User talk:Boghog

Stanford Biochemistry class project

Dear Boghog2,

Thanks so much for working so hard to make Wikipedia's protein and enzyme pages so helpful, accurate, and nicely laid out. You're really doing the community a huge service. My students are editing Wikipedia pages as part of a class project, and are being graded based on their efforts. It will make my work much easier if you could hold up on fixing up their work until after Friday the 21st. Please let me know if this seems reasonable to you. Again, I personally greatly appreciate the effort you've obviously put in to helping out the entire biochemical community.

Best,

Alex Dunn

alex.dunn@stanford.edu

Updated IUPHAR links responding

~Thanks for the work on these links, we have been rather busy and out of touch of late. But I'm still interested in continuing to encourage pharmacologists to fill in the receptor stubs..... Not easy to recruit volunteers! Another suggestion, we have been slowly curating drugs and other experimental chemical modulators of the IUPHAR-receptor set, each compound now boasts a ligand page (e.g.http://www.iuphar-db.org/DATABASE/LigandDisplayForward?ligandId=34) with some interesting information. It would be nice to link out to your growing list of drugs from each page... Please could we have a list of the wikipedia compound_ids and their SMILES? What is the best way to link to your chemicals?

ever SMILING

--Chidochangu (talk) 16:29, 13 April 2010 (UTC)

Good to hear from you again. Implementing the IUPHAR links was rather straight forward.

I could be wrong, however I do not think anyone has constructed a paired list of SMILES strings vs. Wikipedia drug articles. Wikipedia by its vary nature is very diffuse and unless someone makes a special effort to index a topic such as drug articles vs. SMILES stings, these types of indices are generally not available. Concerning ways of finding wikipedia drug articles to link to, I noticed that aripiprazole IUPHAR entry has CAS and PubChem accession numbers. Given either of these IDs, one can do the following types of searches to located the corresonding Wikipedia article name:

• CASNo = 129722-12-9
• PubChem = 60795

If you can supply me a list of CAS and/or PubChem registry numbers, I can return to you a list of corresponding Wikipedia article names.

On a related topic, would it be possible to link IUPHAR receptor and ion channel entries back to the corresponding Wikipedia Gene Wiki articles?

Cheers. Boghog (talk) 18:53, 13 April 2010 (UTC)

Hi Boghog

Thanks for the quick response, (I see you have not lost your touch, efficient as ever !!!)

I certainly will prepare a list of iuphar_id v. pubchem_id for you (this is do able, i may even run a small script to get the appropriate wikipedia article names myself to save you time). If you want to include IUPHAR_IDs in the list of identifiers e.g. chemspider, drugbank etc you are welcome

As for the IUPHAR receptor to wikipedia links I do not have any problem with.. I will have a look at the best way to incorporate the links onto our pages and get back to you.

cheers ever SMILIN--Chidochangu (talk) 07:30, 14 April 2010 (UTC)

Hi Boghog again.. twice in a day!!

Here is the csv file containing the IUPHAR_IDs VS. PubChem_IDs link: relevant file

please can you provide the list of wikipedia article names?

I will get back to you soon on the iuphar_receptor page to wiki_gene links

eva SMILIN --Chidochangu (talk) 14:04, 14 April 2010 (UTC)

Thanks for assembling the list of CAS registry numbers. Unfortunately these have been corrupted by Excel (if you paste a CAS number into Excel, Excel thinks it is a formula and treats the dashes as minus signs, and substracts the second and third fields from the first and displays the result). Before you paste the registry number into Excel, you need to first change the format of the cells to "text". I would appreciate if you would update you file with non-corrupted CAS numbers. Thanks. Boghog (talk) 04:55, 16 April 2010 (UTC)

Hi Boghog

No these are not corrupt CAS numbers by PubChem..... (I would never serve corrupt CAS to anyone)

Ooops did I not mention that we have provided the iuphar_id vs pubchem_ids not the CAS...see csv file again relevant file. Our list of CAS numbers is not exhaustive and we think it better to use the PubChem ones... I also have InCHIs for all iuphar compounds if this helps any?

We have also identified a good place on our pages to link out to all the genes on wikipedia from our receptor pages please could you send us a list of all the wiki_gene ids vs. iuphar_receptor numbers and we should have it on line by mid-week...

I hope to hear from you soon... there are some noises within IUPHAR about getting the stubby ones updated in a more systematic way... please keep nagging me on this..

I have lost my old password and do not have access to the Phamarcology group...arrrrr

yours with SMILEs InCHIs wide --Chidochangu (talk) 10:07, 16 April 2010 (UTC)

Opps, sorry about that. When I responded, I was very tired and I didn't read your message very carefully. I will supply you the PubChem/Wikipage and wiki_gene ids vs. iuphar_receptor numbers this weekend. Cheers. Boghog (talk) 10:39, 16 April 2010 (UTC)

Hi Chidochangu. Per your request, I have compiled a tab delimited list of IUPHARDB ligand IDs vs Wiki pages. Concerning adding returning links from these Wikipedia articles to the IUPHARDB, again I will ask consensus from the community. I don't think there will be any objection, especially since the IUPHARDB ligand entries will link to Wikipedia pages, but nevertheless I still should ask. Concerning linking to Wikipedia receptor/ion channel pages, for the most part, the pages are named after the HUGO symbol or there is a redirect from the HUGO symbol to the Wikipedia article. I am currently double checking this to make sure (so far I found a few missing redirects which I have now added). More later. Cheers. Boghog (talk) 06:38, 19 April 2010 (UTC)

Hi there Boghog we have implemented drug id links to wikipedia on our test database, however we noticed some errors in the list you sent ( please see a few examples below:)

--iuphar_name, iupharId, pubchem, wikipedia, wiki_PubChem

--bromocriptine, 35,2443,Resveratrol,445154

--bupivacaine,2397,2474,Hydroxy-1,4-benzoquinone,151011

I'm sure how this happened but it appears to come form the list you generated IUPHARDB ::::ligand IDs vs Wiki pages.

Can you help me check this on your end before we go live at IUPHAR-DB?

Thanks again (I would trust SMARTS or SMILES InCHIs to link out )

--Chidochangu (talk) 14:52, 23 April 2010 (UTC)

Sorry for the errors. I have now manually checked and corrected the entire list.

The only way I could figure out how to retrieve these records was to use a perl/google script to search Wikipedia for the PubChemIDs:

#!/usr/bin/perl

use Google::Search;
use strict 'subs';

if ($#ARGV != 1) {
   die("\nUsage: infile outfile\n");
}
    
$file1=shift(@ARGV);
open(INFILE,"${file1}") ||
   die("\nTrouble opening $file1\n");
$file2=shift(@ARGV);
open(OUTFILE,">${file2}") ||
   die("\nTrouble opening ${file2}\n");

while (<INFILE>) {
    chomp;
    my @fields = split(/,/);
    my $index   = $fields[0];
    my $PubChem = $fields[1];
    my $query   = "site:en.wikipedia.org PubChem " . $PubChem . " -user:" ;
    my $search  = Google::Search->Web( q => $query );
    my $result  = $search->first;
    if ($result ne '') {
       my $article = $result->uri;
       print OUTFILE "$index\t$PubChem\t$article\n";    
    }
}

Using Google to search Wikipedia for example "site:en.wikipedia.org PubChem 60795 -user:" usually works, but as you can see from all the errors, not always. I don't know a better way of doing this. Searching for InCHIs might be the best way, but unfortunately most of the Wikipedia ligand articles do not contain InCHIs codes. SMILES is more commonly included, but there are many ways of writing a SMILES string for the same structure, so searching for SMILES will not work (there are ways of canonicalizing SMILES strings so that they are identical no matter what the order of the inputed atoms into the SMILES string generator, but unfortunately there is no universally accepted canonical SMILES algorithm). Boghog (talk) 07:06, 24 April 2010 (UTC)

Hi Boghog,

Thanks for the file we have now implemented the links on our production database.. we will let you know as soon as we go

live online.. the links work. I will try the InCHIs just to check if there is something missing or with multiple pubchems

I noticed pubchem is sometimes notorious for this, esp with chiral compounds...(where the chiral specification is dubious)

Any luck with the issue wikipedia links back to IUPHAR-DB.?? Please could you supply a similar list for the receptors as you did with ligands so I can reciprocate the receptor links from IUPHAR-DB.

Thanks again [EVER SMILIN] --Chidochangu (talk) 16:01, 26 April 2010 (UTC)

Hi Chidochangu. Thanks for the update. The search I did is bound to miss some Wikipedia ligand articles since as you point out, there may be more than one PubChem ID for a given chemical. So searching with InCHIs may indeed locate some addition articles. I am kind of busy right now, but I haven't forgotten about my promise to provide you with a list of (1) Gene Wiki articles that link to the IUPHAR-DB and also (2) linking Wikipedia ligand pages to the IUPHAR ligand DB. I should be able to complete both tasks this weekend. Cheers. Boghog (talk) 19:47, 26 April 2010 (UTC)

IUPHAR link update

Hi Chidochangu,

I have compiled a mapping of Wikipedia receptor/ion channel articles to IUPHAR database entries here. (Please note that many of these are piped redirects. You should link to the page name after the pipe to directly link to the Wikipedia article.) If you could add these links to the IUPHAR database, I would greatly appreciate it. In addition, I have made a request here to add a link from the {{Drugbox}} to the IUPHAR database. Cheers. Boghog (talk) 17:43, 2 May 2010 (UTC)

Hi Boghog,

Thanks for the list, we will add the wiki_gene links from IUPHAR-db soon...! As you may already know IUPHAR-db will be adding a :: set of nuclear hormones to the classes they cover in the summer.. we may have to re-do this again sometime soon.

cheers --Chidochangu (talk) 10:49, 3 May 2010 (UTC)

ZM-241,385 wrong structure?

Hi Boghog, Thanks for the request to link out to the IUPHAR ligands, I think this will be beneficial to users! I also think we have an error on wikipedia see [wrong_structure?]. The correct links for this compound can be found on [correct_structure?] see the pubchem_id, cas-number, and chebi_id for this compound on this page. I think the literature you used and the text is correct for the Wikipedia drug page. I hope this is a good example of how we can help each other in the future, as IUPHAR adds new compounds to their database!

--Chidochangu (talk) 10:10, 5 May 2010 (UTC)

Thanks for catching the error. I originally obtained the structure from the PubChem record 5311506 which is in error whereas PubChem 176407 contains the right structure. I have corrected the structure, IUPAC name, and SMILES string in the ZM-241,385 article. Likewise, I think this is a great example of how we can help each other. Cheers. Boghog (talk) 19:15, 6 May 2010 (UTC)

I just noticed that the tritiated ZM-241385 entry in the IUPHAR-DB (see 455) contains the same structural error. Cheers. Boghog (talk) 19:35, 6 May 2010 (UTC)

GPCRs Template

Hey. For Template:G protein-coupled receptors, what would you think of recategorizing the class A/rhodopsin-like section? I was thinking something like the following:

• Small molecules (5-HT, dopamine, adenosine, histamine, acetylcholine, cannabinoids, etc)
• Orphans (self-explanatory)
• Peptides (opioids, oxytocin, melanocortins, and so forth)
• Steroids (testosterone, estrogen, progesterone, etc)
• Others (sigma, whatever else)

Possibly a lipids section as well for cannabinoids and such instead of placing them in small molecules?

I'd do it myself but I'm not quite knowledgeable enough in this entire field.

el3ctr0nika (Talk | Contribs) 08:10, 20 April 2010 (UTC)

Hej! Yes, this template has grown over time and I think a reorganization of the template is long over due. There are a couple of ways of doing this. One possible way is listed here, but the number of subfamilies in that classification is probably too large for a template. Similar to what you have suggested is present here:

• "A phylogenetic tree of all human GPCRs" (PDF). Vassilatis DK, Hohmann JG, Zeng H, Li F, Ranchalis JE, Mortrud MT, Brown A, Rodriguez SS, Weller JR, Wright AC, Bergmann JE, Gaitanaris GA (2003). "The G protein-coupled receptor repertoires of human and mouse". Proc Natl Acad Sci USA. 100 (8): 4903–8. doi:10.1073/pnas.0230374100. PMC 153653. PMID 12679517.{{cite journal}}: CS1 maint: multiple names: authors list (link). Retrieved 2008-08-11. {{cite web}}: Cite has empty unknown parameter: |coauthors= (help); External link in |work= (help); Italic or bold markup not allowed in: |work= (help); templatestyles stripmarker in |work= at position 1 (help)

My suggestion which is very similar to yours is to divide into the following five classes:

• "neurotransmitters" (adrenergics, purinergics, serotonin, etc.)
• peptides
• other hydrophobic "small molecules" including eicosanoids, lipids, steroids
• orphans
• miscellaneous

Does this look reasonable? Boghog (talk) 18:01, 20 April 2010 (UTC)

I am in the process of regrouping the template here. Boghog (talk) 19:02, 20 April 2010 (UTC)

OK, the first draft of the regrouping is finished. How does this look? Please note that I classified the cannabinoid opioid receptors as peptide receptors based on their endogenous ligands. Cheers. Boghog (talk) 19:31, 20 April 2010 (UTC)

Opps, my mistake, moved cannabinoid receptors to small molecule signaling molecule section. Boghog (talk) 04:13, 21 April 2010 (UTC)

After a few more edits, I have gone ahead updated the production version. I hope this version is OK. Of course, feel free to make further adjustments if necessary. Boghog (talk) 20:27, 20 April 2010 (UTC)

Interesting to note that along with GPR55 and GPR119, GPR18 has now also been implicated as a novel cannabinoid / fatty acid amide receptor, meaning we could well have five cannabinoid receptors to deal with! The field just keeps getting more complicated... Meodipt (talk) 04:29, 21 April 2010 (UTC)

Thanks for the heads up. I saw your edits and have added GPR55 and GPR119, GPR18 to the list of cannabinoid receptors in the {{G protein-coupled receptors}} template. Cheers. Boghog (talk) 05:10, 21 April 2010 (UTC)

Help with Pentapeptide repeat page

Dear Boghog2,

Thanks for your help with the Pentapeptide repeat page images and layout. It looks much better now. You are totally awesome :) Alexbateman (talk) 08:45, 2 May 2010 (UTC)

No problem. I just made a couple of quick adjustments with GraphicConverter (image cropping; jpg → png conversion) . Cheers. Boghog (talk) 10:24, 2 May 2010 (UTC)

Thyroxine deiodinase

Hi! I saw you did such a good job with Iodothyronine deiodinase and Iodotyrosine deiodinase entries, you might want to look at a remark I made in the Discussion section of Thyroxine deiodinase. I do not know enough to make the right call, but it seems very likely that you do :) Thank you. -- 83.9.135.174 (talk) 14:06, 3 May 2010 (UTC)

Thanks for the heads up. Per your suggestion, I have merged the contents of the thyroxine deiodinase article into iodothyronine deiodinase and also cleanup slightly the deiodinase article. Cheers. Boghog (talk) 20:21, 3 May 2010 (UTC)

Ezrin

Hi! I'm really a newbe in wiki, and I edit the ERM protein family entry. I was planning to edit Ezrin entry next...but you've done a great job already!

Thanks for updating this entry! Machicoa (talk) —Preceding undated comment added 20:31, 11 May 2010 (UTC).

And thank you for expanding the ERM protein family article! You have done a great job. Please carry on and if I can be of any assistance, please don't hesitate to ask. Cheers. Boghog (talk) 20:41, 11 May 2010 (UTC)

Pyruvate Carboxylase page

boghog, thanks for editing especially fixing my formatting on Pyruvate carboxylase! I'm (extremely) new to wikipedia and working on a class project. as a head's up i'm looking to expand the mechanism and biological significance sections and probably add a role in anaplerosis section.

Sswilson7 (talk) 16:54, 14 May 2010 (UTC)

Your doing a great job of expanding the pyruvate carboxylase article! It looks like you are catching on very quickly. Let me know if you have any questions and I look forward to your additional contributions to the article. Cheers. Boghog (talk) 18:06, 14 May 2010 (UTC)