Hello, The chemistds! Welcome to Wikipedia! Thank you for your contributions to this free encyclopedia. If you decide that you need help, check out Getting Help below, ask me on my talk page, or place {{helpme}} on your talk page and ask your question there. Please remember to sign your name on talk pages by using four tildes (~~~~) or by clicking if shown; this will automatically produce your username and the date. Finally, please do your best to always fill in the edit summary field. Below are some useful links to facilitate your involvement. Happy editing! Dirk BeetstraTC11:35, 4 November 2010 (UTC)[reply]
I'm an organic chemist by training, having specialised in radical chemistry and asymmetric methodology.
I currently work for a chemistry publisher and as well as working on analytical databases I work on ChemSpider. I also curate Chemspider in my own time.
Wikipedia activities
At the moment this is probably mainly going to be adding info into ChemBoxes, ChemSpider Ids, Pubchem Ids, SMILES strings and InChI strings. I also have an interest in flagging and correcting records with incorrectly drawn structures - probably mainly images with incomplete stereochemical configurations.
I'm sure I'll dip into other topics as well.
InChI
Hi! Thank you for the InChIs and ChemSpiderIDs you added to drugboxes. Please be careful when copying them from PubChem – the PubChem entries read
InChI: InChI= ...
which easily leads to editing mistakes like this, ie.,
I've noticed this before and caught it sometimes - the info comes from the ChemSpider Wikibox output, I can get the developers to change this.
However, I wonder if there is reason to examine the way that InChIs are handled in these boxes. The "InChI=1..." is an integral part of the InChI itself - if you remove the "InChI=" part it will not be understood by the current InChI software/resolvers. Even the format that it is displayed in in the Editing view "InChI = 1..." is not handelled. I understand that the wiki box displays the InChI in the correct format, but I would suggest that it makes more sense to store the information in it's original usable state, rather than stripping out information then re-inserting it upon display.
Do you have any thoughts on this, or any suggestions of where it might be best to discuss this further?
Good point. While the {{drugbox}} currently doesn't do anything at all with the InChI/InChIKey parameters, I think they should be in the same format as with the {{chembox}} for possible future uses. The best place for asking about the reasons why the chembox is programmed like this should be Wikipedia talk:Chemical infobox. --ἀνυπόδητος (talk) 16:25, 27 November 2010 (UTC)[reply]
Thanks for uploading File:1,4-dibromobenzene.png. You don't seem to have indicated the license status of the image. Wikipedia uses a set of image copyright tags to indicate this information.
To add a tag to the image, select the appropriate tag from this list, click on this link, then click "Edit this page" and add the tag to the image's description. If there doesn't seem to be a suitable tag, the image is probably not appropriate for use on Wikipedia. For help in choosing the correct tag, or for any other questions, leave a message on Wikipedia:Media copyright questions. Thank you for your cooperation. --ImageTaggingBot (talk) 00:05, 25 November 2011 (UTC)[reply]
Calcium polystyrene sulfonate
Hi! I've just found another ChemSpider entry that is a polymer but shows a monomeric formula: [1]. The feedback tool on ChemSpider somehow doesn't work for me, so I'm telling you here. Cheers! ἀνυπόδητος (talk) 09:52, 25 March 2012 (UTC)[reply]
Thanks, I've ammended the record in question. I don't know why the feedback form wouldn't work. You can always email the chemspider inbox and notify us that way. --The chemistds (talk) 22:31, 26 March 2012 (UTC)[reply]
…see interspersed italic comments, and final proposal at [2]. Written at the time, and just discovered as not posted. Cheers, and respect your involvement. Le Prof Leprof 7272 (talk) 20:19, 29 May 2014 (UTC)[reply]
Hi chemistds. I noticed that you moved benzoyl-CoA to benzoyl-S-Coenzyme A. While I don't have any real preference between those two styles of naming, I think Wikipedia should be consistent across related articles. Currently all the articles in Category:Thioesters of coenzyme A are named in the style of "benzoyl-CoA", so "benzoyl-S-Coenzyme A" is now an outlier. I would suggest starting a discussion to rename the whole set, or otherwise to simply return the moved article back to benzoyl-CoA. Your thoughts? -- Ed (Edgar181) 13:05, 9 October 2014 (UTC)[reply]
Hi Edgar181, I hadn't really noticed that the abbreviation was used on so many titles. I think that it might be a good idea to expand CoA in the other records as if my argument is accepted for this article - it holds true for the rest. I'll try and start a discussion this weekend --The chemistds (talk) 09:39, 10 October 2014 (UTC)[reply]
In the meantime, please revert your renaming, which is to an obscure terminology. I tried to this morning but messed it up. Thanks, --Smokefoot (talk) 12:28, 31 October 2014 (UTC)[reply]
The chemistry project is doing well just to have a decent source for many chemistry articles, so I am skeptical of the advisability of adding a "one source" tag, which might be an idea suited for another project, not chemistry. The tagging could give readers the impression that an article is badly flawed, which is usually untrue. Our articles are reasonably well curated and much of the content is based on generic general or organic chemistry knowledge. If the lack of citations concerns you, then your time might be better spent consulting and then citing gen chem or organic textbook. Finally, if you really think that this one-source tagging is a good idea, you might raise it at the Chemistry project and get some consensus and advice from other editors. Thanks, --Smokefoot (talk) 12:28, 31 October 2014 (UTC)[reply]
Implicit notability of small molecules
The way I see it, small molecules are notable by default by their mere existence. I don't believe they need humans to provide references to establish notability. Moreover, I believe this applies even to molecules that exist for mere fractions of a second, such as at super cold temperatures Of course you will disagree. --IO Device (talk) 20:14, 29 June 2015 (UTC)[reply]
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Hey David, not sure how to use this page, but you just replaced my SMILES for bombesin with one that has cis/trans stereo across the terminal C=NH of arginine. InChI ignores it because it's in a tautomer, and maybe several other toolkits will also, but it should not be present. Separate issue - I've been deleting all non-standard InChIs as they are a legacy of the time before standard InChI and essentially meaningless without knowing the non-standard options, and I thought that was the consensus - am I wrong? Baoilleach (talk) 08:50, 3 August 2016 (UTC)[reply]
Hi Noel, I just saw the message that you left - as I've not been on Wikipedia much the last few weeks. When I update Chemboxes, I just use a number of fields from the ChemSpider record (from the wikibox tool on the record). I tend to replace the SMILES strings in many cases because it is not easy to quickly determine if the SMILES agrees with the structure. In this case as you point out the toolkit that generated the SMILES has captured an alternative tautomer. With regards to non-standard InChIs - I tend to add them as they don't do any harm and in some cases allow the capture of useful structural information. Eg. Grignard reagents - in the non-standard InChI you can have the reconnected layer which will preserve the covalent bonds between the Mg, Br and organic component, rather than as Mg2+, Br- and carbanion. I hope that is a helpful explaination. --The chemistds (talk) 13:32, 31 August 2016 (UTC)[reply]
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I saw you have added InChI and -Keys to drugbox. However, these are already present as |StdInChI= and |StdInChIKey= (with minor changes for being standard, e.g. by the "1S/..." opening. {{Drugbox}} does not use or know |InChI= and |InChIKey=. That is why I removed them (messages 'uknown parameter used'). Anything unclear? -DePiep (talk) 18:00, 23 November 2016 (UTC)[reply]
InChI in the Drugbox
As you might have noticed, in Nandrolone cyclotate I have removed the InChI/Key values you had inserted. As this my be rude, I'll give some background. In {{Drugbox}} we have parameters |StdInChI/Key=. Of course, these are for the standard (1S/...) InChI set. Other, non-canonical InChIs options we do not present. This is mainly because they do not add so much extra. Also, the parameters |InChI/Key= are not available. -DePiep (talk) 21:37, 28 November 2016 (UTC)[reply]
Systematic reviews are basic building blocks of evidence-based medicine, surveys of existing literature devoted typically to a definite question that aim to bring out scientific conclusions. They are principled in a way Wikipedians can appreciate, taking a critical view of their sources.
PRISMA flow diagram for a systematic review
Ben Goldacre in 2014 wrote (link below) "[...] : the "information architecture" of evidence based medicine (if you can tolerate such a phrase) is a chaotic, ad hoc, poorly connected ecosystem of legacy projects. In some respects the whole show is still run on paper, like it's the 19th century." Is there a Wikidatan in the house? Wouldn't some machine-readable content that is structured data help?
Most likely it would, but the arcana of systematic reviews and how they add value would still need formal handling. The PRISMA standard dates from 2009, with an update started in 2018. The concerns there include the corpus of papers used: how selected and filtered? Now that Wikidata has a 20.9 million item bibliography, one can at least pose questions. Each systematic review is a tagging opportunity for a bibliography. Could that tagging be reproduced by a query, in principle? Can it even be second-guessed by a query (i.e. simulated by a protocol which translates into SPARQL)? Homing in on the arcana, do the inclusion and filtering criteria translate into metadata? At some level they must, but are these metadata explicitly expressed in the articles themselves? The answer to that is surely "no" at this point, but can TDM find them? Again "no", right now. Automatic identification doesn't just happen.
Actually these questions lack originality. It should be noted though that WP:MEDRS, the reliable sources guideline used here for health information, hinges on the assumption that the usefully systematic reviews of biomedical literature can be recognised. Its nutshell summary, normally the part of a guideline with the highest density of common sense, allows literature reviews in general validity, but WP:MEDASSESS qualifies that indication heavily. Process wonkery about systematic reviews definitely has merit.
The term Applications Programming Interface or API is 50 years old, and refers to a type of software library as well as the interface to its use. While a compiler is what you need to get high-level code executed by a mainframe, an API out in the cloud somewhere offers a chance to perform operations on a remote server. For example, the multifarious bots active on Wikipedia have owners who exploit the MediaWiki API.
APIs (called RESTful) that allow for the GET HTTP request are fundamental for what could colloquially be called "moving data around the Web"; from which Wikidata benefits 24/7. So the fact that the Wikidata SPARQL endpoint at query.wikidata.org has a RESTful API means that, in lay terms, Wikidata content can be GOT from it. The programming involved, besides the SPARQL language, could be in Python, younger by a few months than the Web.
Magic words, such as occur in fantasy stories, are wishful (rather than RESTful) solutions to gaining access. You may need to be a linguist to enter Ali Baba's cave or the western door of Moria (French in the case of "Open Sesame", in fact, and Sindarin being the respective languages). Talking to an API requires a bigger toolkit, which first means you have to recognise the tools in terms of what they can do. On the way to the wikt:impactful or polymathic modern handling of facts, one must perhaps take only tactful notice of tech's endemic problem with documentation, and absorb the insightful point that the code in APIs does articulate the customary procedures now in place on the cloud for getting information. As Owl explained to Winnie-the-Pooh, it tells you The Thing to Do.
Working With Wikibase From Go, Digital Flapjack blogpost 26 November 2018, Michael Dales, developer for ScienceSource using golang, with a software engineer's view on Wikibase and the MediaWiki API
Talk of cloud computing draws a veil over hardware, but also, less obviously but more importantly, obscures such intellectual distinction as matters most in its use. Wikidata begins to allow tasks to be undertaken that were out of easy reach. The facility should not be taken as the real point.
Coming in from another angle, the "executive decision" is more glamorous; but the "administrative decision" should be admired for its command of facts. Think of the attitudes ad fontes, so prevalent here on Wikipedia as "can you give me a source for that?", and being prepared to deal with complicated analyses into specified subcases. Impatience expressed as a disdain for such pedantry is quite understandable, but neither dirty data nor false dichotomies are at all good to have around.
Issue 13 and Issue 21, respectively on WP:MEDRS and systematic reviews, talk about biomedical literature and computing tasks that would be of higher quality if they could be made more "administrative". For example, it is desirable that the decisions involved be consistent, explicable, and reproducible by non-experts from specified inputs.
What gets clouded out is not impossibly hard to understand. You do need to put together the insights of functional programming, which is a doctrinaire and purist but clearcut approach, with the practicality of office software. Loopless computation can be conceived of as a seamless forward march of spreadsheet columns, each determined by the content of previous ones. Very well: to do a backward audit, when now we are talking about Wikidata, we rely on integrity of data and its scrupulous sourcing: and clearcut case analyses. The MEDRS example forces attention on purge attempts such as Beall's list.
Two dozen issues, and this may be the last, a valediction at least for a while.
It's time for a two-year summation of ContentMine projects involving TDM (text and data mining).
Wikidata and now Structured Data on Commons represent the overlap of Wikimedia with the Semantic Web. This common ground is helping to convert an engineering concept into a movement. TDM generally has little enough connection with the Semantic Web, being instead in the orbit of machine learning which is no respecter of the semantic. Don't break a taboo by asking bots "and what do you mean by that?"
The ScienceSource project innovates in TDM, by storing its text mining results in a Wikibase site. It strives for compliance of its fact mining, on drug treatments of diseases, with an automated form of the relevant Wikipedia referencing guideline MEDRS. Where WikiFactMine set up an API for reuse of its results, ScienceSource has a SPARQL query service, with look-and-feel exactly that of Wikidata's at query.wikidata.org. It also now has a custom front end, and its content can be federated, in other words used in data mashups: it is one of over 50 sites that can federate with Wikidata.
The human factor comes to bear through the front end, which combines a link to the HTML version of a paper, text mining results organised in drug and disease columns, and a SPARQL display of nearby drug and disease terms. Much software to develop and explain, so little time! Rather than telling the tale, Facto Post brings you ScienceSource links, starting from the how-to video, lower right.
Please be aware that this is a research project in development, and may have outages for planned maintenance. That will apply for the next few days, at least. The ScienceSource wiki main page carries information on practical matters. Email is not enabled on the wiki: use site mail here to Charles Matthews in case of difficulty, or if you need support. Further explanatory videos will be put into commons:Category:ContentMine videos.
It was synthesized far earlier than 1989. it was used by the navy and others in the US as a possible rocket propellant as early as 1951. The source is a book called Ignition! By John D. Clark, page 36. ChemTrades (talk) 20:53, 10 August 2019 (UTC)[reply]
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