head. What do you think about the following suggestion (and the accompanying .. 'yes, but how?'): Would it be an idea to make a page comparable to the ISBN search engine (e.g. Special:Booksources&isbn=0002570122) working on the CAS number. Such a page could contain an infinite list with suppliers, making the data easily accessible, as well as (and probably more important) searches into many other search-engines. As announced, if the answer to this question is 'yes!' .. how are special pages made (I saw you are into cheminformatics .. hope I am asking the right person)? --Dirk Beetstra 07:23, 6 June 2006 (UTC)
The correct machine is at Special:Booksources, sometimes these links don't work (may be depending on browser). But that is the type of page I mean.
I read something about the InChI, seems like a good plan. But to implement it maybe less functional (YET!!). I mean, the functionality that I am thinking about is a page, that links into as many external sources as possible, based on one searchterm. E.g. with CAS-number, it is possible to make search-URL's into many suppliers, and a lot of other web-based engines (people really using the link will maybe have to pay when they want to get to the result, but that happens also with some results on the ISBN site). I don't have any objection against the use of InChI (just implement it in the chembox, and make sure that it shows advantages).
But .. the one does not exclude the other!! People can decide whether to search via InChI or CAS, and see for themselves which gives the best result.
It may be worth a thought, it would give the functionality that I (and some others) like to see, does not give an unfair advantage to certain suppliers (no bias from the writers side, suppliers that don't support deeplinking get 'punished'), does not give problems in linking to the wrong isomer when we choose to link to the wrong side of the ocean .. etc. etc. --Dirk Beetstra 21:39, 6 June 2006 (UTC)
P.S. you can answer here, I am watching this page for now. --Dirk Beetstra 21:39, 6 June 2006 (UTC)
I understand this ... there are, however, already tools that search for CAS (remember there are > 10,000,000 compounds so there has to be a significant database and this is beyond Wikipedia). The purpose of WP, IMO, is to gather the most important information and add the sources. CAS is one source but I suspect that relatively few WP entries have actually used a paid CAS search, while I assume that many referenced ISBNs have actually been read by the WP editors.
and, as I have said, I wish to promote InChI...
P. Petermr 23:00, 6 June 2006 (UTC)
¡Hola! You are right, there is a difference. Hmm .. I need to think more and better about this.
About InChI, my opinion, get it added it to the chembox template (or whichever template), implement it on the pages, and try to add functionality, within WP, but also to external sources (as in above example, linking to as many suppliers as possible). If people see it in work, you get your promotion, otherwise it is nothing more than a CAS number, or a poiling point .... --Dirk Beetstra 23:20, 6 June 2006 (UTC)
Another point is that PubChem - which is by far the largest public collection of molecular information - uses InChI and does not use CAS (deliberately, because of copyright concerns). PubChem is rapidly becoming the communal aggregation of chemical information this is one of a few verys sites I would publicly point to on a large-scale basis. Note also that PubChem welcomes contributions (unlike many other sources) and if WP sends a list of WP entries to PubChem I am almost certain they will be delighted to add these links and to publicise that WP has done this. PubChem's sole purpose is to collect and disseminate information, unlike almost all other organisations we have discussed. They are complemented by ChEBI and NIST - these are highly quality, but have many fewer entries.
Petermr 06:04, 7 June 2006 (UTC)
Yesyes, I now get the point of the advantages of the InChI, are you being paid by the number? ;-)
Still, I believe that we could use a centralised way that links directly into as many external sources as possible (suppliers, databases, &c). Even if people have to pay to get into some/most of those databases, the people that have payed, and those that are in a good IP-range (unis, companies) can get in anyway. And free databases can be grouped in front of the pay(-per-view)-databases. For now, I would do that with both InChI ánd CAS, if CAS starts nagging WP, these links are gone fast enough. --Dirk Beetstra 07:30, 7 June 2006 (UTC)
I get paid as much for each InChI as for WP entries...
PubChem already links into as many external sources as are required. And although I am not a WP expert, I got the sense from the correspondence. that it is important to avoid WP becoming a central supplier of *links*
Petermr 17:22, 7 June 2006 (UTC)
The ISBN searchpage is a centralised page to link to 'the outside world'. I think it is meant there that not every page should be flooded with external links (which may/will be biased), but that it is then better to have a central page, that links to as many as possible links based on a single input. And, if only PubChem is linked from the InChI (on every page), that would also be biased (however good PubChem is, what if I want to go to a supplier, do I really have to go through PubChem then .. hmmm .. PubChem might get money then for every link that goes through their page (now or in the future) .. so WP would then sponsor such an institution). --Dirk Beetstra 17:31, 7 June 2006 (UTC)
I am not quite sure where this discussion is going. Firstly it is between just 2 people and I suspect is neither informing or being informed by many others. I obviously haven't got across the main arguments:
- suppliers supply chemicals for money. Some also supply information, but this is not their primary purpose. This information is neither verified nor universally correct.
- chemical information aggregators such as Chmoogle or ChemExper aggregate chemical information on an unpredictable business model (i.e. this may be terminated at any time, or changed to a pay-per-view). As far as I know they do not check information.
- PubChem is part of the US government's funding of public research, in a similar manner to the UK research councils or the Wellcome Trust. All information is free and they are funded to make it freely available. They are part of the US NCBI (National Centre of Biotechnology) which, for example, publishers MEDLINE, a public collection of abstracts in the biomoedical field. Medline is FREE, OPEN ACCESS, infinitely accessible and verified. NIST is another arm of the US goverment, like the Environmental Protection Agency, Food and Drug Administration and many others. They are required (with some minor qualifications) to make all their works copyright free. They are completely non-profit, open and completely different from the other suppliers of information.
Finally I see WP as a supplier of information, not a catalog of suppliers of goods. I am relatively new to WP, but I get the sense that this is a mainstream view. You write: " what if I want to go to a supplier, do I really have to go through PubChem then .. hmmm .. PubChem might get money then for every link that goes through their page (now or in the future) .. so WP would then sponsor such an institution). "
- Pubchem is NOT a supplier.
- It does not get money and never will get money (except from the US goverment for its core research - they are a research organisation; I am collaborating with them in medical research).
I hope this makes it clearer. It is important that the role of PubChem, Reseach Councils, Royal Society, National Science Foundation. etc. are recognised as resrach institutions without a commercial mandate. For example I have been funded to calculate the properties of 250,000 molecules provided by the National Cancer Institute. I have posted the results in DSpace at the University of Cambridge where they are freely available as Open Access for all time. The information is freely available for anyone, including WP editors. It is unbiased (in your terminology) and has been published in peer-reviewed scientific journals. This is entirely different from pointing to a commercial supplier of goods.
It hope we are moving to some convergence - I have a heavy program of student marking in the next few days and am limited in what can write.
Petermr 18:44, 7 June 2006 (UTC)
I don't think we are converging, don't mind. I will try a bit and see what I can come up with. See you around, thanks anyway. Good luck with the student marking! --Dirk Beetstra 18:50, 7 June 2006 (UTC)
I'm a chemist trying to get together thoughts on how chemical publishing may be going in the future, and I can't think of a better person to ask than your good self! I'm approaching it from two directions - one as a chemist who is keeping an eye on things like InChI and CML, and another as a Wikipedian interested in chemical information and assessment of articles. I'm also fresh from discussions on validation and article citations at Wikimania last weekend.
- how exciting! I have been away for ca 10 days so don't take this as lack of interest! Your ideas are spot-on! Petermr 14:28, 20 August 2006 (UTC)
It seems that the best way to approach this is to consider what an ideal chemistry journal would look like given current (or soon-to-be-current) technology. I expect it would be easily updated and corrected, with a fast dynamic peer review process (maybe ongoing, as people run things in the lab) and interlinking of the sort any Wikipedian would be proud of. You should be able to draw in a structure with ChemDraw and search - maybe this is what WWMM will do. You should be able to link to a chemical compound by its structure (as its InChI?) rather than its name. You should be able to see the drawing on a page on a site like Wikipedia or JACS, but behind the image would be the machine-searchable representation of that structure. Would it use CML, and if so, how would that be handled? You should be able to fully interlink citations, perhaps using something along the lines of the DOI and possibly m:Wikicat.
- Yes - this is all abolutely right, except that we are hoping to move away from ChemDraw as it is (a) not-semantic (b) proprietary and therefore non-extensible.Petermr 14:28, 20 August 2006 (UTC)
Of course any new style of journal would have to deal with some of the established features of traditional journals. How would you deal with authorship/attribution, so that an author can receive proper credit for their original research (for tenure & promotion, etc.)? This might be difficult if a paper becomes more fragmented, wiki-style, but it could be done. What would be the new system for peer review, and how would credentials be handled? How could a completely new style of journal establish itself and gain credibility/respect of the chemical community?
- several publishers are starting to think along these lines. There is exceitement about both social publishing (e.g. Wikipedia) and the new technology. Of course they interact. Henry and I have been promoting the "Datument" idea - combined document and data.
So far I've been disappointed at what I've seen from the publishers - we essentially have paper journals scanned onto the web, with subscription requirements and little metadata available. The ACS Chemical Biology wiki is very hard to use, and seems more like a blog than a wiki. However, I think some in the publishing community are very open to ideas right now, and I'd like to try and develop a viable model. I'm not too strong with the heavy technical stuff - anything beyond simple HTML and BASIC tends to be beyond me, so please keep it simple! I'd love to hear some of your ideas on this, many thanks, Walkerma 00:56, 11 August 2006 (UTC)
- There are things I can't say in public, but I am hoping to present much of this at the Sept meeting of the ACS in San Francisco. Essentially we want to show that a mixture of Blue Obelisk and Bioclipse has to be the way forward. As we are a volunteer community I am sure that your contributions - whether technical, content, evangelism, etc. would be highly welcomed.Petermr 14:28, 20 August 2006 (UTC)
If you want to do something in a non-WP context (or work towards tools which can be used in WP - which we really need) suggest you mail me at pm286 atsign cam dot ac dot uk
Hi! I just decided to spam some people directly, who I know are very active on chemicals. There is now a wiki running on http://chemistry.poolspares.com (a site created by Nickj from the wikimedia IRC channel, the site will be taken offline again in a couple of weeks), where I have now hosted a small wikipedia. It runs two extensions I have written to the wikipedia software, a special page (for chemical sources, see also wikipedia:chemical sources and a chemform tag (for easy input of chemical formulae). Could you have a look, and comment on it (if useful I would like to try to let Tim or Brion enable it on wikipedia, though I feel some resistance there). Cheers! --Dirk Beetstra T C 17:52, 26 October 2006 (UTC)
Re: thanks for references
- Thanks for showing me how to do references. Petermr 19:59, 31 October 2006 (UTC)
No problem. I was reading your blog post here (I have a habit of reading Wikipedia-related blog posts just to get an idea of Wikipdia's reputation) and thought I'd check the article to see if anything else needed doing. I thought the post was very good, by the way; obviously I know how to edit Wikipedia myself, but I think it will be of use to first-time contributors – Gurch 20:08, 31 October 2006 (UTC)
- Thanks for your reply (how do I quote it here if I want to - as you quoted mine?). Yes, A blog has many of the aspects that are useful for a communal discussion on a new topic when coupled with a WP aricle. I actually run the Open Data mailing list and am trying to activate it by using WP as a catalyst to define our term. (There is no shortage of usage of "Open Data" now, so it's not a research project but an exercise in communal scholarship. I need additional input from the community.
Petermr 08:25, 1 November 2006 (UTC)
Unfortunately there's no quick shortcut for quoting messages. Many people just reply to messages without quoting, but I find that makes the discussion hard to follow as it's split into two. I usually include the original message in my reply, by copying and pasting it into the edit window, and then formatting it like this:
'''''(name) wrote:''''' :''(message)''
Now that Open Data exists and is linked from other articles, it will inevitably be edited at some point, though how much attention articles will recieve is difficult to predict. If you haven't already done so, I suggest you add the page to your watchlist (click the "watch" tab at the top of the page); that way you can quickly see if there have been any changes – Gurch 11:23, 1 November 2006 (UTC)
I see that you redirected "Open Science" to Open Access. My own feeling is that they are quite distinct and I am interested in creating material for Opwn Science. However I wanted to check whether they was a reason for this before.
But I am new to the rules of redirection :-) Petermr 08:19, 1 November 2006 (UTC)
- There simply was nothing at the open science page. If you have something to put there, please go ahead. AaronSw 14:57, 1 November 2006 (UTC)
Oops. Sorry about the spelling of your name, Peter, Yours, Brian. --Bduke 23:08, 15 November 2006 (UTC)
Hello after MKM
nice to meet you again here – hope you had a safe trip back home :-) Just for fun, I searched Wikipedia for you, and, for the sake of completeness, I added a reference to your homepage and blog to the article about you – until I realised that you also contribute to Wikipedia. So, if you should not like these links to be listed there, just let me know, or remove them again.
BTW, have you seen the OMDoc article I once wrote? Maybe we should eventually add a comment about extending OMDoc towards chemistry there…
Best, Langec 18:30, 1 July 2007 (UTC)
Hi Peter, please take a look at this article which has just been written and now put up for deletion. Regards, Brian Duke. --Bduke 11:27, 19 August 2007 (UTC)
Thanks for telling me about CrystalEye, it looks very useful!
Note that CrystalEye is OpenData so any or all of it could be used in WP without asking permission Petermr 23:44, 6 December 2007 (UTC)
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