User talk:The chemistds

From WikiProjectMed
Jump to navigation Jump to search
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 Beetstra T C 11:35, 4 November 2010 (UTC)[reply]
Getting started
Getting help
Policies and guidelines
The community
Writing articles
Miscellaneous

General Info

Background

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.,

InChI = InChI = ...

instead of

InChI = ...

I just fixed Mozavaptan, could you take care of your other edits? Thanks, ἀνυπόδητος (talk) 11:43, 27 November 2010 (UTC)[reply]


Hi ἀνυπόδητος,
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?
In the meantime, I'll go back and find the examples of this in my previous edits --The chemistds (talk) 14:17, 27 November 2010 (UTC)[reply]
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]

Thank you

The Chemistry Star
I just wanted to say thanks for all the work you are doing to improve chemistry articles. -- Ed (Edgar181) 13:24, 2 January 2011 (UTC)[reply]

License tagging for File:1,4-dibromobenzene.png

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]

Bosseopentaenoic acid

I saw your comments on the talk page of the image that I originally created for this page. I have replied at Talk:Bosseopentaenoic acid. Can you please have a look? Thank you. -- Ed (Edgar181) 13:07, 3 April 2012 (UTC)[reply]

Xylitol

Your minor-flagged change to this on 2012-04-15 broke the page markup so it's now visible to all. Please fix it. Thanks! Jamesday (talk) 02:25, 23 April 2012 (UTC)[reply]

Now fixed. --The chemistds (talk) 07:48, 23 April 2012 (UTC)[reply]

Brexpiprazole

Thank you very much for your edits! It's much appreciated! Jmdault (talk) 13:56, 26 April 2012 (UTC)[reply]

InChIs

Hi! Thanks for adding all these InChIs and other data! Just a note: in the drugbox, InChI and SMILES belong into the Chemical data section because they aren't identifiers. See Template:Drugbox#Single chemical drugs (the full template form). Cheers, ἀνυπόδητος (talk) 18:29, 11 February 2014 (UTC)[reply]

Cyclopentadienyl

Take a look at the history of cyclopentadienyl to get a sense of what we are dealing with. Then search the history of Wikipedia talk:WikiProject Chemistry etc. --Smokefoot (talk) 13:09, 6 May 2014 (UTC)[reply]

In re PP edit controversy

…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]

ORCID

If you have an ORCID identifier, please add it to your user page, using {{Authority control}}. See WP:ORCID for help. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 08:57, 3 October 2014 (UTC)[reply]

Benzoyl-S-Coenzyme A

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]
Update on discussing or reverting this nomenclature change? --Smokefoot (talk) 14:06, 5 November 2014 (UTC)[reply]

One source?

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]

Disambiguation link notification for July 15

Hi. Thank you for your recent edits. Wikipedia appreciates your help. We noticed though that when you edited Tolgabide, you added a link pointing to the disambiguation page INN. Such links are almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. Read the FAQ • Join us at the DPL WikiProject.

It's OK to remove this message. Also, to stop receiving these messages, follow these opt-out instructions. Thanks, DPL bot (talk) 09:30, 15 July 2015 (UTC)[reply]

ArbCom elections are now open!

Hi,
You appear to be eligible to vote in the current Arbitration Committee election. The Arbitration Committee is the panel of editors responsible for conducting the Wikipedia arbitration process. It has the authority to enact binding solutions for disputes between editors, primarily related to serious behavioural issues that the community has been unable to resolve. This includes the ability to impose site bans, topic bans, editing restrictions, and other measures needed to maintain our editing environment. The arbitration policy describes the Committee's roles and responsibilities in greater detail. If you wish to participate, you are welcome to review the candidates' statements and submit your choices on the voting page. For the Election committee, MediaWiki message delivery (talk) 14:23, 24 November 2015 (UTC)[reply]

Reference errors on 24 December

Hello, I'm ReferenceBot. I have automatically detected that an edit performed by you may have introduced errors in referencing. It is as follows:

Please check this page and fix the errors highlighted. If you think this is a false positive, you can report it to my operator. Thanks, ReferenceBot (talk) 00:19, 25 December 2015 (UTC)[reply]

Disambiguation link notification for April 21

Hi. Thank you for your recent edits. Wikipedia appreciates your help. We noticed though that when you edited Fospropofol, you added a link pointing to the disambiguation page INN. Such links are almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. Read the FAQ • Join us at the DPL WikiProject.

It's OK to remove this message. Also, to stop receiving these messages, follow these opt-out instructions. Thanks, DPL bot (talk) 09:51, 21 April 2016 (UTC)[reply]

SMILES for bombesin and non-standard InChIs

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]

ArbCom Elections 2016: Voting now open!

Hello, The chemistds. Voting in the 2016 Arbitration Committee elections is open from Monday, 00:00, 21 November through Sunday, 23:59, 4 December to all unblocked users who have registered an account before Wednesday, 00:00, 28 October 2016 and have made at least 150 mainspace edits before Sunday, 00:00, 1 November 2016.

The Arbitration Committee is the panel of editors responsible for conducting the Wikipedia arbitration process. It has the authority to impose binding solutions to disputes between editors, primarily for serious conduct disputes the community has been unable to resolve. This includes the authority to impose site bans, topic bans, editing restrictions, and other measures needed to maintain our editing environment. The arbitration policy describes the Committee's roles and responsibilities in greater detail.

If you wish to participate in the 2016 election, please review the candidates' statements and submit your choices on the voting page. MediaWiki message delivery (talk) 22:08, 21 November 2016 (UTC)[reply]

Standard InChI/Key values

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]

LOL after saving I saw I wrote the above post too. About the same. Well, shows I care. -DePiep (talk) 21:39, 28 November 2016 (UTC)[reply]

KCN in ChemSpider

Hello - could you perhaps comment on this post about ChemSpider on WT:Chemicals? Thanks! Walkerma (talk) 20:53, 6 December 2016 (UTC)[reply]

Facto Post – Issue 21 – 28 February 2019

Facto Post – Issue 21 – 28 February 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer.
Back numbers are here.
What is a systematic review?

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?

File:Schittny, Facing East, 2011, Legacy Projects.jpg
2011 photograph by Bernard Schittny of the "Legacy Projects" group

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.

Links
If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page.
Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 10:02, 28 February 2019 (UTC)[reply]

Facto Post – Issue 22 – 28 March 2019

Facto Post – Issue 22 – 28 March 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer.
Back numbers are here.
When in the cloud, do as the APIs do

Half a century ago, it was the era of the mainframe computer, with its air-conditioned room, twitching tape-drives, and appearance in the title of a spy novel Billion-Dollar Brain then made into a Hollywood film. Now we have the cloud, with server farms and the client–server model as quotidian: this text is being typed on a Chromebook.

File:Cloud-API-Logo.svg
Logo of Cloud API on Google Cloud Platform

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.

Links
If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page.
Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 11:46, 28 March 2019 (UTC)[reply]

Facto Post – Issue 23 – 30 April 2019

Facto Post – Issue 23 – 30 April 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer.
Back numbers are here.
Completely clouded?
Cloud computing logo

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.

Links
If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page.
Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 11:27, 30 April 2019 (UTC)[reply]

Facto Post – Issue 24 – 17 May 2019

Facto Post – Issue 24 – 17 May 2019
Text mining display of noun phrases from the US Presidential Election 2012
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer.
Back numbers are here.
Semantic Web and TDM – a ContentMine view

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.

ScienceSourceReview, introductory video: but you need run it from the original upload file on Commons
Links for participation

The review tool requires a log in on sciencesource.wmflabs.org, and an OAuth permission (bottom of a review page) to operate. It can be used in simple and more advanced workflows. Examples of queries for the latter are at d:Wikidata_talk:ScienceSource project/Queries#SS_disease_list and d:Wikidata_talk:ScienceSource_project/Queries#NDF-RT issue.

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.

If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page.
Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 18:52, 17 May 2019 (UTC)[reply]

Hydrazine nitrate

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]

ArbCom 2020 Elections voter message

Hello! Voting in the 2020 Arbitration Committee elections is now open until 23:59 (UTC) on Monday, 7 December 2020. All eligible users are allowed to vote. Users with alternate accounts may only vote once.

The Arbitration Committee is the panel of editors responsible for conducting the Wikipedia arbitration process. It has the authority to impose binding solutions to disputes between editors, primarily for serious conduct disputes the community has been unable to resolve. This includes the authority to impose site bans, topic bans, editing restrictions, and other measures needed to maintain our editing environment. The arbitration policy describes the Committee's roles and responsibilities in greater detail.

If you wish to participate in the 2020 election, please review the candidates and submit your choices on the voting page. If you no longer wish to receive these messages, you may add {{NoACEMM}} to your user talk page. MediaWiki message delivery (talk) 02:30, 24 November 2020 (UTC)[reply]

Retrieved from "https://mdwiki.org/wiki/User_talk:The_chemistds"