![]() | This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 1 | Archive 2 | Archive 3 | Archive 4 | Archive 5 | Archive 6 | → | Archive 10 |
Hey Boghog, I hope that you and your family have a Happy New Year. :-- Literaturegeek | T@1k? 10:03, 2 January 2010 (UTC)
Hope you had a good start into the new year. Besides, I only wanted to ask what you think of my considerations and questions regarding protein and gene names. Cheers, ἀνυπόδητος ( talk) 20:21, 16 January 2010 (UTC)
There appear to be two articles with the same enzyme name:
Should the second article be merged into the first? -- Robert.Allen ( talk) 01:23, 20 January 2010 (UTC)
Hi again! Do you know whether an immunoglobulin fold is the same as an immunoglobulin domain? Looks like it to judge from the Pfam boxes, I'm just irritated by the term "Immunoglobulin-like domain" in the latter article. -- ἀνυπόδητος ( talk) 10:52, 20 January 2010 (UTC)
Hello. Could you possibly do me a favor? I've been trying to start this (it's red I know but click it anyway) article for months. I've requested unprotection 2-3 times but for whatever reason nobody ever does anything about it. Maor Levi is one of my favorite electronic artists of all time and I'd like to give him a place here on Wikipedia. Here's his Last.fm profile. If you can do so thanks a ton! el3ctr0nika ( Talk | Contribs) 04:59, 1 February 2010 (UTC)
Could someone else check out Beta clamp? I suggested redirecting it to DNA clamp at MCB talk but I don't want to be judge, jury and executioner to an article written in good faith by a new contributor. Adrian J. Hunter( talk• contribs) 01:48, 31 January 2010 (UTC)
Thanks for that, Boghog. Sorry I don't have more time right now to help with the merge. Adrian J. Hunter( talk• contribs) 03:57, 4 February 2010 (UTC)
Hi! Just saw that you nominated Nyctalopin for deletion but I have to admit I don't understand the reason. Because NYX_(gene) should be moved to nyctalopin? What's the official wiki policy? Should one name the main article after the gene or the protein? It is quite mixed now as far as I can see. Usually the article is named after the gene but about the protein. Thanks, Panoramix303 ( talk) 20:17, 12 February 2010 (UTC)
![]() |
The Chemistry Star | |
I just wanted to let you know that all your contributions to chemistry articles has not gone unnoticed. Thank you for all your efforts at improving articles in this corner of Wikipedia. -- Ed ( Edgar181) 20:43, 24 February 2010 (UTC) |
I have re-instated it - on hold for seven days. There is a lot of work to be done. Jezhotwells ( talk) 01:54, 27 February 2010 (UTC)
Wow, we did a good job on that entry. Just compare the January version with the latest one. Just in time, too. We got >4,000 hits after that New York Times story. -- Nbauman ( talk) 06:20, 3 March 2010 (UTC)
Hello! Your submission of
Cereblon at the
Did You Know nominations page has been reviewed, and there still are some issues that may need to be clarified. Please review the comment(s) underneath
your nomination's entry and respond there as soon as possible. Thank you for contributing to Did You Know!
SusanLesch (
talk) 00:44, 12 March 2010 (UTC)
Materialscientist ( talk) 06:03, 15 March 2010 (UTC)
If the information is not provided, the image may eventually be proposed for deletion, a situation which is not desirable, and which can easily be avoided.
If you have any questions please see Help:Image page. Thank you. Sfan00 IMG ( talk) 12:04, 16 March 2010 (UTC)Hi Boghog2. I came across this recently discovered endogenous polypeptide agonist for CB1 cannabinoid receptors and figured it was fairly significant seeing as all previous endogenous CB1 agonists have been lipids. I don't suppose you could give us a hand with the data box for the page? As it is clearly better classified as a protein rather than a chemical or drug it should have a protein box, but I'm not sure what should go in there... Meodipt ( talk) 00:11, 22 March 2010 (UTC)
Yeah that looks great, thanks. I suspect the number of short polypeptide fragments that turn out to have important physiological roles will become rather large over the next few years, so perhaps a new template will be needed at some stage! Meodipt ( talk) 08:49, 22 March 2010 (UTC)
Hi Boghog2. Given lack of progress with the thymosin page over years I was surprised and delighted to find my beginner's efforts getting instant support. Am specially grateful re citations. Lots more to be done re remaining cut-and-pastes. And lots for me to learn re Wikipedia. Jgedwards ( talk) 08:45, 24 March 2010 (UTC)
Hi Boghog. Good to point up 15A and 15B. However, it probably needs to be included that in humans the proteins off A and B genes are identical. (Though silent diffs in coding sequence). Happens it was me who spotted there were two genes and pointed out to Bruce Zetter at Harvard Med. School. In due course the b15 story can take on board that the Harvard group have it as a possible clinical marker for aggressive prostate cancer.
May be a little while before I get the actin binding stuff dealt with Jgedwards ( talk) 23:08, 24 March 2010 (UTC)
Thanks for the structure box on the CBS domain page! Much appreciated. Alexbateman ( talk) 09:24, 26 March 2010 (UTC)
Hey, thanks for your fine work with the SEGRA article! Any idea whether SEGRAs interact with membrane GRs? Cheers, ἀνυπόδητος ( talk) 09:59, 30 March 2010 (UTC)
Hi boghog Simplification OK and thanks for citation/punctuation. As a lecturer I sometimes got panned for use of metaphors. Don't actually agree that para was pure peacock, though. There's a big difference between starting with a specific protein and seeing what it can do, and pursuing an unknown factor and finding what it is after all. Maybe I'll try to write that more prosaically sometime. but priority has to be the multiple activities of b4. With promotion of hair growth, repair after heart attack, neurological function..... begins to read like "snake oil" - another metaphor to avoid! . You'll have gathered I did some edits having forgotten to sign in. Jgedwards ( talk) 10:34, 2 April 2010 (UTC)
Hi boghog No call to apologise. I continue to value your help and advice, particularly re what is appropriate for Wikipedia. Latest is that I've received very positive feedback via email from the original discoverer of thymosins, who is also the pre-eminent world authority. He's provided me with a rich vein of further material relating to the biological activities and clinical/medical applications, the latter which will very likely be of interest to general readers. He would like me to Wikify it as appropriate rather than getting directly involved himself. I'm also working on some images of solved structures of thymosin bound to actin. I'm really enjoying this, but please don't hesitate to be WP:BOLD if I stray into inappropriate! Jgedwards ( talk) 11:41, 4 April 2010 (UTC)
Hi. :) Since you seem to have done such a good job on that article, I just wanted to let you know that permission has not yet been verified, so contributions by the contributor who added the copied passages have been removed. I've done my best to salvage the content subsequently placed by you and User:Mary Foster, but I realize this is probably a set-back for the article. Sorry about that! I always hate to see content lost for copyright concerns. :/ Since this is far out of my field, I did want to let you know that the purge is complete. If and when you have a chance, I'd be grateful if you could take a look to make sure that my clumsy cleanup hasn't cost the article vital sense. (I know you probably would anyway, since you've been hanging out there for a while, but I did want to let you know. :)) -- Moonriddengirl (talk) 21:31, 9 April 2010 (UTC)
Boghog, would "Oral care" be more accurate? Mary Foster ( talk) 20:05, 11 April 2010 (UTC)
Function and Applications needs to be summarized in the lede. Mary Foster ( talk) 01:16, 12 April 2010 (UTC)
![]() |
The Copyright Cleanup Barnstar | |
For going above and beyond to rescue Lactoperoxidase after copyright concerns led to the significant loss of content. Your extraordinary efforts are appreciated! Moonriddengirl (talk) 22:33, 12 April 2010 (UTC) |
Hi! You're sure to know this — can you tell me whether the "structure weight" in entries like PDB: 1TTG means the glycoprotein (as opposed to the polypeptide alone)? Cheers, ἀνυπόδητος ( talk) 09:25, 17 April 2010 (UTC)
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:
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:
{{
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:
Does this look reasonable? Boghog ( talk) 18:01, 20 April 2010 (UTC)
~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)
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 = $fields0];
my $PubChem = $fields1];
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)
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)
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! 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)
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)
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).
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)
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
email redacted, visible via dif] —Preceding unsigned comment added by 171.66.82.245 ( talk) 02:15, 18 May 2010 (UTC)
Would you like to receive some computer-generated and partly wikified files from me about protein families (see my recent edits)? Or maybe someone else would? If so, please send me a message through my WP email. Ideally, this should be done by a bot, but I am not really in this business. Great job you are doing! Warm regards. Biophys ( talk) 20:41, 25 May 2010 (UTC)
Regarding the merger proposal. GiftigerWunsch [TALK] 09:48, 6 June 2010 (UTC)
Hi Boghog, thanks a lot for expanding the centrosome template and adding the navbox to the proteins pages. I was just wondering if you did this manually or with some sort of script. best, MichaK ( talk) 07:39, 7 June 2010 (UTC)
Thank you!!!! -- for making all those protein boxes. I am in your debt!! ~ Ciar ~ (Talk) 20:24, 14 June 2010 (UTC)
Hi! You reverted on Endorphin but the simplified text is back again. I don't want to revert again, because I have too many reverts there as it is (even though one of the reverts was a revert of my own revert). Maybe you could revert to a previous version? Thank you! Lova Falk talk 18:57, 19 June 2010 (UTC)
Hey! Thanks for the edits to Ribonuclease T1. Do you have any experience with using images from PDB on Wikipedia? The PDB Policies & References page seems to allow this, but I can't find the right image copyright tag. Eigma ( talk) 21:22, 16 June 2010 (UTC)
Looks like great resource [2]. However, the author is rather eccentric. Biophys ( talk) 20:07, 20 June 2010 (UTC)
Heya, I've been going through the protein domains and I've come across an inconsistency: the field PROSITE is written in lowercase (Prosite) on a lot of pages. I could go through and correct them all, but that would be a pretty big task. The other option (which I suspect would be a lot easier to achieve) would be to make a change to the template and allow either PROSITE or Prosite as valid options. I know you've put a lot of work into the protein domain pages and have a lot more experience on wikipedia that me, so i was wondering if you might want to help with this little tweak. Ta Abergabe ( talk) 12:45, 24 June 2010 (UTC)
Hi! Seeing that your bot is running on Python: Do you know a good way of adding parameters to templates, or of modifying existing ones (like a PyWikipediabot function or some code you have already written)? Just wanted to ask before I start reinventing the wheel. -- ἀνυπόδητος ( talk) 18:37, 25 June 2010 (UTC)
if not ( regexp_er.search(line) or regexp_cas.search(line) or regexp_go.search(line) or regexp_el.search(line) ):
if ( regexp_template.search(line) ):
ReferringPageGenerator
in pagegenerators.py produces the same list of pages as the "what links here" function. Cheers,
ἀνυπόδητος (
talk) 10:55, 26 June 2010 (UTC)Dear BogHog2,
Thank you for your message, and please forgive my uninitiated editing. I should have left existing pages alone. My main objective is to complete the set of human alpha defensin pages, and to make redirect pages so that the many synonyms all point to well-referenced pages named after each defensin protein or gene. The style of antimicrobial peptide pages should be as similar as possible to entries of other proteins such as enzymes. However, defensins aren't enzymes. Perhaps antimicrobial peptides should be treated a little differently than enzymes.
My objection to the language "in humans" in the leading sentence defining each defensin gene is the implication of standardization of gene names across more than one species, which isn't the case. For example, DEFA1 encodes human alpha defensin 1--human only. Mouse alpha defensin 1 is far less similar to DEFA1 than it is to other mouse defensins.
Best regards,
Bcericksen ( talk) 13:20, 15 June 2010 (UTC)
Hi,
I saw that you have been editing Colipase. I really like the further reading sections. In fact I added one last week to the GcvB RNA article. But I did that manually by searching pubmed and then cutting and pasting each pubmed id into the online template filler. It was pretty tedious to do. But it was super useful for the expansion of that article that I have underway. I'd quite like to do this for some other non-coding RNA articles so if you have a less manually intensive approach I'd love to hear about it. Alexbateman ( talk) 21:48, 13 July 2010 (UTC)
#!/usr/bin/perl
use WWW::Wikipedia::TemplateFiller;
my $filler = new WWW::Wikipedia::TemplateFiller();
my $source = $filler->get( pubmed_id => '8566796' )->fill;
my $string = $source->output( add_ref_tag => 1,
vertical => 0,
add_accessdate => 0,
dont_use_etal => 1,
omit_url_if_doi_filled => 1,
extended => 0,
add_param_space => 1 );
print "$string\n";
The following is a Python scripting solution:
#!/usr/bin/python
import re
import string
from Bio import Entrez
from Bio import Medline
Entrez.email = "your_email@domain.com"
months = {'01': "Jan", '02': "Feb", '03': "Mar", '04': "Apr", '05': "May", '06': "Jun", '07': "Jul", '08': "Aug", '09': "Sep", '10': "Oct", '11': "Nov", '12': "Dec"}
def PubMed_Citation(PubMed_ID):
handle = Entrez.efetch(db="pubmed",id=PubMed_ID,rettype="medline",retmode="text")
records = Medline.parse(handle)
ref = ""
for record in records:
if record.has_key("AU"):
author_list = ""
for author in record"AU"]:
author_list = author_list + ", " + author
author_list = author_list2:]
else:
author_list = ""
if record.has_key("TI"):
title = record"TI"
if (title-1:] == "."):
title = title[:-1
else:
title = ""
if record.has_key("TA"):
journal = record"TA"
else:
journal = ""
if record.has_key("VI"):
volume = record"VI"
else:
volume = ""
if record.has_key("IP"):
issue = record"IP"
else:
issue = ""
if record.has_key("PG"):
pages = record"PG"
else:
pages = ""
if record.has_key("DA"):
year = record"DA"][:4
month = monthsrecord"DA"][4:6]]
else:
year = ""
month = ""
if record.has_key("PMID"):
pmid = record"PMID"
else:
pmid = ""
if record.has_key("PMC"):
pmc = record"PMC"][3:]
else:
pmc = ""
if record.has_key("AID"):
doi = ""
for item in record"AID"]:
elements =item.split(" ")
if (len(elements) == 2):
if elements1 == "[doi]":
doi = elements0
else:
doi = ""
ref = ref + "<ref name=\"pmid" + record"PMID" + "\">{{cite journal | author = " + author_list + " | title = " + title + " | journal = " + journal + " | volume = " + volume + " | issue = " + issue + " | pages = " + pages + " | year = " + year + " | month = " + month + " | pmid = " + pmid + " | pmc = " + pmc + " | doi = " + doi + " }}</ref>"
return ref
I hope that you find at least one of these suggestions useful. Cheers. Boghog ( talk) 20:25, 14 July 2010 (UTC)
What do you think about this: [5]? Biophys ( talk) 22:02, 21 July 2010 (UTC)
<16 minutes! Not bad. Many thanks. -- Paul ( talk) 20:34, 31 July 2010 (UTC)
I've moved {{ TCACycle WP78 offset}} for you so that "Template:" isn't repeated twice. — Jeremy ( v^_^v Carl Johnson) 21:10, 2 August 2010 (UTC)
Hi, this [6] has left a broken template '"{{PDB Gallery|genei' on CFL2 (gene). Can't fix it by myself as I have absolutely no clue about genetics. Found the error on [7]. Thanks -- Ben Ben ( talk) 15:04, 4 August 2010 (UTC)
Heya, i'm just wondering about the opening line; would be better to put the gene as the focus of the article:
The '''BTRC''' (beta-transducin repeat containing) '''gene''' in humans encodes for the protein F-box/WD repeat-containing protein 1A, also known as '''pIkappaBalpha-E3 receptor subunit'''.
Than the protein it encodes for:
The '''F-box/WD repeat-containing protein 1A''' also known as '''pIkappaBalpha-E3 receptor subunit''' is a [[protein]] that in humans is encoded by the ''BTRC'' (beta-transducin repeat containing) [[gene]].
Dear wise, glorious and noble Boghog, I have been doing a bit of work on the SMK_box_riboswitch page. This riboswitch has a number of pdb structures but the Infobox_rfam doesn't seem to work in quite the same way as Infobox protein family. Do you have any hints on how I should deal with this?-- Paul ( talk) 22:17, 25 August 2010 (UTC)
Could you check Template_talk:Did_you_know#Protein pigeon homolog? Thanks Smartse ( talk) 16:34, 2 September 2010 (UTC)
![]() | On 11 September 2010, Did you know? was updated with a fact from the article Protein pigeon homolog, which you created or substantially expanded. You are welcome to check how many hits the article got while on the front page ( here's how, quick check ) and add it to DYKSTATS if it got over 5,000. If you know of another interesting fact from a recently created article, then please suggest it on the Did you know? talk page. |
Materialscientist ( talk) 07:19, 11 September 2010 (UTC)
Hi! Can you please fix a little error? The shaded area (AUC) should stretch down to y=0 (not only to Cmin). → Alfie ±Talk 14:32, 13 September 2010 (UTC)
Boghog2, I'd really appreciate it if you would stop reformatting Protein C to fit your aesthetic. I'm working very heavily on this article, and every time you make a change, it makes my work significantly harder. I don't see any benefit to your modifications (except the wikilinking, which has been useful), and I assure you there are reasons for my conventions. If you have a suggestion, please suggest it on the talk page, where we can discuss which way works better. In the mean time, please don't make changes that have no effect except to make my editing more difficult. The article is not done, and if I'm the one currently adding material, I need to be able to read the syntax. -- Rmrfstar ( talk) 16:36, 13 September 2010 (UTC)
Hi there Boghog2, I was making PNG images from PyMol for a class and came across your upload for NFkB. Your rendering looks nice, but I think you cited the wrong PDB ID. The image you rendered was actually 3d07 (NFkB p100/RelB/DNA) rather than 1svc (NFkB p50/DNA). As my homework is due tomorrow, it would be a great help if you could update the PDB ID before 22-Sept-2010, 8am, since I've already rendered an image of 1svc. Thank you! NguyenJB ( talk) 20:43, 21 September 2010 (UTC)NguyenJB
Hi Boghog2. I just spent the last hour checking the release dates as well, and I apologize for the misunderstanding. I think I figured out why my rendering looks different from yours -- you were astute enough to find the correct symmetry mate and generate a homodimer, while I just showed the p50 monomer. Do you think there is a place for me on the website to deposit the new ternary complex? NguyenJB ( talk) 21:28, 21 September 2010 (UTC)NguyenJB
Right. Thank you for the suggestion. I just displayed all symmetry mates within 4 angstrom and selected the one that completed the DNA structure, and I think that should work fine due to the inherent symmetry in the space group. Have you taken a look at the ternary complex that was deposited 2009-07-21? The structure looks very similar (which explains why I was initially confused by your rendering) and the sequence of RelB and NFkB p50 are ~41% identical. Since you've spent some time editing this page and presumably know some molecular science, would you mind critiquing my recent upload ( http://en.wikipedia.org/wiki/NF-κB#Activation) to the NF-kB page? NguyenJB ( talk) 22:40, 21 September 2010 (UTC)
Hi Boghog2. Are you sure the structure for this compound is correct? this link shows a related but different structure for the compound, although the one on the page has a pubchem hit which the other one doesn't... Meodipt ( talk) 13:32, 22 September 2010 (UTC)
^ Any progress on getting the commons ducks in a row? – xeno talk 15:40, 24 September 2010 (UTC)
Hello, I confirm that I'd like to usurp de:User:Boghog. Thank you. Boghog ( talk) 20:04, 25 September 2010 (UTC)
Can you read thoughts [8] [9] or have you just seen my edits to SALL1 and 4? By the way, congratulations to your new name! Is there a baptizing party? -- ἀνυπόδητος ( talk) 11:22, 26 September 2010 (UTC)
I never knew that, thank you for correcting my "correction". - 2/0 ( cont.) 17:26, 3 October 2010 (UTC)
Thanks for helping out with the ABCC2 article. I am busy with other stuff which, sadly, leaves me little time for OAT1 and ABCC2. I recommend that the ABCC2 article be renamed "multidrug resistance-associated protein 2". Now that we know what the MRP2 protein does, it is receiving more attention than the gene.
Googling Canalicular multispecific organic anion transporter 1 generates about 3,400 hits.
Googling ABCC2 generates about 4,700 hits.
Googling MRP2 generates about 14,500 hits and
googling multidrug resistance-associated protein 2 generates about 22,000 hits.
KBlott ( talk) 16:02, 7 October 2010 (UTC)
Hi Boghog: I have added the molecular structures of some known MRP2 inhibitors to the ABCC2 page. All of the image files (so far) are svg type except for one, which is png type. The svg images have a light blue background while the png image has a white background. Do you know how to convert the png file to an svg file? KBlott ( talk) 00:53, 8 October 2010 (UTC)
Hi Boghog. I resumed some activity and created this page: [10]. Any comments or help would be very welcome. Biophys ( talk) 19:27, 9 October 2010 (UTC)
If the information is not provided, the image may eventually be proposed for deletion, a situation which is not desirable, and which can easily be avoided.
If you have any questions please see Help:Image page. Thank you. -- ARTEST4ECHO ( talk | contribs) 17:39, 11 October 2010 (UTC)Hi. I see that you are active in the pharma project. (I know virtually nothing about it.) Do you think agomelatine should be pared down by someone who knows what s/he is doing? The project has it listed as Start class. IMO it is just too much. Thanks, Hordaland ( talk) 10:47, 5 November 2010 (UTC)
Yes this is for an assignment. I put that info in there because it is one of the options for the guidelines on the project. It is due on Monday so if you want to delete info after December 17th 2010 you can (this will give her enough time to see what I did to the page). I just want to make sure I hit the guidelines and get a good grade. Thanks for the help. jviess —Preceding unsigned comment added by Jviess14 ( talk • contribs) 23:39, 20 November 2010 (UTC)
Spaghettimonster ( talk) 21:24, 26 November 2010 (UTC)
I just wanted to say thanks for the advice with the Hepcidin and how to use Wikipedia a little bit better. This is the first time I've had to do this for a class to wikipedia and I always knew it could be edited, but never knew how. Once again, thanks for the advice hopefully the shortcuts will help next time I have to do this for Biochemistry and I'm not sure if I am writing to you the correct way, but it's worth a shot! Duossm49 —Preceding unsigned comment added by Duossm49 ( talk • contribs) 07:30, 30 November 2010 (UTC)
Hi Boghog
It makes sense to have separate entries for thymosin alpha and the beta thymosins (as split out by Arcadian). I've tried to improve some of the wording necessitated by the split, but am not yet happy with it. (Problem of historic versus contemporary usage).
Also good to bring together the otherwise separate references to prothymosin alpha. Thanks for that! However, virtually all the "extra reading" now listed under thymosin alpha1 is actually about prothymosin, which has function/properties besides those of its alpha1 fragment. A separate entry for prothymosin alpha would be a good fix, but this is a daunting prospect given that its conserved function is mysterious. Jgedwards ( talk) 16:30, 30 November 2010 (UTC)
Hi Boghog
No call to apologise! Separate sections within single article, at least for time being, sounds fine. Meanwhile a group at Harvard may have found the holy grail re beta thymosins: a candidate cell surface receptor (Kd 12 nm) and a putative signalling pathway. PMID: 21106936 Gives me a lot else to think about! Jgedwards ( talk) 01:41, 1 December 2010 (UTC)
Thanks for all the edits and advice. I appreciate it.
One question though - SERPINA14 is on bovine chromosome 21 but does not exist in human. Therefore, should it be listed in the chromosome 21 category or be listed as chromosome 21 in the protein table? Ufpete ( talk) 02:00, 2 December 2010 (UTC) Ufpete ( talk) 01:55, 2 December 2010 (UTC)
Hey since im new at this sort of thing, i was wondering if you could walk me through the rationalle for some of the updates you made on the glycogen synthase and ppp1r3c pages. Some proper use feedback would be great. If easier feel free to email me, "dave dot bridges at gmail dot com" Davebridges ( talk) 17:26, 8 December 2010 (UTC)
re: PP1 should be no problem, Ill take a look at that page plus see if i can add anything to PP2A while I'm at it Davebridges ( talk) —Preceding undated comment added 02:33, 10 December 2010 (UTC).
![]() | On 11 December 2010, Did you know? was updated with a fact from the article Kunitz domain, which you created or substantially expanded. The fact was ... that Kunitz domains, the active protein domains of certain protease inhibitors, are used for the development of new drugs? You are welcome to check how many hits the article got while on the front page ( here's how, quick check) and add it to DYKSTATS if it got over 5,000. If you know of another interesting fact from a recently created article, then please suggest it on the Did you know? talk page. |
The DYK project ( nominate) 12:03, 11 December 2010 (UTC)
Just a quick note of Thanks for the 'removal of those "tortured analogies" '. ~ Betaclamp ( talk) 06:54, 23 November 2010 (UTC)
When I said Thanks I really meant it, no sarcasm this time! I'm glad that you could recognize the effect that they had on me/us.
While there is little time now for me to really scour your messages, I just have time to say that whereas my thorough article betaclamp (with no extraneous material) is based upon passages found in a major book, the term Dna-clamp appears to be merely a misnomer. Can we recruit a specialist for this point? Much obliged. ~ Betaclamp ( talk) 07:57, 12 December 2010 (UTC) P.S. my non-contestation is an artifact of 'being new and not wanting to 'step-on-another's-toes' ". May I suggest that you put on your safety shoes?
P.P.S. I do feel the need to placate my 'hack' comment, this will be done by my explanation of why I said it.
I'm delighted to say we have to talk; for now I am working on the supposition that there is no such thing as a Dna clamp that is not also a beta-clamp and I'm working towards proving this. Until then I'll expect Beta clamp to be treated as a separate Article, unless you have another opinion! Merci!
As well, my original 1,000 word beta clamp article contained NO extraneous material. ~ Betaclamp ( talk) 07:47, 9 December 2010 (UTC)
Dna-clamp does not contain the info in Betaclamp. It mentions only prokaryotes and condenses my elucidation of the Greek alphabet into a string of gibberish. 1,000 words diminished to 100 cannot be positive. Time is all that stops me from more elucidation! ~ Betaclamp ( talk) 08:35, 12 December 2010 (UTC) Except for this: I told Adrian that the 'one thing' from the merge that I loved was the addition of the trimer pictograph that he told me that you inserted. Please do the same for the version that you just reinstated, please. Now I can explain the delay that I've mentioned: at the end of the six pages that I took beta-clamp from there is a short section on PCNA, the label on your trimer pictograph; I've yet to study this, it could be that PCNA is a betaclamp.
Yes it does. The eight or so points made lately by myself are all tied together; I've a few unanswered questions that I'll need to prioritize before making another submission. Meanwhile, would you like me to continue here or would a New Section be preferable? ~ Betaclamp ( talk) 06:34, 13 December 2010 (UTC)
And thank you for helping to make Wikipedia a worthwhile place to collaborate! Best wishes.
Boghog (
talk) 16:38, 24 December 2010 (UTC)
![]() | This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 1 | Archive 2 | Archive 3 | Archive 4 | Archive 5 | Archive 6 | → | Archive 10 |
Hey Boghog, I hope that you and your family have a Happy New Year. :-- Literaturegeek | T@1k? 10:03, 2 January 2010 (UTC)
Hope you had a good start into the new year. Besides, I only wanted to ask what you think of my considerations and questions regarding protein and gene names. Cheers, ἀνυπόδητος ( talk) 20:21, 16 January 2010 (UTC)
There appear to be two articles with the same enzyme name:
Should the second article be merged into the first? -- Robert.Allen ( talk) 01:23, 20 January 2010 (UTC)
Hi again! Do you know whether an immunoglobulin fold is the same as an immunoglobulin domain? Looks like it to judge from the Pfam boxes, I'm just irritated by the term "Immunoglobulin-like domain" in the latter article. -- ἀνυπόδητος ( talk) 10:52, 20 January 2010 (UTC)
Hello. Could you possibly do me a favor? I've been trying to start this (it's red I know but click it anyway) article for months. I've requested unprotection 2-3 times but for whatever reason nobody ever does anything about it. Maor Levi is one of my favorite electronic artists of all time and I'd like to give him a place here on Wikipedia. Here's his Last.fm profile. If you can do so thanks a ton! el3ctr0nika ( Talk | Contribs) 04:59, 1 February 2010 (UTC)
Could someone else check out Beta clamp? I suggested redirecting it to DNA clamp at MCB talk but I don't want to be judge, jury and executioner to an article written in good faith by a new contributor. Adrian J. Hunter( talk• contribs) 01:48, 31 January 2010 (UTC)
Thanks for that, Boghog. Sorry I don't have more time right now to help with the merge. Adrian J. Hunter( talk• contribs) 03:57, 4 February 2010 (UTC)
Hi! Just saw that you nominated Nyctalopin for deletion but I have to admit I don't understand the reason. Because NYX_(gene) should be moved to nyctalopin? What's the official wiki policy? Should one name the main article after the gene or the protein? It is quite mixed now as far as I can see. Usually the article is named after the gene but about the protein. Thanks, Panoramix303 ( talk) 20:17, 12 February 2010 (UTC)
![]() |
The Chemistry Star | |
I just wanted to let you know that all your contributions to chemistry articles has not gone unnoticed. Thank you for all your efforts at improving articles in this corner of Wikipedia. -- Ed ( Edgar181) 20:43, 24 February 2010 (UTC) |
I have re-instated it - on hold for seven days. There is a lot of work to be done. Jezhotwells ( talk) 01:54, 27 February 2010 (UTC)
Wow, we did a good job on that entry. Just compare the January version with the latest one. Just in time, too. We got >4,000 hits after that New York Times story. -- Nbauman ( talk) 06:20, 3 March 2010 (UTC)
Hello! Your submission of
Cereblon at the
Did You Know nominations page has been reviewed, and there still are some issues that may need to be clarified. Please review the comment(s) underneath
your nomination's entry and respond there as soon as possible. Thank you for contributing to Did You Know!
SusanLesch (
talk) 00:44, 12 March 2010 (UTC)
Materialscientist ( talk) 06:03, 15 March 2010 (UTC)
If the information is not provided, the image may eventually be proposed for deletion, a situation which is not desirable, and which can easily be avoided.
If you have any questions please see Help:Image page. Thank you. Sfan00 IMG ( talk) 12:04, 16 March 2010 (UTC)Hi Boghog2. I came across this recently discovered endogenous polypeptide agonist for CB1 cannabinoid receptors and figured it was fairly significant seeing as all previous endogenous CB1 agonists have been lipids. I don't suppose you could give us a hand with the data box for the page? As it is clearly better classified as a protein rather than a chemical or drug it should have a protein box, but I'm not sure what should go in there... Meodipt ( talk) 00:11, 22 March 2010 (UTC)
Yeah that looks great, thanks. I suspect the number of short polypeptide fragments that turn out to have important physiological roles will become rather large over the next few years, so perhaps a new template will be needed at some stage! Meodipt ( talk) 08:49, 22 March 2010 (UTC)
Hi Boghog2. Given lack of progress with the thymosin page over years I was surprised and delighted to find my beginner's efforts getting instant support. Am specially grateful re citations. Lots more to be done re remaining cut-and-pastes. And lots for me to learn re Wikipedia. Jgedwards ( talk) 08:45, 24 March 2010 (UTC)
Hi Boghog. Good to point up 15A and 15B. However, it probably needs to be included that in humans the proteins off A and B genes are identical. (Though silent diffs in coding sequence). Happens it was me who spotted there were two genes and pointed out to Bruce Zetter at Harvard Med. School. In due course the b15 story can take on board that the Harvard group have it as a possible clinical marker for aggressive prostate cancer.
May be a little while before I get the actin binding stuff dealt with Jgedwards ( talk) 23:08, 24 March 2010 (UTC)
Thanks for the structure box on the CBS domain page! Much appreciated. Alexbateman ( talk) 09:24, 26 March 2010 (UTC)
Hey, thanks for your fine work with the SEGRA article! Any idea whether SEGRAs interact with membrane GRs? Cheers, ἀνυπόδητος ( talk) 09:59, 30 March 2010 (UTC)
Hi boghog Simplification OK and thanks for citation/punctuation. As a lecturer I sometimes got panned for use of metaphors. Don't actually agree that para was pure peacock, though. There's a big difference between starting with a specific protein and seeing what it can do, and pursuing an unknown factor and finding what it is after all. Maybe I'll try to write that more prosaically sometime. but priority has to be the multiple activities of b4. With promotion of hair growth, repair after heart attack, neurological function..... begins to read like "snake oil" - another metaphor to avoid! . You'll have gathered I did some edits having forgotten to sign in. Jgedwards ( talk) 10:34, 2 April 2010 (UTC)
Hi boghog No call to apologise. I continue to value your help and advice, particularly re what is appropriate for Wikipedia. Latest is that I've received very positive feedback via email from the original discoverer of thymosins, who is also the pre-eminent world authority. He's provided me with a rich vein of further material relating to the biological activities and clinical/medical applications, the latter which will very likely be of interest to general readers. He would like me to Wikify it as appropriate rather than getting directly involved himself. I'm also working on some images of solved structures of thymosin bound to actin. I'm really enjoying this, but please don't hesitate to be WP:BOLD if I stray into inappropriate! Jgedwards ( talk) 11:41, 4 April 2010 (UTC)
Hi. :) Since you seem to have done such a good job on that article, I just wanted to let you know that permission has not yet been verified, so contributions by the contributor who added the copied passages have been removed. I've done my best to salvage the content subsequently placed by you and User:Mary Foster, but I realize this is probably a set-back for the article. Sorry about that! I always hate to see content lost for copyright concerns. :/ Since this is far out of my field, I did want to let you know that the purge is complete. If and when you have a chance, I'd be grateful if you could take a look to make sure that my clumsy cleanup hasn't cost the article vital sense. (I know you probably would anyway, since you've been hanging out there for a while, but I did want to let you know. :)) -- Moonriddengirl (talk) 21:31, 9 April 2010 (UTC)
Boghog, would "Oral care" be more accurate? Mary Foster ( talk) 20:05, 11 April 2010 (UTC)
Function and Applications needs to be summarized in the lede. Mary Foster ( talk) 01:16, 12 April 2010 (UTC)
![]() |
The Copyright Cleanup Barnstar | |
For going above and beyond to rescue Lactoperoxidase after copyright concerns led to the significant loss of content. Your extraordinary efforts are appreciated! Moonriddengirl (talk) 22:33, 12 April 2010 (UTC) |
Hi! You're sure to know this — can you tell me whether the "structure weight" in entries like PDB: 1TTG means the glycoprotein (as opposed to the polypeptide alone)? Cheers, ἀνυπόδητος ( talk) 09:25, 17 April 2010 (UTC)
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:
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:
{{
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:
Does this look reasonable? Boghog ( talk) 18:01, 20 April 2010 (UTC)
~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)
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 = $fields0];
my $PubChem = $fields1];
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)
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)
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! 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)
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)
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).
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)
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
email redacted, visible via dif] —Preceding unsigned comment added by 171.66.82.245 ( talk) 02:15, 18 May 2010 (UTC)
Would you like to receive some computer-generated and partly wikified files from me about protein families (see my recent edits)? Or maybe someone else would? If so, please send me a message through my WP email. Ideally, this should be done by a bot, but I am not really in this business. Great job you are doing! Warm regards. Biophys ( talk) 20:41, 25 May 2010 (UTC)
Regarding the merger proposal. GiftigerWunsch [TALK] 09:48, 6 June 2010 (UTC)
Hi Boghog, thanks a lot for expanding the centrosome template and adding the navbox to the proteins pages. I was just wondering if you did this manually or with some sort of script. best, MichaK ( talk) 07:39, 7 June 2010 (UTC)
Thank you!!!! -- for making all those protein boxes. I am in your debt!! ~ Ciar ~ (Talk) 20:24, 14 June 2010 (UTC)
Hi! You reverted on Endorphin but the simplified text is back again. I don't want to revert again, because I have too many reverts there as it is (even though one of the reverts was a revert of my own revert). Maybe you could revert to a previous version? Thank you! Lova Falk talk 18:57, 19 June 2010 (UTC)
Hey! Thanks for the edits to Ribonuclease T1. Do you have any experience with using images from PDB on Wikipedia? The PDB Policies & References page seems to allow this, but I can't find the right image copyright tag. Eigma ( talk) 21:22, 16 June 2010 (UTC)
Looks like great resource [2]. However, the author is rather eccentric. Biophys ( talk) 20:07, 20 June 2010 (UTC)
Heya, I've been going through the protein domains and I've come across an inconsistency: the field PROSITE is written in lowercase (Prosite) on a lot of pages. I could go through and correct them all, but that would be a pretty big task. The other option (which I suspect would be a lot easier to achieve) would be to make a change to the template and allow either PROSITE or Prosite as valid options. I know you've put a lot of work into the protein domain pages and have a lot more experience on wikipedia that me, so i was wondering if you might want to help with this little tweak. Ta Abergabe ( talk) 12:45, 24 June 2010 (UTC)
Hi! Seeing that your bot is running on Python: Do you know a good way of adding parameters to templates, or of modifying existing ones (like a PyWikipediabot function or some code you have already written)? Just wanted to ask before I start reinventing the wheel. -- ἀνυπόδητος ( talk) 18:37, 25 June 2010 (UTC)
if not ( regexp_er.search(line) or regexp_cas.search(line) or regexp_go.search(line) or regexp_el.search(line) ):
if ( regexp_template.search(line) ):
ReferringPageGenerator
in pagegenerators.py produces the same list of pages as the "what links here" function. Cheers,
ἀνυπόδητος (
talk) 10:55, 26 June 2010 (UTC)Dear BogHog2,
Thank you for your message, and please forgive my uninitiated editing. I should have left existing pages alone. My main objective is to complete the set of human alpha defensin pages, and to make redirect pages so that the many synonyms all point to well-referenced pages named after each defensin protein or gene. The style of antimicrobial peptide pages should be as similar as possible to entries of other proteins such as enzymes. However, defensins aren't enzymes. Perhaps antimicrobial peptides should be treated a little differently than enzymes.
My objection to the language "in humans" in the leading sentence defining each defensin gene is the implication of standardization of gene names across more than one species, which isn't the case. For example, DEFA1 encodes human alpha defensin 1--human only. Mouse alpha defensin 1 is far less similar to DEFA1 than it is to other mouse defensins.
Best regards,
Bcericksen ( talk) 13:20, 15 June 2010 (UTC)
Hi,
I saw that you have been editing Colipase. I really like the further reading sections. In fact I added one last week to the GcvB RNA article. But I did that manually by searching pubmed and then cutting and pasting each pubmed id into the online template filler. It was pretty tedious to do. But it was super useful for the expansion of that article that I have underway. I'd quite like to do this for some other non-coding RNA articles so if you have a less manually intensive approach I'd love to hear about it. Alexbateman ( talk) 21:48, 13 July 2010 (UTC)
#!/usr/bin/perl
use WWW::Wikipedia::TemplateFiller;
my $filler = new WWW::Wikipedia::TemplateFiller();
my $source = $filler->get( pubmed_id => '8566796' )->fill;
my $string = $source->output( add_ref_tag => 1,
vertical => 0,
add_accessdate => 0,
dont_use_etal => 1,
omit_url_if_doi_filled => 1,
extended => 0,
add_param_space => 1 );
print "$string\n";
The following is a Python scripting solution:
#!/usr/bin/python
import re
import string
from Bio import Entrez
from Bio import Medline
Entrez.email = "your_email@domain.com"
months = {'01': "Jan", '02': "Feb", '03': "Mar", '04': "Apr", '05': "May", '06': "Jun", '07': "Jul", '08': "Aug", '09': "Sep", '10': "Oct", '11': "Nov", '12': "Dec"}
def PubMed_Citation(PubMed_ID):
handle = Entrez.efetch(db="pubmed",id=PubMed_ID,rettype="medline",retmode="text")
records = Medline.parse(handle)
ref = ""
for record in records:
if record.has_key("AU"):
author_list = ""
for author in record"AU"]:
author_list = author_list + ", " + author
author_list = author_list2:]
else:
author_list = ""
if record.has_key("TI"):
title = record"TI"
if (title-1:] == "."):
title = title[:-1
else:
title = ""
if record.has_key("TA"):
journal = record"TA"
else:
journal = ""
if record.has_key("VI"):
volume = record"VI"
else:
volume = ""
if record.has_key("IP"):
issue = record"IP"
else:
issue = ""
if record.has_key("PG"):
pages = record"PG"
else:
pages = ""
if record.has_key("DA"):
year = record"DA"][:4
month = monthsrecord"DA"][4:6]]
else:
year = ""
month = ""
if record.has_key("PMID"):
pmid = record"PMID"
else:
pmid = ""
if record.has_key("PMC"):
pmc = record"PMC"][3:]
else:
pmc = ""
if record.has_key("AID"):
doi = ""
for item in record"AID"]:
elements =item.split(" ")
if (len(elements) == 2):
if elements1 == "[doi]":
doi = elements0
else:
doi = ""
ref = ref + "<ref name=\"pmid" + record"PMID" + "\">{{cite journal | author = " + author_list + " | title = " + title + " | journal = " + journal + " | volume = " + volume + " | issue = " + issue + " | pages = " + pages + " | year = " + year + " | month = " + month + " | pmid = " + pmid + " | pmc = " + pmc + " | doi = " + doi + " }}</ref>"
return ref
I hope that you find at least one of these suggestions useful. Cheers. Boghog ( talk) 20:25, 14 July 2010 (UTC)
What do you think about this: [5]? Biophys ( talk) 22:02, 21 July 2010 (UTC)
<16 minutes! Not bad. Many thanks. -- Paul ( talk) 20:34, 31 July 2010 (UTC)
I've moved {{ TCACycle WP78 offset}} for you so that "Template:" isn't repeated twice. — Jeremy ( v^_^v Carl Johnson) 21:10, 2 August 2010 (UTC)
Hi, this [6] has left a broken template '"{{PDB Gallery|genei' on CFL2 (gene). Can't fix it by myself as I have absolutely no clue about genetics. Found the error on [7]. Thanks -- Ben Ben ( talk) 15:04, 4 August 2010 (UTC)
Heya, i'm just wondering about the opening line; would be better to put the gene as the focus of the article:
The '''BTRC''' (beta-transducin repeat containing) '''gene''' in humans encodes for the protein F-box/WD repeat-containing protein 1A, also known as '''pIkappaBalpha-E3 receptor subunit'''.
Than the protein it encodes for:
The '''F-box/WD repeat-containing protein 1A''' also known as '''pIkappaBalpha-E3 receptor subunit''' is a [[protein]] that in humans is encoded by the ''BTRC'' (beta-transducin repeat containing) [[gene]].
Dear wise, glorious and noble Boghog, I have been doing a bit of work on the SMK_box_riboswitch page. This riboswitch has a number of pdb structures but the Infobox_rfam doesn't seem to work in quite the same way as Infobox protein family. Do you have any hints on how I should deal with this?-- Paul ( talk) 22:17, 25 August 2010 (UTC)
Could you check Template_talk:Did_you_know#Protein pigeon homolog? Thanks Smartse ( talk) 16:34, 2 September 2010 (UTC)
![]() | On 11 September 2010, Did you know? was updated with a fact from the article Protein pigeon homolog, which you created or substantially expanded. You are welcome to check how many hits the article got while on the front page ( here's how, quick check ) and add it to DYKSTATS if it got over 5,000. If you know of another interesting fact from a recently created article, then please suggest it on the Did you know? talk page. |
Materialscientist ( talk) 07:19, 11 September 2010 (UTC)
Hi! Can you please fix a little error? The shaded area (AUC) should stretch down to y=0 (not only to Cmin). → Alfie ±Talk 14:32, 13 September 2010 (UTC)
Boghog2, I'd really appreciate it if you would stop reformatting Protein C to fit your aesthetic. I'm working very heavily on this article, and every time you make a change, it makes my work significantly harder. I don't see any benefit to your modifications (except the wikilinking, which has been useful), and I assure you there are reasons for my conventions. If you have a suggestion, please suggest it on the talk page, where we can discuss which way works better. In the mean time, please don't make changes that have no effect except to make my editing more difficult. The article is not done, and if I'm the one currently adding material, I need to be able to read the syntax. -- Rmrfstar ( talk) 16:36, 13 September 2010 (UTC)
Hi there Boghog2, I was making PNG images from PyMol for a class and came across your upload for NFkB. Your rendering looks nice, but I think you cited the wrong PDB ID. The image you rendered was actually 3d07 (NFkB p100/RelB/DNA) rather than 1svc (NFkB p50/DNA). As my homework is due tomorrow, it would be a great help if you could update the PDB ID before 22-Sept-2010, 8am, since I've already rendered an image of 1svc. Thank you! NguyenJB ( talk) 20:43, 21 September 2010 (UTC)NguyenJB
Hi Boghog2. I just spent the last hour checking the release dates as well, and I apologize for the misunderstanding. I think I figured out why my rendering looks different from yours -- you were astute enough to find the correct symmetry mate and generate a homodimer, while I just showed the p50 monomer. Do you think there is a place for me on the website to deposit the new ternary complex? NguyenJB ( talk) 21:28, 21 September 2010 (UTC)NguyenJB
Right. Thank you for the suggestion. I just displayed all symmetry mates within 4 angstrom and selected the one that completed the DNA structure, and I think that should work fine due to the inherent symmetry in the space group. Have you taken a look at the ternary complex that was deposited 2009-07-21? The structure looks very similar (which explains why I was initially confused by your rendering) and the sequence of RelB and NFkB p50 are ~41% identical. Since you've spent some time editing this page and presumably know some molecular science, would you mind critiquing my recent upload ( http://en.wikipedia.org/wiki/NF-κB#Activation) to the NF-kB page? NguyenJB ( talk) 22:40, 21 September 2010 (UTC)
Hi Boghog2. Are you sure the structure for this compound is correct? this link shows a related but different structure for the compound, although the one on the page has a pubchem hit which the other one doesn't... Meodipt ( talk) 13:32, 22 September 2010 (UTC)
^ Any progress on getting the commons ducks in a row? – xeno talk 15:40, 24 September 2010 (UTC)
Hello, I confirm that I'd like to usurp de:User:Boghog. Thank you. Boghog ( talk) 20:04, 25 September 2010 (UTC)
Can you read thoughts [8] [9] or have you just seen my edits to SALL1 and 4? By the way, congratulations to your new name! Is there a baptizing party? -- ἀνυπόδητος ( talk) 11:22, 26 September 2010 (UTC)
I never knew that, thank you for correcting my "correction". - 2/0 ( cont.) 17:26, 3 October 2010 (UTC)
Thanks for helping out with the ABCC2 article. I am busy with other stuff which, sadly, leaves me little time for OAT1 and ABCC2. I recommend that the ABCC2 article be renamed "multidrug resistance-associated protein 2". Now that we know what the MRP2 protein does, it is receiving more attention than the gene.
Googling Canalicular multispecific organic anion transporter 1 generates about 3,400 hits.
Googling ABCC2 generates about 4,700 hits.
Googling MRP2 generates about 14,500 hits and
googling multidrug resistance-associated protein 2 generates about 22,000 hits.
KBlott ( talk) 16:02, 7 October 2010 (UTC)
Hi Boghog: I have added the molecular structures of some known MRP2 inhibitors to the ABCC2 page. All of the image files (so far) are svg type except for one, which is png type. The svg images have a light blue background while the png image has a white background. Do you know how to convert the png file to an svg file? KBlott ( talk) 00:53, 8 October 2010 (UTC)
Hi Boghog. I resumed some activity and created this page: [10]. Any comments or help would be very welcome. Biophys ( talk) 19:27, 9 October 2010 (UTC)
If the information is not provided, the image may eventually be proposed for deletion, a situation which is not desirable, and which can easily be avoided.
If you have any questions please see Help:Image page. Thank you. -- ARTEST4ECHO ( talk | contribs) 17:39, 11 October 2010 (UTC)Hi. I see that you are active in the pharma project. (I know virtually nothing about it.) Do you think agomelatine should be pared down by someone who knows what s/he is doing? The project has it listed as Start class. IMO it is just too much. Thanks, Hordaland ( talk) 10:47, 5 November 2010 (UTC)
Yes this is for an assignment. I put that info in there because it is one of the options for the guidelines on the project. It is due on Monday so if you want to delete info after December 17th 2010 you can (this will give her enough time to see what I did to the page). I just want to make sure I hit the guidelines and get a good grade. Thanks for the help. jviess —Preceding unsigned comment added by Jviess14 ( talk • contribs) 23:39, 20 November 2010 (UTC)
Spaghettimonster ( talk) 21:24, 26 November 2010 (UTC)
I just wanted to say thanks for the advice with the Hepcidin and how to use Wikipedia a little bit better. This is the first time I've had to do this for a class to wikipedia and I always knew it could be edited, but never knew how. Once again, thanks for the advice hopefully the shortcuts will help next time I have to do this for Biochemistry and I'm not sure if I am writing to you the correct way, but it's worth a shot! Duossm49 —Preceding unsigned comment added by Duossm49 ( talk • contribs) 07:30, 30 November 2010 (UTC)
Hi Boghog
It makes sense to have separate entries for thymosin alpha and the beta thymosins (as split out by Arcadian). I've tried to improve some of the wording necessitated by the split, but am not yet happy with it. (Problem of historic versus contemporary usage).
Also good to bring together the otherwise separate references to prothymosin alpha. Thanks for that! However, virtually all the "extra reading" now listed under thymosin alpha1 is actually about prothymosin, which has function/properties besides those of its alpha1 fragment. A separate entry for prothymosin alpha would be a good fix, but this is a daunting prospect given that its conserved function is mysterious. Jgedwards ( talk) 16:30, 30 November 2010 (UTC)
Hi Boghog
No call to apologise! Separate sections within single article, at least for time being, sounds fine. Meanwhile a group at Harvard may have found the holy grail re beta thymosins: a candidate cell surface receptor (Kd 12 nm) and a putative signalling pathway. PMID: 21106936 Gives me a lot else to think about! Jgedwards ( talk) 01:41, 1 December 2010 (UTC)
Thanks for all the edits and advice. I appreciate it.
One question though - SERPINA14 is on bovine chromosome 21 but does not exist in human. Therefore, should it be listed in the chromosome 21 category or be listed as chromosome 21 in the protein table? Ufpete ( talk) 02:00, 2 December 2010 (UTC) Ufpete ( talk) 01:55, 2 December 2010 (UTC)
Hey since im new at this sort of thing, i was wondering if you could walk me through the rationalle for some of the updates you made on the glycogen synthase and ppp1r3c pages. Some proper use feedback would be great. If easier feel free to email me, "dave dot bridges at gmail dot com" Davebridges ( talk) 17:26, 8 December 2010 (UTC)
re: PP1 should be no problem, Ill take a look at that page plus see if i can add anything to PP2A while I'm at it Davebridges ( talk) —Preceding undated comment added 02:33, 10 December 2010 (UTC).
![]() | On 11 December 2010, Did you know? was updated with a fact from the article Kunitz domain, which you created or substantially expanded. The fact was ... that Kunitz domains, the active protein domains of certain protease inhibitors, are used for the development of new drugs? You are welcome to check how many hits the article got while on the front page ( here's how, quick check) and add it to DYKSTATS if it got over 5,000. If you know of another interesting fact from a recently created article, then please suggest it on the Did you know? talk page. |
The DYK project ( nominate) 12:03, 11 December 2010 (UTC)
Just a quick note of Thanks for the 'removal of those "tortured analogies" '. ~ Betaclamp ( talk) 06:54, 23 November 2010 (UTC)
When I said Thanks I really meant it, no sarcasm this time! I'm glad that you could recognize the effect that they had on me/us.
While there is little time now for me to really scour your messages, I just have time to say that whereas my thorough article betaclamp (with no extraneous material) is based upon passages found in a major book, the term Dna-clamp appears to be merely a misnomer. Can we recruit a specialist for this point? Much obliged. ~ Betaclamp ( talk) 07:57, 12 December 2010 (UTC) P.S. my non-contestation is an artifact of 'being new and not wanting to 'step-on-another's-toes' ". May I suggest that you put on your safety shoes?
P.P.S. I do feel the need to placate my 'hack' comment, this will be done by my explanation of why I said it.
I'm delighted to say we have to talk; for now I am working on the supposition that there is no such thing as a Dna clamp that is not also a beta-clamp and I'm working towards proving this. Until then I'll expect Beta clamp to be treated as a separate Article, unless you have another opinion! Merci!
As well, my original 1,000 word beta clamp article contained NO extraneous material. ~ Betaclamp ( talk) 07:47, 9 December 2010 (UTC)
Dna-clamp does not contain the info in Betaclamp. It mentions only prokaryotes and condenses my elucidation of the Greek alphabet into a string of gibberish. 1,000 words diminished to 100 cannot be positive. Time is all that stops me from more elucidation! ~ Betaclamp ( talk) 08:35, 12 December 2010 (UTC) Except for this: I told Adrian that the 'one thing' from the merge that I loved was the addition of the trimer pictograph that he told me that you inserted. Please do the same for the version that you just reinstated, please. Now I can explain the delay that I've mentioned: at the end of the six pages that I took beta-clamp from there is a short section on PCNA, the label on your trimer pictograph; I've yet to study this, it could be that PCNA is a betaclamp.
Yes it does. The eight or so points made lately by myself are all tied together; I've a few unanswered questions that I'll need to prioritize before making another submission. Meanwhile, would you like me to continue here or would a New Section be preferable? ~ Betaclamp ( talk) 06:34, 13 December 2010 (UTC)
And thank you for helping to make Wikipedia a worthwhile place to collaborate! Best wishes.
Boghog (
talk) 16:38, 24 December 2010 (UTC)