Talk:Transporter Classification Database

original proposal

The PubMed link has the wrong PMID. --Ayacop (talk) 15:20, 16 November 2008 (UTC)

Strange capitalisation in name?

Why is it "Transporter Classification database" and not "Transporter classification database" ? BenJWoodcroft (talk) 14:41, 7 May 2011 (UTC)

Listing other transporter databases in the "See Also"

I note that the link to the Guide to Pharmacology has been removed. This is, to quote from the current site

"an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules. The Guide to PHARMACOLOGY is developed as a joint venture between the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), and replaces and expands upon the IUPHAR Database"

Membrane transporter proteins are a subset of "biological targets of licensed drugs", so deleting the link on the grounds of "totally unrelated to subject of this page" (edit summary of My very best wishes) seems surprising. As IUBMB categorizes transporters through Transporter Classification Database, so IUPHAR categorizes transporters through Guide to Pharmacology. I argue that comparing different ways of categorizing transporter is relevant and should be included under a "See Also". Klbrain (talk) 10:04, 26 April 2016 (UTC)

I see. First of all, this should be another link. That one. Secondly, it should be placed to another page (Carrier protein or Membrane transport protein, theses pages probably should be merged). So, that belong to other pages. This page is about only one specific classification. So, yes, comparing different ways of categorizing transporters is relevant, but it is relevant on the general page about transporters. My very best wishes (talk)

Normally on Wikipedia, see also sections do in fact link to pages that are about related topics instead of about the specific topic of a page, so I agree with Klbrain. Links to pages that are specifically about this database should normally be in the main text. The see also section is for readers who want to find out about related topics, not covered on the page. --Tryptofish (talk) 22:45, 26 April 2016 (UTC)

Do you mean that Guide to Pharmacology is somehow related to this classification of transmembrane transporters? Yes, sure, just like page Medicine and a lot of others. My very best wishes (talk) 03:15, 27 April 2016 (UTC)

Yes, Guide to Pharmacology is used a method of classifying and regularizing the nomeclature of transporter. IUPHAR publishes review and nomenclature guidelines for all proteins (including transporters, exchangers and ion channels) in scientific journal like Pharmacological Reviews (see, for example, their categorization of calcium-activated chloride channels), which are then distributed freely on the IUPHAR/BPS Guide to Pharmacology. I suppose the purpose of the See Also is to include different perspectives on how transporters can be categorized, recongising that these differ between different scientific disciplines; hopefully these approaches are complementary! Klbrain (talk) 08:38, 27 April 2016 (UTC)

Guide to Pharmacology is not a method of anything. This is website about human proteins that serve as pharmacological targets. Yes, some transporters (less than 0.00000001% of them) are pharmacological targets. I am giving such small % because most of them are not human proteins. I do not see how this justifies inclusion, especially on this page, which is not about classification of transporters in general. Of course, it might be completely rewritten to become a page about classification of transporters in general, which I do not mind. My very best wishes (talk) 12:41, 27 April 2016 (UTC)

You're quite right that scope of the IUPHAR nomenclature is on human proteins, but it doesn't just cover those that are current pharmacological targets. Rather, it coverer "all the targets of current and future" drugs. Even ligand-gated ion channels, not traditionally seen as druggable are covered, and rightly so given the modern interest in allosteric modulation. So, it is accepted that the scope of the two databases differs, but that they intersect over all human transporter proteins; that is why I think that a "See Also" link to Guide to Pharmacology is worthwhile. Klbrain (talk) 13:06, 27 April 2016 (UTC)

In any case, it would be very appropriate for the see also section of this page to link to pages about other databases dealing with membrane proteins. --Tryptofish (talk) 23:38, 27 April 2016 (UTC)

We have some of them on page Membrane protein, but we can also include them here, no objections. My very best wishes (talk) 02:59, 28 April 2016 (UTC)

Rename?

How about renaming this page to Transporter Classification and changing its scope to a page about classification of TM transporters in general? It will appear that TCDB is actually the only comprehensive classification of TM transporters, wheres classifications used in other good resources are not significantly different from that in TCDB. Hence, the classification currently provided on this page will remain practically the same. My very best wishes (talk) 15:12, 27 April 2016 (UTC)

I think that the Transporter Classification Database deserves its own page; there could be a Transporter classificiation page, but that should be a comparision or critique of different methods of classifying or characterizing transporter. For example, in the field of Pharmacology, the term 'transporter' doesn't include ion channels, but only those proteins that use active transport (directly or indirectly). Klbrain (talk) 20:56, 27 April 2016 (UTC)

And in neuroscience as well as in physiology, anyone calling an ion channel a "transporter" would be regarded as mistaken (or ignorant). A more general page might be something like Membrane protein classification, but I think the rename proposed here would end up being a WP:POV-fork. --Tryptofish (talk) 23:37, 27 April 2016 (UTC)

OK, let's keep it as it is, no problem. My very best wishes (talk) 02:52, 28 April 2016 (UTC)

Linking

Of course it would be best to have a WP page about every protein family. However, if we do not have such page I think it would be helpful to link every family in the list (this is really a list) to the corresponding entities in the TCDB database itself and possibly to other resources that describe same family. What rules prevent us from doing this? I think there is only one criterion here: would such linking be helpful for a reader? I am sure it definitely would, at least on this page. If and when a corresponding WP page will be developed, it will be used to provide internal, instead of the external linking. Why not? My very best wishes (talk) 22:26, 22 November 2016 (UTC)

It is never done that way in Wikipedia articles, per Wikipedia:Manual of Style#External links. That's a Wikipedia-wide consensus, that really should not be overruled here. But there is an easy solution (which is what I did in this edit: [1]). Just make the link a citation, in the reference list. That accomplishes the same result! --Tryptofish (talk) 22:33, 22 November 2016 (UTC)

See Wikipedia:Manual of Style/Embedded lists. It tells about "lists of links, data or information that are either included in the text of an article or appended to the end of an article. Embedded lists may be in table format." OK. I do not really see why we can not make the list of families on this page as a list of links. But the list of references (as you suggested) would also work; I have no strong opinion about it.My very best wishes (talk) 22:44, 22 November 2016 (UTC)

I looked at the Embedded lists page, and it does not seem to me to endorse external links except as citations in references or as links in an External links section. Thanks about the references. --Tryptofish (talk) 23:01, 22 November 2016 (UTC)

I added more families, and a lot of them can be linked to corresponding WP pages we have, but I do not have time for that right now. What I do not understand in TCDB is why certain families are classified as belonging to the top "categories" 8. and 9. (there are actually a lot of them) rather than to 1-5. This page also needs some text explaining how and why these (super)families were classified to functional categories (1-5).My very best wishes (talk) 13:45, 2 December 2016 (UTC)

Licensing

An FYI re the licensing of this database, which is likely relevant to editors editing other articles (not this one--but they're most likely to see this notice if it's here). Though the database is labeled CC-BY, it often copies content from copyrighted journal articles (likely in good faith, because the people who wrote the database entries also wrote the copyrighted journal articles--but a problem nonetheless). Just wanted to get the word out so that we don't accidentally import copyright violations from this source. See Wikipedia:Contributor copyright investigations/Transporter Guy for more information. Calliopejen1 (talk) 21:34, 6 June 2017 (UTC)