Template talk:Drugbox

Monoclonal antibodies

I have come across infliximab and note that we give a blue link to Monoclonal antibody. We do not typically use blue links in headings and thus feel we should remove it.Doc James (talk · contribs · email) 04:46, 15 August 2011 (UTC)

Just come across this... does anyone else have thoughts on the matter? Personally I agree since it does give a blue link to 'monoclonal antibody' in the main text and I imagine most if not all other MAB articles will do as well. ῤerspeκὖlὖm in ænigmate_(talk)(spy) 12:15, 21 September 2011 (UTC)

I have no stong opinion on this matter, but if we do delink it, we should also delink the header "Vaccine description" (eg. in Measles vaccine) for consistency's sake. --ἀνυπόδητος (talk) 12:26, 21 September 2011 (UTC)

Question marks on display

I just noticed Botulinum toxin, where the infobox contains two '?' (resulting from code in the template). I presume that they were included so editors/readers are invited to get that data, and put it there. However, for some requesting that data seems plain silly to me: does it have a reasonable legal status (except for the use in botox), and I would not suggest to use it as a drug on pregnant women. Note, the legal status says "? (US)" - it is defaulting to US when there is a '?').

That aside, I do think that those '?' are unnecessary and mere clutter. Empty fields should simply not display, and question marks should not be put into fields in mainspace to 'request' the data (then leave the field in the box, but without parameter, or with a comment-like parameter as it is in Botulinum toxin. Can we consider changing this behaviour of the drugbox, please (and maybe also remove '?' from mainspace where they occupy fields)? --Dirk Beetstra ^{T C} 13:50, 16 September 2011 (UTC)

See Template_talk:Drugbox/Archive_7#Missing_fields_should_be_omitted. In short (if I remember correctly): there was no consensus to omit the fields "Pregnancy cat., Legal status, ATC code", and hiding the chemical formula was beyond my template editing capabilities. No objections from me to hide all the ?'s. --ἀνυπόδητος (talk) 14:24, 16 September 2011 (UTC)

No objection from me, although I will leave the template editing to someone else. ῤerspeκὖlὖm in ænigmate_(talk)(spy) 11:17, 19 September 2011 (UTC)

this version of the sandbox should do it. I'll wait for some more input (but feel free to update). --Dirk Beetstra ^{T C} 11:39, 19 September 2011 (UTC)

I've experimentally hidden the headers "Pharmacokinetic data" and "Identifiers" in the sandbox if the sections are empty. Could/should probably also be done with "Chemical data", but I'm not sure whether this is worth the trouble. --ἀνυπόδητος (talk) 12:13, 19 September 2011 (UTC)

Let's just do that as well .. clean it up. --Dirk Beetstra ^{T C} 12:15, 19 September 2011 (UTC)

I hope it worked. --Dirk Beetstra ^{T C} 12:28, 19 September 2011 (UTC)

It is broken .. --Dirk Beetstra ^{T C} 12:36, 19 September 2011 (UTC)

Edit request from Aljogryph, 20 September 2011

|- {{#if: | ! NIAID-AIDS# | {{{NIAID-AIDS#}}}{Template:NIAID-AIDS |-

Aljogryph (talk) 20:21, 20 September 2011 (UTC)

Before implementing the above, this needs to be discussed and tested. I have added a slightly modified version to the {{drugbox/sandbox}} and an example NIAID_ChemDB link can be seen here (near the bottom of the identifiers section in the drugbox displayed on the righthand side). Finally I have created a stub NIAID ChemDB article briefly describing the database. This looks like a useful link, but I worry about the proliferation of parameters in the drugbox. Thoughts? Boghog (talk) 03:28, 21 September 2011 (UTC)

Legal Status (UK)

Legal status for the US, Canada, and Australia allows specification of which Schedule a drug is in. The UK, however, only allows a drug to be specified as a "controlled drug", which is rather vague. I'm pretty sure that the UK equivalent of Schedules is Classes - Class A is most illegal, with heroin, cocaine, LSD, MDMA etc, Class B is less harshly punished, with cannabis, amphetamines, etc, and Class C is the least illegal, most benzodiazepines are in this class (and illegal unless prescribed). Schedules in the UK just relate to how drugs have to be stored, prescribed etc, what safeguards must be in place at pharmacies and hospitals, things like that. In either case, the Legal Status for the UK allows neither Class nor Schedule to be displayed, and I believe this should be fixed, as currently the UK legal status shows far less information for illegal drugs than US/Aus/Canada legal status. Xmoogle (talk) 14:31, 23 October 2011 (UTC)

Problem at Hydroxocobalamin.

When looking at https://en.wikipedia.org/wiki/Hydroxocobalamin most of the drugbox is not visible, off the left side of the page, causes lots of whitespace where you have to scroll down to see the actual article. https://secure.wikimedia.org/wikipedia/en/wiki/Hydroxocobalamin shows fine. May this be caused by a problem with the data for the InChI or StdInChI parameters on that page? Using Firefox 7.0.1 on Ubuntu 11.10. -- Jeandré, 2011-11-16t08:27z

This is a known problem if you have JavaScript disabled. (I know that doesn't help much.) --ἀνυπόδητος (talk) 08:37, 16 November 2011 (UTC)

???? What, is there a difference in display between the secure server and the normal server? Does that mean that the secure server has something enabled that we can enable here as well so things do work here as well? --Dirk Beetstra ^{T C} 09:23, 24 November 2011 (UTC)

For me, it's broken on the secure server as well (Firefox 8, Win XP). --ἀνυπόδητος (talk) 12:56, 24 November 2011 (UTC)

That is what I would expect when Java is turned off. Why can't we force in a hard way that a box (table, i.e.) can NEVER be wider than e.g. 25% of a page, whatever the content of a cell would 'force' it to do. Otherwise we either need to break an important parameter (with all problems associated with it) or take it out (which is unfortunate). Note, this is also true for the chembox, which has exactly the same problem. --Dirk Beetstra ^{T C} 13:01, 24 November 2011 (UTC)

Can't we have a CSS attribute "display:none" by default and use JS to display the content? This would mean that there isn't a way of displaying the InChI if JS is turned of, but that might be better than a page with a completely broken layout. --ἀνυπόδητος (talk) 13:19, 24 November 2011 (UTC)

WHEEE .. try again. I think the trick is to wrap long-unbreakable strings in

<p style="word-wrap: break-word;">

and

</p>

. For me it works, the table (with JAVA enabled) does not change form or shape when clicking show/hide. Please test. --Dirk Beetstra ^{T C} 13:34, 24 November 2011 (UTC)

Nope. Still gets wide for me. --ἀνυπόδητος (talk) 14:26, 24 November 2011 (UTC)

)-: ... should it be 'overflow-wrap' maybe, per http://www.w3.org/TR/css3-text/#overflow-wrap0 ?? --Dirk Beetstra ^{T C} 14:33, 24 November 2011 (UTC)

Tried, but that does not work even for me. My Opera perfectly follows it, but others seem to be broken.  :-( --Dirk Beetstra ^{T C} 14:40, 24 November 2011 (UTC)

Hm... Your link points to a CSS Level 3 working draft from September, and word-wrap is also CSS3. I've no idea which versions (if any) of which browsers support that. But it may be a solution for the future. (Or it might not work at all, of course.) Interestingly, IE increases the width only by a few centimetres, while under Firefox the box gets wider than the screen. --ἀνυπόδητος (talk) 15:10, 24 November 2011 (UTC)

What if InChI is too large?

Over at cortisol the drugbox is perversely wide, because the InChI is too long. Is there a way to hide long InChI's? Thanks, AxelBoldt (talk) 02:20, 12 December 2011 (UTC)

See the thread above. It should work fine when JavaScript is switched on, but unfortunately gets broken when JS is turned off. --ἀνυπόδητος (talk) 11:48, 12 December 2011 (UTC)

Sorry, I didn't read the above thread before asking. In my case Javascript is running on Firefox 8.0. I saw the wide-drugbox-problem only on Firefox 8, not on Chrome 16, and only when I was logged in. I tracked it down to some old code in my vector.js. AxelBoldt (talk) 17:51, 12 December 2011 (UTC)

Remove "AIDSNO:" from NIAID_ChemDB field

Please update from sandbox. This will remove the text "AIDSNO:" from the NIAID_ChemDB field (per WT:PHARM#Support NIAID-AIDS parameter in the drugbox, last few lines). Tx --ἀνυπόδητος (talk) 09:12, 22 January 2012 (UTC)

Y Done, thanks. Chris Cunningham (user:thumperward) (talk) 16:09, 3 February 2012 (UTC)

DailyMed

Have people considered adding a DailyMed (NCBI) link to this template? It seems to provide some very good information and claims to index 33265 different drugs. An example URL is http://dailymed.nlm.nih.gov/dailymed/search.cfm?startswith=allopurinol&x=0&y=0 - note that we can just drop a {{PAGENAME}} in there, with an option to override the search term or just shut it off if there's nothing coming, and voila, patients interested in thirty thousand different drugs are pointed to this very useful resource. Wnt (talk) 21:23, 23 January 2012 (UTC)

Edit request on 24 January 2012

{{edit protected}} in order to correct the misuse of the term trade name as it relates to drugs

{{#if:| ! Trade names

should be changed to

{{#if:| ! Brand names

(This will eliminate the need to correct each individual page)

and

{{#if:| ! Brand names

should be added

24.6.51.171 (talk) 18:05, 24 January 2012 (UTC)

Sorry for deactivating your request, but this needs consensus. Many, if not most drug articles start on the lines of "X (trade name Y) is a...". The redirect category is termed Category:Redirects from trade names. And the page Trade name mentioned (although unsourced) the use of the term "trade name" for drugs' brand names. I'm neutral as a non-native speaker. --ἀνυπόδητος (talk) 11:35, 25 January 2012 (UTC)

• Oppose but only because everything else refers to trade name. I feel that brand name is a more accurate term but I feel the need for consistency is more overriding in this case. ῤerspeκὖlὖm in ænigmate_(talk)(spy) 17:34, 25 January 2012 (UTC)

Adding drug mechanism data to drug boxes

vemurafenib
Drug mechanism
Crystallographic structure of B-Raf (rainbow colored, N-terminus = blue, C-terminus = red) complexed with vemurafenib (spheres, carbon = white, oxygen = red, nitrogen = blue, chlorine = green, fluorine = cyan, sulfur = yellow).
Therapeutic use	melanoma
Biological target	BRAF
Mechanism of action	protein kinase inhibitor
External links
ATC code	L01XE15
PDB ligand id	032: PDBe, RCSB PDB
LIGPLOT	3og7

The Drugbox info is really useful. Many small molecule drugs have had their structures solved bound to their protein targets and these are available in the PDB. Could this info be added? it would just need a link to the Compound browser would be needed, eg sildenafil or aspirin to be continuously up to date with the PDB archive. I have a mapping between Inchi and the PDB three letter ligand code which would aid doing it automatically. larger proteinaceous drugs are of course in the PDB too. A2-33 (talk) 17:49, 30 January 2012 (UTC)

It might be better to create a new infobox for drug mechanism that can be placed in the mechanism of action section of drug articles. An additional advantage of using a separate infobox is that an image of the drug/protein complex can be added to it. See an example prototype infobox to the right. Alternatively we could add a new "pharmacodynamic data" section to the drugbox containing similar information as this prototype template. Thoughts? Boghog (talk) 06:59, 26 February 2012 (UTC)

Integrate improvements and corrections

Hello,

I have made improvements and corrections to this template at en.wikipedia.org/w/index.php?title=User:Nnemo/Drugbox&oldid=478751180. Please integrate this in the template. I was going to do it myself, but it's locked. Here are the changes.

Thanks,

--Nnemo (talk) 10:03, 25 February 2012 (UTC)

Hi Nnemo, and thanks for your work! I copied your version to Template:Drugbox/sandbox. This is a good place for such things, as people can easily compare the new code to the old one on Template:Drugbox/testcases. To request updating a protected page with your code, just place {{Edit protected}} on its talk page, followed by a short explanation.

What is your reason for replacing simple spaces with {{sp}}? --ἀνυπόδητος (talk) 12:05, 25 February 2012 (UTC)

Otherwise, MediaWiki eats the spaces — which, by the way, is a bad thing.

--Nnemo (talk) 17:49, 25 February 2012 (UTC)

Y Done Tra (Talk) 14:44, 26 February 2012 (UTC)

Adding drug mechanism data to drug boxes: take 2

vemurafenib

Clinical data
Trade names	Zelboraf
AHFS/Drugs.com	FDA Professional Drug Information
Licence data	US FDA:link
Pregnancy cat.	D (US)
Legal status	℞-only (US)
Routes	Oral
Mechanism & use
Mechanism	Protein kinase inhibitor
Biological target	BRAF
Therapeutic use	Melanoma
Identifiers
CAS number	1029872-54-5
ATC code	L01XE15
PubChem	CID 42611257
ChemSpider	24747352 Y
UNII	207SMY3FQT
ChEMBL	CHEMBL1229517
PDB ligand ID	032 (PDBe, RCSB PDB)
Chemical data
Formula	C23H18ClF2N3O3S
Mol. mass	489.92 g/mol
InChI InChI=1S/C23H18ClF2N3O3S/c1-2-9-33(31,32)29-19-8-7-18(25)20(21(19)26)22(30)17-12-28-23-16(17)10-14(11-27-23)13-3-5-15(24)6-4-13/h3-8,10-12,29H,2,9H2,1H3,(H,27,28) Y Key:GPXBXXGIAQBQNI-UHFFFAOYSA-N Y
Y (what is this?)  (verify)

IMHO, one major omission from the drugbox is information about the biological target and mechanism of action (i.e., "pharmacodynamic data"). This data could be added in a separate infobox as proposed above or incorporated directly into the drugbox (see example to the right). Is there support for adding this type of data directly to the drugbox? Boghog (talk) 21:01, 27 February 2012 (UTC)

• Note the "PDB drug" link provides a list of all the structures of proteins that have been complexed with this drug while the "PDB target" link contains information about how the drug interacts with its target (depicted as a LIGPLOT diagram).
• Also note this previous proposal to add class of drug or mechanism. The objection raised at that time was there was not room and it could not be explained properly. I agree that in some cases (especially for drugs with unknown mechanism of action), adding this data would not be appropriate, but in the case to the right where the drug has a well defined mechanism of action, I think the explanation is fairly clear.
• There is also this previous discussion where the argument against adding drug class information is that it duplicates information that should be contained in the lead and in addition, many drugs have more than one use (and by extension, possibly more than one mechanism of action). While this information should be contained in the lead (and also a mechanism of action section), often it isn't, Even if it is, it is often presented in an unstructured way this is difficult figure out what the mechanism of action is. If this information is in the drugbox, the reader can quickly figure out how this drug works. In cases where the MOA is not known or if the drug works through multiple mechanisms, I would agree it would not be appropriate to display this section in the drug box. Boghog (talk) 06:33, 28 February 2012 (UTC)

Support adding these data to the drugbox. That's clearer and quicker to find (and edit) than if we had two boxes. We could mention in the drugbox documentation that more than 2 or 3 uses/mechanisms are discouraged. Perhaps we could link from the drugbox to the appropriate section in such cases (especially in long articles).

I think the header Pharmacodynamic data is suboptimal. This section contains data that are interesting for the general readers, and not many people know the word pharmacodynamic. What about Use and mechanism? Any better ideas? --ἀνυπόδητος (talk) 08:33, 28 February 2012 (UTC)

Briefly as I don't have a huge amount of time to comment right now. I think we are in danger of second guessing (incorrectly) what the user might want. By putting PDB info in a 'mechanism of action' section assumes that all drug structures in the PDB relate to the pharmacological target, and that users looking for protein-drug complexes require this information. The PDB structure might be of the target, or a resistance mechanism, or the last step of the biosynthesis pathway. Equally, this might be the information the user is looking for. Perhaps therefore the box name isn't quite right. For instance there are 16 structures containing chloramphenicol, most are not the ribosome.

If there are several structures of a drug in complex with the target, which ligplot is linked to?

Does the link to 032 page provide much more information than is available in the drug box anyway? — Preceding unsigned comment added by A2-33 (talk • contribs) 12:00, 28 February 2012 (UTC)

┌────────────────────────────────────────────────────────────────────────────────────────────────────┘ It is not clear to me how cases with more than one mechanism will be handled in this box. There may be structures in PDB for which the exact mechanism is not well understood. Also from discussion above it would be good to be clear n what exactly we want to achieve by adding the extra information.

• Do we want to give easy access to "mechanism" information?
• Do we want to give information about "interaction" of drug with macromolecules?

I also think that adding a link to PDB which only describes the molecule is not adding any extra information instead if we add a link to PDB structures e.g. http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/ligand/?ligand=AIN for aspirin so then it shows all structures that have the molecule and the extra information about domains, assemblies etc. and something like http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/drugport/GetPage.pl?template=drug.html&drug_id=DB01614. This would be more useful in drugbox. A2-25 (talk) 13:00, 28 February 2012 (UTC)

Thanks everyone for your comments. Obviously the proposal needs to be fined tuned before it is put into production. I agree that "pharmacodynamics data" section heading is not ideal, but one advantage of this heading is that it is consistent with the "pharmacokinetic data" heading that is already contained in the drugbox (unfortunately this cannot be seen in the example to the right because this data is apparently not yet available for this drug). All the structures in the PDB containing a given drug may not relevant to the mechanism (but may be relevant to pharmacokinetic, e.g., drug metabolizing enzymes, transport proteins, etc.). The idea of the LigPlot link is that would be specific to the known target of the drug. The idea of the PDB ligand ID link is that it would provide links to all the structures containing the drug , some of which may be relevant to mechanism, others of which might be relevant to pharmacokinetics. In the current link, one has to click through to see the structures so that I agree that it is not ideal. I don't have much more time to comment at the moment, but I will resume experimenting in a day or two to try to incorporate your suggestions and address your concerns. Boghog (talk) 17:59, 28 February 2012 (UTC)

Thanks Boghog. A2-25 (talk) 21:48, 1 March 2012 (UTC)

• Per the above discussion, I have changed the title of the "pharmacodynamic data" section "mechanism & use" and moved the PDB links to the identifiers section and link changed the links so that list of all structures containing a particular PDB ligand ID are displayed. My original thought for including the PDB target links (as a LigPlot diagram which in turn linked to the PDB structure) in the mechanism section is that it provided better context for the links. Now the query link will provide a list of all structures complexed with the ligand, and it is up to the reader to determine whether the associated biopolymer is a target, metabolizing enzyme, transport protein, or has some other function. The changes can be seen in the infobox to the right. Does this look OK?
• Concerning mechanism/target data, I was (and still am) hesitant to include this type of data for drugs that have more than one mechanism of action because it would be difficult to locate and explain this data. However I recently noticed that the DrugBank database maintains a comprehensive list of targets for many drugs (see for example amiodarone targets). Furthermore one can download this data. Hence it would be possible for a bot to systematically add this data to drugboxes. In addition, this data could be displayed as a optionally collapsible table of Actions/Target pairs. Thoughts? Boghog (talk) 11:23, 3 March 2012 (UTC)

From my point of view (working in a pharmacy), "Mechanism: Class III antiarrhythmic" would be enough. I'd even say the CYPs and ABCs given on the DrugBank page are more interesting than to which subunit of the Ca channel amiodarone binds. What about a data page like the ones from WP:CHEM (eg. Ethanol (data page)), or a table (formatted by template) in the mechamism/pharmacokinetics sections? If people want to have all the pharmacodynamics data in the drugbox, a possibility would be to condense the mechanism/target fields into "Mechanism: BRAF inhibitor" (for vemurafenib), "Mechanism: Class III antiarrhythmic (hERG)" or something (for amiodarone). Just ideas. --ἀνυπόδητος (talk) 15:56, 3 March 2012 (UTC)

The new changes look good. I was looking at drugbank data and it would be good idea to add these links using a bot. A2-25 (talk) 17:27, 3 March 2012 (UTC)