User talk:Boghog/Archive 6

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Trypsin

Thank you for tidying and summarising my entry for trypsin use in food. Unfortunately, it appears to me as though your summary is just the original with parts missing. In particular, my whole reason for editing the article, the use of trypsin in baby food, along with the detailed reasons for its use, has disappeared altogether.

Certainly, the article is better now than it was before I deleted the original baby food thing, in that it says nothing, but in England and Wales this is part of the curriculum for more than half of our school students, and I believe that they would appreciate a full explanation of the reason for protease enzymes in this application.

I'll leave it to you. — Preceding unsigned comment added by LittleStretton (talk • contribs) 03:49, 2 January 2012 (UTC)

Per your request, I have re-added detail about baby food in this edit. Please note that the original material is marked as "© 2012 by GMO Compass. All rights reserved." Hence per WP:CV it is not permissible to copy and paste this material into Wikipedia. I tried to summarize and paraphrase this material to remove the copyright concerns. Cheers. Boghog (talk) 04:11, 2 January 2012 (UTC)

Thanks

Thank you for your help with the citations on genome-wide association study. I'm really trying to get them to work, but they keep causing problems. --LasseFolkersen (talk) 12:15, 17 January 2012 (UTC)

No problem. I have been using User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article. If you want to include the citation "in-line", be sure that the "add ref tag" option of the template tool is turned on. If you want to include a reference in the further reading section, the "add ref tag" option should be left off. Cheers. Boghog (talk) 20:39, 17 January 2012 (UTC)

PDB links

Hi, thanks for your message. I really like the enzyme browser that I've modified the link for. It would be good to modify the infobox for pfam similarly to go to PDBe's browser ebi.ac.uk/pdbe-srv/PDBeXplore/pfam/?pfam= but the template is protected so I can't edit it.

Yes the problem with PBB/3043 was the links. I can get a search term encoded in the URL at PDBe, but not from the RCSB site, and I want to be fair to both. RCSBs search results have some kind of session ID as the URL and I've no idea how to code the search in the link from wikipedia. (though the Pfam infobox manages it) Would be excellent to apply that to all the Genewiki articles if we can sort out the search URL to have uptodate PDB info from the different PDB sites. Uniprot ID isn't ideal, but until there's a homologene search I guess its better than a long list of four letter codes. I'll do some digging and see if I can work out the RCSB's URL issue. A2-33 — Preceding unsigned comment added by A2-33 (talk • contribs) 21:46, 20 January 2012 (UTC)

New IUPHAR links

~ Hi

The IUPHAR Database team would like to update Wikipedia with information on recent updates to receptors and ligands as well as inform the community about a new project which IUPHAR are involved in that might be of interest to Wikipedia readers.

As you know, IUPHAR experts and database curators are continuously working to maintain and grow IUPHAR-DB with up-to-date information on the properties of receptors and their recommended experimental and approved drugs and endogenous ligands. The links on Wikipedia to IUPHAR-DB pages provide readers with detailed information and literature references on the recommended nomenclature, function, expression, pathophysiology and pharmacology of GPCRs, Ion Channels and Nuclear Receptors. Links from Wikipedia drug pages to IUPHAR-DB ligand pages provide literature data for ligand actions and affinities at the receptors.

In order to ensure that Wikipedia readers have access to the current information we are attaching up-to-date files of our ligands and receptors containing all the information that you should need to add links to new ligands and receptors in IUPHAR-DB or update links that might have changed. do you think it will be OK for me to send you the appropriate ligand lists and new receptors as we did the last time-- It would be great if you could use the information to add links to Wikipedia and then send us back these files with mappings to Wikipedia URLs so we can add reciprocal links.

We would like to let you know about a new online portal, the Guide to Pharmacology, being jointly developed by IUPHAR and the British Pharmacological Society. The Guide to Pharmacology includes a searchable database of information from IUPHAR-DB and the BPS Guide to Receptors and Channels (GRAC), published every 1-2 years in the British Journal of Pharmacology and providing a succinct summary of the properties, key references and selective ligands of ~1600 drug targets and related proteins. The first version of the Guide to Pharmacology includes data for GPCRs, Ion Channels and Nuclear Receptors, with Enzymes, Catalytic Receptors and Transporters under development for release in 2012 Chidochangu

Hi Chidochangu, sounds great. Please send me the list of IUPHAR-DB links and I will see to it that corresponding Wikipedia articles are updated. In return, I will send you mappings from Wikipedia articles to the IUPHAR-DB. Cheers. Boghog (talk) 21:16, 10 January 2012 (UTC)

Hi Boghog, sorry for the delay. Please have a look at the following lists [iuphar receptors -- iuphar ligands] and see if they are suitable for you. I will certainly look forward to the wikipedia links so that we can reciprocate the links on IUPHAR-DB and the sister portal (guide to pharmacology) Chidochangu —Preceding undated comment added 09:13, 26 January 2012 (UTC).

Thanks for the data files which I have down loaded. I should have some time this week end to write a bot script to go through Wikipedia protein and drug articles and update the IUPHAR links. At the same time, I will compile a mapping between Wikipedia article names and IUPHAR database entries and forward that list when I am done. Cheers. Boghog (talk) 05:27, 27 January 2012 (UTC)

IUPHAR links

Hi B, any progress with the IUPHAR links? Are the files ok for you? Chidochangu —Preceding undated comment added 09:00, 23 February 2012 (UTC).

Hi Chidochangu. Your files are perfect. I have already updated the {{IUPHAR}} template. The {{drugbox}} links are more complicated. Things have been incredably complicated for me in real life over the last several weeks and will take one or two more weeks for me to sort it out. I will get back to you in a week or two. Please have patience. Cheers. Boghog (talk) 20:19, 23 February 2012 (UTC)

New IUPHAR links

Hi any more progress with the IUPHAR links? Cheers

Chidochangu

Well done!

		The Tireless Contributor Barnstar
		For having contributed a thousand new articles to Wikipedia. Properly sourced, too - at least those I looked at. Keep it up; I'm sure you have hundreds more in you! ;) Aridd (talk) 18:56, 25 January 2012 (UTC)

Thanks. Much appreciated. Good grief! I had no idea that I had created that many. Anyway, the Gene Wiki project has created articles for 10,000 human genes. There are still 10,000 genes left which should keep me busy ;-) Boghog (talk) 20:22, 25 January 2012 (UTC)

Template:Infobox protein family

Just seen that you've implemented the change to Template:Infobox protein family to point to the PDBe Pfam browser. Like the enzyme info box, definitely an improvement. Thanks. — Preceding unsigned comment added by A2-33 (talk • contribs) 22:45, 5 February 2012 (UTC)

Pramiracetam copyvio

Looks like it came from http://www.antiaging-systems.com/articles/189-pramiracetam-the-ultimate-smart-drug --Gwern (contribs) 00:02 9 February 2012 (GMT)

Thanks. I have left a message on the users talk page. Boghog (talk) 07:18, 9 February 2012 (UTC)

Derp!

Thanks for catching that! - I'm a bit out of practice :) - Alison ^❤ 07:59, 10 February 2012 (UTC)

Vitamin D Page

Thanks, Boghog, for tedious work on the citations... I had done it on 2-12-12, but jmh649 decided it wasn't useful so reverted back to less accurate info, destroying my edits. Appreciate your effort! --Zefr (talk) 05:14, 17 February 2012 (UTC)

Citing patents

Thank you for your work on {{Citation/patent}} and {{cite patent}}. Note that I changed "dash" to "slash" in your post at Template talk:Citation/patent#Proposal to add DisplayedPublicationNumber parameter as I believe that is what you meant. Note also that patameters in {{cite patent}} are all lower case, so |DisplayedNumber= should probably be |displayednumber=. (Please respond either here or, better, at Template talk:Citation/patent.) HairyWombat 20:50, 11 March 2012 (UTC)

Later. I also corrected your link to discussion. HairyWombat 20:58, 11 March 2012 (UTC)

I am rapdily loosing patience with your obsessive nitpicking. The purpose of the proposals (unindexed inventor parameter and DisplayedPublicationNumber) is to first to determine if there is support for these changes. If there is support, we can then make sure all the "i's are dotted and the t's are crossed". Please also keep in mind WP:TPO. Thank you. Boghog (talk) 07:30, 12 March 2012 (UTC)

WP:TPO states, "This page in a nutshell: Talk pages are for improving the encyclopedia, not for expressing personal opinions on a subject or an editor." I did not express a personal opinion on a subject or on an editor. What you call "nitpicking", I call accuracy; undotted 'i's and non-crossed 't's can cause confusion, and so are unhelpful when gathering support. I mentioned my corrections to your proposal here only as a courtesy. HairyWombat 17:10, 12 March 2012 (UTC)

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PDB links in drug box

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

Hi. I see that you have some edits to drugbox in sandbox2. I was wondering if we could add links to PDB entries with molecules. There is no information in these boxes on "bound structure". I was wondering if the following kind of link woul dbe useful to add to this box - e.g. for Nicotine I have added http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/ligand/?ligand=NCT under external links. I can easily provide mapping between PDB three letter codes and InCHI string or keys or mapping to ChEMBL id's. A2-25 (talk) 20:42, 25 February 2012 (UTC)

Yes, this certainly could be done and I would personally support it. My only reservation is that the {{drugbox}} is becoming incredibly complex and we must be careful of feature creep. Another issue is where to place the link. Incredibly this infobox does not currently contain any information about target or mechanism other than the ATC code. Perhaps we should add a mechanism section (perhaps called "pharmacodynamic data") that includes the ATC code, a wiki link to the biological target, and other basic information (whether the drug acts as agonist, antagonist, irreversible inhibitor, etc.). The adding the PDB link to this section would make the most sense. There are a lot of editors who have strong opinions about this template, so we need to build consensus before making any changes. Boghog (talk) 21:59, 25 February 2012 (UTC)

On second thought, it might be better to create a new infobox containing drug mechanism information. I have created a prototype {{infobox drug mechanism}} template and a filled out example can be seen to the right. The advantage of having a separate infobox is that it can be placed in the mechanism of action section of the drug article and in addition, we can add a image of the drug/protein complex. Thoughts? Boghog (talk) 06:43, 26 February 2012 (UTC)

This would be a better way of doing it. A new box woud allow us to add extra information later. e.g. I would very much like to start adding information about the binding sites etc. Have a look at - http://www.ebi.ac.uk/pdbe-srv/pdbexpress/ligandEnvironment/showEnvironment?ligand=RTL which gives more information on binding residues. Another such analysis that might be useful is - http://www.ebi.ac.uk/pdbe-srv/pdbexpress/EC/showEnzymes?ligand=MAN. We can also add extra information on targets if such information is easily accessible via link. So I support adding an extra box. One of the images below is ligand interaction image so we can add that as you suggest. Suggestions/thoughts? A2-25 (talk) 08:42, 26 February 2012 (UTC)

While there are exceptions, most drugs bind with high affinity to a single biological target that in turn is responsible for the therapeutic effect. Hence for drugs, I think a link to a LigPlot or PoseView representation of the binding cavity (see for example LigPlot O32/3og7 or PoseView O32/3og7) would be more relevant. The links that you have provided above to composite binding site information may be of more relevant for promiscuous ligands that bind to many different types of proteins, and hence would be more appropriate to add for example to the {{chembox}} template in the manose article. Boghog (talk) 10:06, 26 February 2012 (UTC)

That sounds like a good plan. I don't think we should add two links Ligplot and poseView since both show same/very similar information and LigPlot is something people are more familier with so I prefer adding link to LigPlot but do not have any objection if you think both links are useful. Let me know what information you need to implement this. Another suggestion I have is to link the ligand id to something like http://pdbe.org/chem/032 so users can see PDB definition of the molecule with atom names etc. A2-25 (talk) 12:37, 26 February 2012 (UTC)

Thanks for the suggestions. I agree Ligplot is more widely known and the PDBe ligand ID link that you mentioned is more appropriate. I have implemented both in the prototype template and in the example to the right. Is the LIgplot link OK? Boghog (talk) 14:24, 26 February 2012 (UTC)

I am close to getting the server to give best image picture. I wanted to know your opinion on adding extra picture in wikimedia. I am thinking of adding all images similar to ones on http://www.ebi.ac.uk/pdbe-apps/widgets/PDBimages/cb/1s/index.html which are images for 1cbs or http://www.ebi.ac.uk/pdbe-apps/widgets/PDBimages/e9/14/index.html for 1e94. We can then think about using these in other pages e.g. showing Pfam domain on structures or CATH and SCOP domains. In any case all these images are freely available. Let me know your opinion A2-25 (talk) 20:42, 25 February 2012 (UTC)

Great! Perhaps we should first concentrate on adding graphics to {{GNF Protein box}} templates that currently do not have graphics. For that purpose, a bot could download as needed graphics and upload them to Wikimedia commons. A tricker question is what to do about templates that already have graphics. Some of these were manually added and I would be very hesitant on replacing those. The remainder are high quality ray traced PyMol images that User:Emw worked very hard at producing. In some cases, these have small coverage of the UniProt sequence and better alternatives exist. These images should be replaced. However I would be reluctant to replace the remainder. Thoughts? Boghog (talk) 21:59, 25 February 2012 (UTC)

I agree we will not use all the images immediately. I will still upload all the images so if we want image we do not have to wait for adding these images. We at EBI must have enough band width to do this. I am also taking help from other wiser wikipedia users to see how this can be done. If nothing comes off it then we anyway have a plan for uploading these images. I maintain the SIFTS (pdbe.org/sifts) project which keeps up-to-date information on links between PDB and all other databases. This information is used by most databases (RCSB, Pfam, CATH, SCOP to name a few) so I suppose I am in a position to give all information about mappings and any changes to those mappings. So in summary, I agree with you that we can not use all the images and replace old ones but then will it be useful to create a new box with title "representative structure" and add the image. We could even make it (I don't know if that is possible) such that we add all the extra images that show mappings to other databases mentioned above. suggestions/thoughts? A2-25 (talk) 08:42, 26 February 2012 (UTC)

One needs to be careful about uploading large numbers of images to Wikimedia commons since images that are not used in articles tend to get deleted. It appears that you have already generated and stored these images at the EBI. Hence it might be a better solution to upload these images to Wikipedia only as needed. The extra links also are of interest, particularly Pfam. Since Wikipedia article already exist for many Pfam entries, the links should preferably take the form of internal Wiki links. Boghog (talk) 10:06, 26 February 2012 (UTC)

No problem. As you have noticed all images are ready so we can add it as necessary. I wanted to add them since these are freely available so if someone is searching for a particular image they can find it easily. But if unused images get deleted it is not that useful to upload all images. As you suggest adding Pfam mapping might be useful so I can concentrate on uploading best structure images first and once we have that working then Pfam mapping images. I have no problem if these are internal wiki links. A2-25 (talk) 12:37, 26 February 2012 (UTC)

Sounds good. Just to clarify, it would be useful to have the Pfam accession numbers so that the relevant Wikipedia Pfam articles can be identified and if the corresponding Wikipedia article has not yet been created, we can include an external link using the {{Pfam}} template. Boghog (talk) 14:24, 26 February 2012 (UTC)

I am not sure I replied to this. Have a look at -

• ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/text/pdb_chain_pfam.lst
• http://www.ebi.ac.uk/pdbe/docs/sifts/quick.html

These pages give all the mappings from PDB to other databases.A2-25 (talk) 15:06, 17 March 2012 (UTC)

WikiThanks

WikiThanks

You are among the top 5% of most active Wikipedians this month! 66.87.2.119 (talk) 16:04, 31 March 2012 (UTC)

WikiProject Immunology

I see you have edited some of the pages within the scope of immunology. Please have a look at the proposal for a WikiProject Immunology WP:WikiProject Council/Proposals/Immunology and give your opinion (support or oppose). Thank you for your attention. Kinkreet^{~♥moshi moshi♥~} 09:28, 4 April 2012 (UTC)

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Image request

Crystallographic structure of the human κ-opioid receptor homo dimer (4djh) imbedded in a cartoon representation of a lipid bilayer. Each monomer is individually rainbow colored (N-terminus = blue, C-terminus = red). The receptor is complexed with the ligand JDTic that is depicted as a space-filling model (carbon = white, oxygen = red, nitrogen = blue).

Hi Boghog! I'm preparing the article "GPCR oligomer" for the german wikipedia in my sandbox. I'd like to ask you whether you could make a sectional drawing of a model of a receptor heterodimer embedded in a membrane. --Hm20 (talk) 10:24, 1 April 2012 (UTC)

Hi Hm20! I would be happy to help, but I am not exactly sure how to do this. If an experimental structure of a heterodimer were available, this would be very straight forward. Correct me if I am wrong, but I believe no such experimental structures exists. Lacking an experimental structure, do you known if some one has created a model of a heterodimeric structure? Lacking a heterodimer structure, are there any structures (experimental or modeled) of homodimers available (parallel, not anti-parallel)? Boghog (talk) 11:16, 1 April 2012 (UTC)

Hi, The kappa opioid receptor PDB 4djh is a parallel homodimer in the crystal. It was published in Nature a couple of weeks ago (epub. don't think its in print yet PMID 22437504). Most GPCRs though tend to crystallise as head-to-tail dimers, which is biologically irrelevant. ~~A2-33

Excellent! I take this one. Hm20 (talk) 17:11, 1 April 2012 (UTC)

Wow, hot off the presses! Thanks A2-33! Hm20, I assume that you want something analogous to the image in TRPV. I will see what I can do. Boghog (talk) 18:08, 1 April 2012 (UTC)

Initial attempt to the right. How does this look? Boghog (talk) 20:22, 1 April 2012 (UTC)

Thank you very much, Boghog! I love your drawings. Hm20 (talk) 20:56, 1 April 2012 (UTC)

I just noticed that the 4djh crystal structure is of a artificial fusion protein between the κ-opioid receptor and lysozyme. In the original graphic, lysozyme appeared to be an intracellular domain which obviously is not right. I have updated the graphic to suppress the display of lysozyme. Sorry about that. Boghog (talk) 06:34, 7 April 2012 (UTC)

IUPHAR links

Have you managed to make any progress with the IUPHAR links?

regards Chidochangu (talk) 14:56, 28 March 2012 (UTC)

Hi Chidochangu. The mapping of Wikipedia drug articles to IUPHAR pages is very difficult since Wikipedia does not have any database mechanism (although Wikidata may provide such functionality in the future).

I was able to locate a number of Wikipedia drug articles that were not yet linked to IUPHAR. I have since then added these links. A mapping of Wikipedia drug articles to IUPHAR ligand IDs may be found here (please note that this list does not include mappings that were already in your list).

I have also updated the {{IUPHAR}} template and activated the new links. A mapping of Wikipedia Gene Wiki articles (that link to the IUPHAR database) to Entrez Gene IDs may be found here. Boghog (talk) 15:51, 10 April 2012 (UTC)

Hi Thank for your help with this list.. I will see what we can do to get the receprocal links set up on IUPHAR-db and will try to send an example to you soon... Chidochangu (talk) —Preceding undated comment added 08:39, 11 April 2012 (UTC).

Great! Again, I apologize for taking so long but I have been busy in real life and determining the drugbox mappings was non-trivial. Thank you for your help in establishing the reciprocal links. Cheers. Boghog (talk) 18:53, 11 April 2012 (UTC)

Resolving KCNMA1

Hi Boghog, I noticed your change to KCNMA1 and realized that there are partially redundant articles on this channel. I worked on this channel for 5 years during my PhD and participated the publication of it crystal structure 7 years later, so it's dear to my heart :) I'd like to propose merging BK channel and KCNMA1, and using 'KCNMA1' as the title. This will reduce redundancy and unify the Gene Wiki article nomenclature with KCNMB1, KCNMB2, etc. Do you have recommendations on how best to proceed? For example, after merging content, should I just add redirects to the old articles? AlexanderPico (talk) 17:49, 11 April 2012 (UTC)

Hi Alexander. It is great to have some experts like yourself contributing to these Gene Wiki articles! Concerning Calcium-activated potassium channel subunit alpha-1, I have no objection renaming this article to KCNMA1. I am not so sure about merging the BK channel article into KCNMA1 however. The later is a gene/protein specific article while the former is about the alpha tetramer + optional beta subunits. I think it makes some sense to have one parent article that covers both alpha and beta subunits (BK channel) plus separate gene/protein specific articles (KCNMA1, KCNMB1, KCNMB2, KCNMB3, KCNMB4). One thing that probably should be moved is the {{Infobox protein family}} (Pfam calcium-activated BK potassium channel alpha subunit) from BK channel to KCNMA1. Thoughts? Boghog (talk) 18:37, 11 April 2012 (UTC)

I had the same thought initially, but actually the entire BK article is only relevant to the alpha subunit and doesn't say anything substantial about the beta subunits. I was also persuaded by the fact that other articles and templates already provide overview of the complex and list the beta subunits: Calcium-activated_potassium_channel and Template:Ion_channels. AlexanderPico (talk) 19:22, 11 April 2012 (UTC)

Approaching the issue from the other direction... I'd like to copy the content from BK channel to the KCNMA1 article (since it equally applies), but I'm not sure how best to handle this redundancy and increased maintenance burden. Should I transclude? Should one of the articles just have minimal information and reference the other? AlexanderPico (talk) 20:46, 11 April 2012 (UTC)

I was feeling bold and went ahead and migrated all the appropriate content from BK channel. I've asked for feedback on the best title for the Gene Wiki article and will proceed by consensus. Then I will likely redirect BK channel to the Gene Wiki article since it will no longer contain unique information. Thanks again for advice. Please feel free to toss a wrench into these plans of mine if they cause you any concern. Cheers, AlexanderPico (talk) 03:40, 12 April 2012 (UTC)

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Image of C. albicans – we live and learn... --ἀνυπόδητος (talk) 11:31, 17 April 2012 (UTC)

Disambiguation pages can lead to interesting surprises ;-) Cheers. Boghog (talk) 18:00, 17 April 2012 (UTC)

Thank you for your contributions on the Roundabout (gene) page

Hello Boghog,

I wanted to thank you for your contributions to the Roundabout (gene) page. I am collaborating with a couple others on improving the page as a research-type project, and your editing has certainly helped improve the page, and our project. If you have any other suggestions for the page, be it formatting or information, they would be much appreciated. Again, thank you!

Kaleinonen (talk) 20:38, 19 April 2012 (UTC)

Hi Kaleinonen. You guys have done an excellent job of expanding the roundabout (gene) article! It looks like it is in pretty good shape. My only suggestion is that there are two sections (guidance of non-neural cells and dyslexia) that only contain one sentence apiece. It would be good if these two sections were expanded somewhat. Again, very nice work. Cheers. Boghog (talk) 20:56, 19 April 2012 (UTC)

We will certainly work on expanding those two sections, thank you for the suggestion!

Kaleinonen (talk) 13:22, 20 April 2012 (UTC)

Using plain English, and not your prefered jargon

I would prefer it if you could use language which is easily to understand rather than your preferred jargon, it would help those who may have various forums of communication disability, such as myself, so that we can contribute to Wikipedia without others using nonsense language to create unneeded communication complications. So please use more lay language common to all who use English around the world and less nonsense specific jargon dolfrog (talk) 11:07, 25 April 2012 (UTC)

Estrogenics / Estrogens and Progestogens templates

Hello. See here for discussion. el3ctr0nika (Talk | Contribs) 10:47, 2 May 2012 (UTC)

Extra care needed on ref formatting

Please try to take a bit more care with ref formatting, e.g. here you've lost |doi=10.1186/gb-2000-1-4-reviews0004 and duplicated |doi=10.1126/science.1190414. Thanks Rjwilmsi 15:43, 8 May 2012 (UTC)

MED13

This is an automated message from MadmanBot. I have performed a web search with the contents of MED13, and it appears to include material copied directly from http://www.uscnk.com/directory/Thyroid-Hormone-Receptor-Associated-Protein-1(THRAP1)-7026.htm.

It is possible that the bot is confused and found similarity where none actually exists. If that is the case, you can remove the tag from the article. The article will be reviewed to determine if there are any copyright issues.

If substantial content is duplicated and it is not public domain or available under a compatible license, it will be deleted. For legal reasons, we cannot accept copyrighted text or images borrowed from other web sites or printed material. You may use such publications as a source of information, but not as a source of sentences. See our copyright policy for further details. (If you own the copyright to the previously published content and wish to donate it, see Wikipedia:Donating copyrighted materials for the procedure.) MadmanBot (talk) 05:30, 12 May 2012 (UTC)

Added {{NLM content}} template to article to indicate that the material is in the public domain. Boghog (talk) 05:35, 12 May 2012 (UTC)

Reference reformatting.

reformat in question

I do a lot of reference addition, expansion with templates and reformatting myself. I'm a little curious about a few things.

• Do you use any specific tool to help you reformat and rename a huge number of references at once? I find wikiED + proveit kinda insufficient.
• Author names in the cite journal template: any reason you go with a single string of authors? (I stuck with the zotero default- Last,first, coauthors) Should I reprogram the zotero output? If there is a consensus /majority choice on how it should be...
• The renaming of the reference names: Each editor uses a different naming style. I have found the name=pmid to be particularly cryptic when further changes need to be made to the article. Is there an automated tool to do this renaming? Are there any style guides you know of so everyone can stick to the same naming style e.g AuthorLastYYYY orAuthor_YYYY?

CheerioStaticd (talk) 09:17, 13 May 2012 (UTC)

Hi. For citations, I use User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article. I agree that the reference tags that Diberri produces (e.g., "pmid123456") is cryptic, so that in cases where a reference tag is used more than once, I have manually changed these to "author_year". As far as I know, there is no style guide pertaining to reference tags. Concerning the format of the citations, WP:CITEVAR is the relevant guideline. It looks like there was no consistent reference style used in the phage display article, so I converted everything to the less verbose Vancouver System that uses a single author parameter. Using the "last1, first1, ..." parameters produces very long citation templates that IMHO start to overwhelm the rest of the raw wiki text. Boghog (talk) 09:39, 13 May 2012 (UTC)

Opsoclonus Myoclonus Syndrome and Ataxia

Hi I just looked at Opsoclonus myoclonus syndrome which appears to have much research which seems to relate to Ataxia, which is outside my area of interest, but i was wondering if you knew of how these issues may be linked and how these articles may or may not be linked. dolfrog (talk) 23:39, 17 May 2012 (UTC)

Ref formatting

Wondering if you could help me with some references. I have been spending the last few years working on improving these 80 articles Book:Health care 11 of which I have so far helping bring to GA/FA (two up for nomination currently). Over the next few years as part of this project I hope to bring the rest to GA/FA [1]. Have been and planning on in the future using the diberri formatting for the references. As reference formating get changed around can we this format on these articles? They form a 2000 page textbook which I am going to work on publishing when done. Doc James (talk · contribs · email) 22:22, 5 May 2012 (UTC)

And of course any help improving the articles in question is much appreciated. --Doc James (talk · contribs · email) 22:24, 5 May 2012 (UTC)

Wow! That is an incredibly noteworthy and ambitious project. I will try to help out with ref formatting and copyedit as I find time. Boghog (talk) 23:00, 5 May 2012 (UTC)

Thanks :-) I am planning on spending the next 5-8 years on it. If it is a success than many expand to further articles. --Doc James (talk · contribs · email) 00:26, 6 May 2012 (UTC)

Hello - I wonder if you could rapidly point me to an explanation/indication of why Template:Cite pmid is less than ideal. I struggle to get to grips with different WP citation practices and I'm just curious to know. Thanks in advance, —MistyMorn (talk) 20:13, 22 May 2012 (UTC)

Hi. The most relevant guideline is WP:CITEVAR which states "citations within a given article should follow a consistent style". The dominate citation style in the prostate-specific antigen article has been for quite some time the compact Vancouver System. Using the {{Cite pmid}} in turn invokes User:Citation bot which uses a somewhat more verbose citation format (<Last_Name_1>, <First_Initial_1>. <Middle_Initial_1>.; ...). One can still use the {{Cite pmid}} template and still be compatible with the Vancouver System by editing the template (see for example this edit). Boghog (talk) 20:53, 22 May 2012 (UTC)

Thanks very much. I appreciate that. —MistyMorn (talk) 22:12, 22 May 2012 (UTC)

Raymond P. Ahlquist

Hi Bog! Nice article -- can you source that his work was initially ignored / rejected? An inline citation immediately after the sentence that is relevant for the hook would be required by DYK guidelines. Also, what is the license for the image? Cheers, ἀνυπόδητος (talk) 10:01, 24 May 2012 (UTC)

PDE4A

Why did you remove the workover I gave it? You even removed the pdfs which are not pmc links? 70.137.135.95 (talk) 08:08, 26 May 2012 (UTC)

Besides what you are doing is not really Vancouver style. You are merely mangling the initials, which is not explicitly reqd in Vancouver style. You are truncating the journal names. Both these "compact" notations make the refs less usable for the lay reader. This is not your damn masters thesis, and it is not to be read by an Asst. Professor. It is to be read by the average reader, or optimistically by the educated reader. So keep the damn jargon of the craft out of it, it makes refs harder to find and to follow. I linked a bunch of non-pmc pdfs, you removed them. Even in the case of pmc-based pdfs they are much easier to open and to read than to page through the pmc link one by one, thats why I added them. The pmc link is still accesible if someone wants to absolutely use it, by clicking on pmc. All from the viewpoint of the lay reader. The average educated lay reader will be better served with the less "compact" format. We are not in school any more for Christs sake. 70.137.135.95 (talk) 08:42, 26 May 2012 (UTC)

As I explained in my edit summary, I removed the URL to PMC articles since the PMC parameter already generate the link to PMC. Also removed URLs for citations that had a DOI since these URLs are redundant. Also why did you find it necessary to change the pre-existing author format? Boghog (talk) 08:44, 26 May 2012 (UTC)

Please note WP:CITEVAR and in particular "Editors should not attempt to change an article's established citation style merely on the grounds of personal preference, or without first seeking consensus for the change. If the article you are editing is already using a particular citation style, you should follow it; if you believe it is inappropriate for the needs of the article, seek consensus for a change on the talk page." Boghog (talk) 08:48, 26 May 2012 (UTC)

Because a link on the pdf is convenient for the lay reader, even if redundant by the doi. A link is also more convenient for the lay reader than to open the pmc link and click through it pagewise. We are optimizing for readability, not for disc space. also authors like Wurtz PK Fart MY Hell FI are abbreviations, at least the dots and commas make this more readable, again for the lay reader. Redundance means less context and background needed for reading, and besides less eye strain.

certainly "J. Toi. Ur." is less readable than "Journal of Toilets and Urinals", if you see what I mean. At least for the lay reader who is not an insider of the craft. Please also try the pmc links, compared to the pdf fulltext regarding ease of access, not to talk about someone who does not know pmcs.

Apart from expanding the acronyms and the mangled names no change of citation style has taken place. The pdfs are added convenience. 70.137.135.95 (talk) 08:58, 26 May 2012 (UTC)

Look, I am so long out of school, I do not need to edit here to throw my time and effort away, so to say pearls for the swine. I leave this now to the kids who know everything better, yes even they invented it. If you take pride in jargon, then keep the wiki for yourself. You are anyway not responding to the points I made, as if you do not understand. 70.137.135.95 (talk) 09:05, 26 May 2012 (UTC)

First of all, I have no problem with including full journal names and we can include these if you like. I do have an issue with changing the pre-existing author name format. User:Diberri's Wikipedia template filling tool (instructions) is widely used by the WP:MCB and WP:MED projects to generate citations and this tool formats citations using the Vancouver system. Furthermore the citation format in the other ~10,000 Gene Wiki articles also use this system. Hence the formatting changes that you have made are inconsistent with the format used in a large majority of other gene/protein articles. While removing periods from initials is not explicitly mandated in the Vancouver system, in all the examples used in the system's authoritative guide do. Also I think you are underestimating the intelligence of the average reader. Finally DOI are preferred over URLs links since the former are guaranteed not to change while the later may change. Using URLs may introduce maintenance problems. Likewise, if PubMed ever changes the URL for PMC articles, this will also cause maintenance problems. Using the PMC parameter is safer since any change in the PMC URL can easily be fixed in the {{cite journal}} template. Boghog (talk) 10:21, 26 May 2012 (UTC)

The diberri tool actually allows a choice of separators and punctuation if I remember correctly. The cite doi and cite pmid bot uses the format as I did. I do not underestimate the IQ of the average reader, so I hope, as I took myself as an average reader.(but maybe I am senile? You do not notice yourself. You just notice the Alzheimers by finding an unknown wonderful woman in your bed every morning, in an apartment where you do not remember ever to have been. But it surely is cozy and the woman is so nice as if she has known you forever.) Maintenance problems point is granted in case of doi links vs. urls, but again maintenance counts less than user convenience and the doi is not replaced but augmented, so there is always the doi as a fallback. In case of pmc links the urls are believed to be permalinks i.e. they keep backward compatibility there even when changing the format. (as they did before, and there they kept compatibility) See the point from a customers view. Ease and convenience. The wiki is also hopefully attracting readers even less educated and intelligent than I am, who will need it most and are profiting most by taking a bite from this wonderful teaching text. One day they will maybe study science, inspired by this experience. This is how I started myself. So reconsider. We are not writing a teaching text for academics, it is for everyone who maybe once will become an academic too. And this is IMO worth the slightly increased efforts in maintenance, if these are real. Remember: WP:NoTEXTBOOK. If you put the computer with the wiki in a monkey stable and they suddenly start typing the Feynman Lectures, THEN you got it right. (NOT the Bible! They already did that. It is redundant.) 70.137.135.95 (talk) 10:50, 26 May 2012 (UTC)

The diberri tool does support full journal names as an option but does not support a choice of punctuation and separators (other than padding parameters and values with spaces). Regardless of whether or not the tool supports alternative author punctuation as an option, what is relevant is how the citations in other Gene Wiki articles are currently formatted. Finally I do not buy the argument that average people can only understand "Smith, A.L." and not "Smith AL". I think you underestimate the intelligence of the average reader. Boghog (talk) 11:31, 26 May 2012 (UTC)

I do not claim "they do not understand", I claim "it is easier on the eye". At least for me. Now do what you want. The cite pmid and cite doi bot does it different. I see that you work transcluded templates manually to conform with the article to which they are transcluded. - What if they are transcluded to several articles, with different puctuation styles? This should tell you that there is a problem.

I will likely not waste my time on wiki any more. 70.137.134.249 (talk) 18:38, 26 May 2012 (UTC)

IMHO, "Smith AL, ..." is less cluttered and easier on the eye than "Smith, A.L.; ...". The vast majority of templates that I have manually edited are only transcluded into one article. If they are transcluded into more than one article, they are very likely to be within the scope of the WP:MCB or WP:MED projects that are also likely to use the Vancouver style. The real problem is that DOI bot does not support the Vancouver style as an option when creating new templates. The DOI bot does however respect the Vancouver style if it is already present and will not over write it. Boghog (talk) 18:54, 26 May 2012 (UTC)

I am more a lay person than you are, I presume. So what is easier on the eye may differ. I believe the diversity of citation styles is a problem, including free style citations, if you really want a unified citation style over a topic, like proteins. It took me lots of work to clean up citations in articles from 10 editors, including endless variations of punctuation, ordering of names, "year = a, volume= x, issue = y, pages = z" notations and spelling variations. Either we can only fix it for every article in question individually and keep the artistic freedom, following the first contributor or the majority of contributors of the article in unification - as it is now. Or we have to standardize tools and notations for defined groups of articles. Otherwise poor Sysiphus will be rolling the stone uphill, and it will roll back over night with the new edits, as you can see. The rules as they are do not lead themselves to coherence over the wiki or even groups of articles. This is largely unsupported. But even use of the templates will help to make it less chaotic. However, templates are not preferred over free style to the taste, as it is now. You see what I mean. At least we agree on the goal to make it more readable for lay persons, I believe, as I said, it is not for an Asst. prof. 70.137.134.249 (talk) 20:14, 26 May 2012 (UTC)

Far more important than the format of further reading citations is the articles content. The purpose of the further reading section in Gene Wiki articles is primarily to provide a seed material to encourage others to add content and the hope is that some of the citations would be brought in-line to support the articles text while unused citations would eventually be deleted. Without content to provide context, citations are of very limited value. Rather than having extended discussion about citation formatting, I think a more productive use of our time would be to add content. Boghog (talk) 20:36, 27 May 2012 (UTC)

DYK for Raymond P. Ahlquist

Casliber (talk · contribs) 00:06, 30 May 2012 (UTC)

number of columns fo refs

just as an example Ataxia the references from my perspective are visually a mess, and " The colwidth parameter dynamically adjusts the number of columns to the width of the browser window." does not seem to improve matters. However using two columns as per Auditory processing disorder is much easier on the eye, and easier to read as each reference appears as a visual block which is visually easier to process than following whole lines across a wide screen. dolfrog (talk) 07:49, 3 June 2012 (UTC)

This may be a browser specific problem. It looks fine in Safari and Firefox. What browser are you using? For normal font size and browser window widths, it should look identical to the two column ref list. Try expanding or contracting the width of your browser window. For very narrow widths, you should see one column, for wider widths, you should see two or more columns. Boghog (talk) 07:56, 3 June 2012 (UTC)

I am using Firefox, however I have a play with the |colwidth in one of my sandboxes and the issue woouls appear to be more the wide of screen used by the browser, i used a setting of 30em which best suited the size of display use, where say 10 or 20 has too may narrow columns, can this set up be customised by each user to best suite the size of screen they use, or size of browser they work with they use. until i played around with colwidth in my sandpit I had no idea that the size of screen determined the number of columns you see. would non editors know about this option when visiting an article. dolfrog (talk) 08:14, 3 June 2012 (UTC)

The whole purpose of dynamically adjustable number of columns is to automatically display an appropriate number of columns for the browser window width and font size. Furthermore the user should not have to worry about this. For example, if someone is viewing a Wikipedia page from a smart phone, it would be appropriate to display only one column of citations. If one is viewing an article with a large number of citations using a wide screen monitor, more than two columns would be appropriate. I have had previous discussions with the sight impaired who used large fonts and complained about the appearance citations when the number of columns is fixed at two. In these cases, two columns ref list were too narrow for their web browser window and they strongly preferred when the number of columns was automatically reduced to one. Boghog (talk) 08:35, 3 June 2012 (UTC)

See also Template:Reflist#Browser_support_for_columns. However as I understand it, all browsers that support "fixed number of columns" will also support "dynamically adjustable number of columns". Conversely browsers like Internet Explorer that do not support "fixed number of columns > 1" will also not support "dynamically adjustable number of columns" and vice versa. Boghog (talk) 08:10, 3 June 2012 (UTC)

The big problem i have with Wikipedia is all these long winded pages of verbiage, which due to my communication disability are more or less no go areas for me. I am more "try it and see" and pictures, diagrams and charts. Not your fault. dolfrog (talk) 08:23, 3 June 2012 (UTC)

Sorry for the detailed explanation, but this is a technical issue that is difficult to explain in plain language. Boghog (talk) 08:35, 3 June 2012 (UTC)

I suppose from my perspective reflist|2 provides two columns regardless of other technical issues that can come into play, which for me makes life easier. such is progress lol dolfrog (talk) 09:18, 3 June 2012 (UTC)

Wikipedia Help Survey

Hi there, my name's Peter Coombe and I'm a Wikimedia Community Fellow working on a project to improve Wikipedia's help system. At the moment I'm trying to learn more about how people use and find the current help pages. If you could help by filling out this brief survey about your experiences, I'd be very grateful. It should take less than 10 minutes, and your responses will not be tied to your username in any way.

Thank you for your time,
the wub (talk) 18:08, 14 June 2012 (UTC) (Delivered using Global message delivery)

"Lung cancer" references

Hi, Boghog. I see that you changed a number of references in "Lung cancer". The article has a prevailing citation format. You have changed the authorship fields, removed url links, and added random spaces to several references. Why have you done this? Axl ¤ [Talk] 17:53, 17 June 2012 (UTC)

OK, sorry. Checking the history of lung cancer, I now see that the last/first/coauthor format has been established for sometime, therefore per WP:CITEVAR, I have undone my edit. The reason I was prompted to do this was by this request above. The rationale to chaining the authorship fields was to streamline them. The URLs were removed from citations that already have DOIs (the URLs for the most part point to the same web page; furthermore URLs may change whereas DOIs are guaranteed not too). The spaces are not random. They are merely to uniformly pad the parameters with spaces so that the templates are easier to read. Boghog (talk) 18:53, 17 June 2012 (UTC)

Thank you for the explanation and for reverting your edit.

I am surprised by your justification for removing urls. These are clearly included in citation templates. The solution to potential broken links is not to pre-emptively delete all links; it is to remove links after they break. (Actually, the full solution is more complex and probably includes a form of archiving.) The presence of these links helps readers and editors to check the source and confirm verifiability. While readers may be able to find sources without the links, surely the links make this easier? Axl ¤ [Talk] 19:43, 17 June 2012 (UTC)

The DOI is a link. If a citation has a DOI, normally there should be no reason to include a URL since the later becomes redundant. See for example this discussion which lead to David Iberri modifying his citation filler tool so that if a DOI is present, the URL is not included. Boghog (talk) 20:45, 17 June 2012 (UTC)

Ah, I see. Thanks. Axl ¤ [Talk] 21:45, 17 June 2012 (UTC)

Authority Control Integration

Hi, I've been researching the intersection of Wikipedia and Authority Control, and have just recently made a Village Pump Proposal to create a bot to expand the usage of a template. I've identified you as someone in the sphere of interest to this project and would appreciate your input at the Village Pump. Thanks, Maximiliankleinoclc (talk) 18:36, 18 June 2012 (UTC)

History of Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)

Hi, again. The View History button of Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) gives this weird URL and the history seems not to exist. A "Last updated ..." message in the upper right corner of the article page gives the same URL. Can you figure this out? J G Campbell (talk) 18:26, 19 June 2012 (UTC)

That history link is bizarre. When I hit the history tab, I get this link which works as it should. Either Wikipedia or your web browser had a temporary glitch. Please try it again. Boghog (talk) 19:25, 19 June 2012 (UTC)

I suppose that you will now have to amend your no complaints statement. ;-) Boghog (talk) 19:38, 19 June 2012 (UTC)

I was complaining that I hadn't received complaints. J G Campbell (talk) 15:46, 20 June 2012 (UTC)

If you insist, we can quickly fix that :-) Boghog (talk) 20:39, 20 June 2012 (UTC)

Must be bolder. ;-) J G Campbell (talk) 16:00, 20 June 2012 (UTC)

Adding a trivia section to an enzyme article will likely elicit a swift retort ;-)

I neglected to say that the behavior has been somewhat erratic. "Last updated ... " has been, however, consistently present on the article page. I've not noticed it on other pages. J G Campbell (talk) 23:55, 19 June 2012 (UTC)

That indeed is very strange. I have not noted this type of behavior before. The only difference in the link that you provided is that "25" is inserted in "%2B" (a plus character) to produce "%252B". Interestingly "%25" is the HTML character code for "%". In html links, any non standard characters are supposed to be replaced by html character codes. The first character in the character code is "%" so that it appears that there was an unnecessary double substitution (i.e., "+" → "%2B" → "%252B"). I have no idea why that would happen. Boghog (talk) 20:39, 20 June 2012 (UTC)

Enzyme infobox

Thanks for adding the enzyme infobox to Fructose-bisphosphate aldolase. And thanks for improving the infobox template. J G Campbell (talk) 13:32, 19 June 2012 (UTC)

And thank your major contributions to the article. Your rewrite is a huge improvement! My contribution was relatively minor. Cheers. Boghog (talk) 17:59, 19 June 2012 (UTC)

I wouldn't have thought to add it. J G Campbell (talk) 16:23, 21 June 2012 (UTC)

I mean that I wasn't bold enough. You were. J G Campbell (talk) 20:54, 22 June 2012 (UTC)

File:Nr alignment tree.png listed for deletion

A file that you uploaded or altered, File:Nr alignment tree.png, has been listed at Wikipedia:Files for deletion. Please see the discussion to see why this is (you may have to search for the title of the image to find its entry), if you are interested in it not being deleted. Thank you. Fredlyfish4 (talk) 03:02, 30 June 2012 (UTC)

Credo Reference Update & Survey (your opinion requested)

Credo Reference, who generously donated 400 free Credo 250 research accounts to Wikipedia editors over the past two years, has offered to expand the program to include 100 additional reference resources. Credo wants Wikipedia editors to select which resources they want most. So, we put together a quick survey to do that:

• Link to Survey (should take between 5-10 minutes): http://www.surveymonkey.com/s/N8FQ6MM

It also asks some basic questions about what you like about the Credo program and what you might want to improve.

At this time only the initial 400 editors have accounts, but even if you do not have an account, you still might want to weigh in on which resources would be most valuable for the community (for example, through WikiProject Resource Exchange).

Also, if you have an account but no longer want to use it, please leave me a note so another editor can take your spot.

If you have any other questions or comments, drop by my talk page or email me at wikiocaasi@yahoo.com. Cheers! Ocaasi ^{t | c} 17:10, 11 July 2012 (UTC)

July 2012 Study of authors of health-related Wikipedia pages

Dear Author/Boghog

My name is Nuša Farič and I am a Health Psychology MSc student at the University College London (UCL). I am currently running a quantitative study entitled Who edits health-related Wikipedia pages and why? I am interested in the editorial experience of people who edit health-related Wikipedia pages. I am interested to learn more about the authors of health-related pages on Wikipedia and what motivations they have for doing so. I am currently contacting the authors of randomly selected articles and I noticed that someone at this address recently edited an article on Vacuatiner. I would like to ask you a few questions about you and your experience of editing the above mentioned article and or other health-related articles. If you would like more information about the project, please visit my user page (http://commons.wikimedia.org/wiki/User:Hydra_Rain) and if interested, please reply via my talk page or e-mail me on nusa.faric.11@ucl.ac.uk. Also, others interested in the study may contact me! If I do not hear back from you I will not contact this account again. Thank you very much in advance. Hydra Rain (talk) 13:09, 14 July 2012 (UTC)

Hello Boghog, I saw your questionnaire response. Thank you! Can you please send me an email to nusa.faric.11@ucl.ac.uk in order for me to send you the ethics form and the interview questions. Many thanks. Nuša

Hydra Rain (talk) 15:14, 14 July 2012 (UTC)

User:JonSDSUGrad/Sandbox

It looks like your MfD nomination at User:JonSDSUGrad/Sandbox was never completed. Its a month old now with no action and I can't find the related MfD subpage. Monty₈₄₅ 18:17, 14 July 2012 (UTC)

Opps. I forgot to finish what I started. Sorry about that. The MfD subpage now exists. Cheers. Boghog (talk) 20:26, 14 July 2012 (UTC)

Search and replace

Hey Bog Where is this "search and replace" function? This is something I have been looking for. Doc James (talk · contribs · email) (if I write on your talk page please reply on mine) 16:00, 18 July 2012 (UTC)

Splitting list of human proteins up on FYVE domain page

Hi BogHog, I was just looking at the article for the FYVE domain and noticed that the list of human proteins seems to take up a lot of room in the article. Looking back in the revision list it used to appear like this:

ANKFY1; EEA1; FGD1; FGD2; FGD3; FGD4; FGD5; FGD6; FYCO1; HGS; MTMR3; MTMR4; PIP5K3; PLEKHF1; PLEKHF2; RUFY1; RUFY2; WDF3; WDFY1; WDFY2; WDFY3; ZFYVE1; ZFYVE16; ZFYVE19; ZFYVE20; ZFYVE21; ZFYVE26; ZFYVE27; ZFYVE28; ZFYVE9;

The it looks like you split it onto several lines as in the current article. I prefer the more compact representation, but I know you are an expert editor so was wondering what the rationale for the change was? Thanks for all your great work! Alexbateman (talk) 15:15, 20 July 2012 (UTC)

Hi Alex, I don't have any strong opinions one way or the other on how these lists are displayed. Splitting these long sentences into bulleted lists makes them easier for the human eye to parse, but I agree that these bulleted lists do take a lot of room. I have therefore changed it back. Boghog (talk) 05:48, 21 July 2012 (UTC)

Erythropoietin and Epoetin alfa

No one seems to have shown any interest in your suggestion. Based on your analogy with insulin, I think it is a sensible suggestion. Are you willing to make the changes? Unfortunatly, a non expert is going to struggle otherwise. Op47 (talk) 20:08, 20 July 2012 (UTC)

 Done Hi. Thanks for reminding me. Since no one has objected to the suggestion, I have gone ahead and moved the drug specific material from Erythropoietin to Epoetin alfa and reorganized both articles a bit. Cheers. Boghog (talk) 06:13, 21 July 2012 (UTC)

Thankyou. Op47 (talk) 11:34, 21 July 2012 (UTC)

Adrenodoxin reductase

First of all as I am new to editing, I do not know if this the right place to send a message, but I couldn't find another more discrete way. I noticed that you changed adrenodoxin reductase to adrenal ferredoxin. Adrenodoxin reductase is an enzyme and adrenodoxin (or adrenal ferredoxin) is an electron transfer protein. These two proteins are completely different. Please return the PBB geneid to what it was and approve adrenodoxin reductase as a new entry. — Preceding unsigned comment added by Redactor271 (talk • contribs) 21:56, 22 July 2012 (UTC)

Hi. Yes, this is good place to place a message. The classification of adrenodoxin reductase is confusing. Searching HUGO only lead to adrenal ferredoxin. After digging around more it appears that adrenodoxin reductase (ADXR) for which an article already exists is identical to ferredoxin reductase (FDXR). I realize that you have written:

• Adrenodoxin reductase has been also called a ferredoxin-NADP+ reductase. But, determination of the sequence and structure of the enzyme revealed that it is completely different from ferredoxin reductase.

Please note that the EC classification is not based on sequence or structure but rather the reaction that is catalyzed. According to all the databases (HUGO, UniProt, etc.), adrenodoxin reductase is classified as EC 1.18.1.2 (ferredoxin—NADP(+) reductase). Another name listed for ferredoxin—NADP(+) reductase by the Enzyme Commission is adrenodoxin reductase (see nomenclature). Furthermore, according to HUGO, FDXR and OMIM (ferredoxin reductase) = ADXR (adrenodoxin reductase). Hence the article you wanted to create already exists (it was previously named FDXR which I have rename to adrenodoxin reductase). Boghog (talk) 04:33, 23 July 2012 (UTC)

Hi Boghog. Thank you very much for the change. You did the right thing. I am working on changing the nomenclature and this will take some time. Best regards, Redactor271 (talk) 09:31, 23 July 2012 (UTC)

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Rootletin protein family

Thank you very much Boghog for your help with Rootletin protein family. I would like to enlist your help in both Rootletin protein family and CROCC articles. CROCC is the name of the gene that encodes Rootletin. For some reason typing in Rootletin into the search box leads to a re-direct to the CROCC gene. Is there anyway to remove this, as I would like to move Rootletin protein family to a new page entitled Rootletin. Many thanks Kfh123 (talk) 08:08, 22 August 2012 (UTC)

Hi. I also wanted to complete the same page move, but was prevented since rootletin page already exists as a redirect. I have requested that the rootletin page be deleted. As soon as an administrator completes this request, we can complete the page move. Cheers. Boghog (talk) 16:53, 22 August 2012 (UTC)

Shelf life: Revision history

Why would it not be practical to include a table of the shelf lives of different products? I am personally always searching for this information and have a hard time finding it on the net. — Preceding unsigned comment added by YounesB3 (talk • contribs) 12:35, 23 August 2012 (UTC)

(Number of types of products) X (number of brands) X (number of countries) = (an enormous number) that would completely overwhelm the shelf life article. Furthermore, if you are interested in the shelf life of a particular product, why not simply look at the product packaging? Boghog (talk) 21:01, 23 August 2012 (UTC)

I understand your point. That is why I tried to make a new article with just this table, but it got deleted and I've been redirected to the shelf life article. Also, most of the products (in Canada at least) have a "best before" date and not a "use by" date which is completely different. If I want to know if I can eat an aliment regardless of its quality without having any health impact on my system, I can't know with only the "best before" date. That is why I wanted to create this table. What do you suggest me to do? — Preceding unsigned comment added by YounesB3 (talk • contribs) 19:34, 25 August 2012 (UTC)

The obvious solution is to place this information in a product specific article, but even this I think is a really bad idea (see WP:NOTMANUAL, WP:NOTSTATSBOOK, and WP:MEDICAL). If you want this information about the shelf life of product that you purchased (shelf life ≈ use before ≈ best before date), please read the product packaging or insert. An encyclopedia is not an appropriate place to list such information. Boghog (talk) 20:41, 25 August 2012 (UTC)

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A bot to add tags to talk pages

Hey Boghog Wondering if you could help with a possible bot. We are looking at the possibility of adding a template to talk pages pertaining to diseases / pharmaceuticals to help editors find high quality references. TRIP database breaks down references by quality as does Pubmed (there is a review tab and a last 10 years tab). If we could add a template to talk pages within the project linking to these two with the search term being the article in question I think that would be useful. Discussion is taking place here. [2] Doc James (talk · contribs · email) (if I write on your page reply on mine) 12:32, 3 September 2012 (UTC)

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Nice work

I tried to address some of the ENCODE stuff at the end of my editing day and I'm pleased to see how much you've improved it in the same direction I was going. Thanks. I'm no geneticist, and I don't try to play one on TV or Wikipedia, but the blatant misinformation being pumped out about the ENCODE findings was just too much! See also some of my comments here at Talk:Noncoding DNA. I'd appreciate it if you took a look at some of the changes I made at Noncoding DNA yesterday to make sure they're in-line with your work at ENCODE. Cheers, — Scientizzle 14:04, 11 September 2012 (UTC)

Likewise, nice work with Noncoding DNA! I am embarrassed to admit that I initially took the press releases at face value until I read the ARS Technica article. I am certainly not a geneticist either, so I am doing a bit of research in parallel with editing. I don't have much time at the moment, but I will take a closer look at both articles this weekend. Cheers. Boghog (talk) 18:29, 11 September 2012 (UTC)

tool

hello there! you gave me some advice about template-filling for pubmed articles a few weeks ago. I was wondering now that the tool's down, if you knew of any others. cheers! FoCuSandLeArN (talk) 22:35, 1 October 2012 (UTC)

The tool is back up! Boghog (talk) 19:01, 4 October 2012 (UTC)

Category:Top 200 US Drugs of 2011 is undergoing deletion review

Thank you for your input on the WHO Model Lists of Essential Medicines. I'm notifying everybody who has been part of that discussion about a pending Categories for Discussion review regarding the newly created Category:Top 200 US Drugs of 2011. I've also put a notice on the project talk page here. Thanks again. - Stillwaterising (talk) 05:51, 7 October 2012 (UTC)

Thank you for your participation in the Cfd. I find it unacceptable that this discussion was not announced to me or the project talk page. Frustrations like this are part of why I resign/retired from June 2010 untul last month. It's possible to spend more time defending your work from deletion instead of creating and improving. It's soul crushing to have your hard work secretely demolished by a clique of admins who can't even take the time to click on a few links and read a few lines. I'm considering putting this to AN. - Stillwaterising (talk) 08:44, 7 October 2012 (UTC)

de-bloating the controversies article

Thank you! i wrote a note on his talk page, to that Chris Capoccia guy, who was adding so much detail to the refs and asked him to stop... the article is so long already and editing it was just looking uglier and uglier. He did some good work in adding detail that was lacking but man I hate that style of referencing. bloatorama. anyway thanks!!! Jytdog (talk) 20:04, 10 October 2012 (UTC)

Sorry for not responding sooner as I have been busy in real life. I realize that reference style is a very controversial topic. According to WP:CITEVAR, if there is disagreement about which style is best, defer to the style used by the first major contributor. The first major contributor to Genetically modified food controversies introduced bare URLs which is not an acceptable style. After that, a variety of styles were introduced including a sizeable number of {{cite}} templates that generally conformed to the more compact Vancouver System. The advantage of using the {{cite}} templates is that they (1) insure that the formatting of the references is consistent, (2) are maintained by bots, and (3) provide machine readable bibliographic metadata. The usefulness of the last item is IMHO very questionable since the method used, WP:COinS, results in significant increases in loading times while editing and there is very little evidence that anyone actually uses COinS. COinS slows down editing for a lot of people for the theoretical advantage of a very few (see for example this discussion). Furthermore to take full "advantage" of COinS, the first1, last1, ... author parameters should also be used which IMHO is ugly and generates a lot of unnecessary clutter.

So my edits were to reformat the {{cite}} templates to use the more compact Vancouver System consistent with the previously established citation style that used a single author parameter. An additional advantage of using the Vancouver System is that the {{cite}} template can be replaced with the much faster {{vcite}} templates. This could be a real advantage for the Genetically modified food controversies article whose citation list has grown very long. Boghog (talk) 21:06, 12 October 2012 (UTC)

Thanks for your note! I SO hear you on the questionability of 3 and the goodness of 1 and 2. I've been having a discussion with Chris on his talk page... woo man he is committed to these bloaty templates! Anyway thanks again for working on cleaning up that article and even more for the explanation!Jytdog (talk) 23:38, 12 October 2012 (UTC)

Notice of Edit warring noticeboard discussion

Hello. This message is being sent to inform you that there is currently a discussion involving you at Wikipedia:Administrators' noticeboard/Edit warring regarding a possible violation of Wikipedia's policy on edit warring. Thank you. ... this is regarding Keerthi78 at Insulin. Zad68 21:13, 12 October 2012 (UTC)

Thanks for filing the notice. Boghog (talk) 21:43, 12 October 2012 (UTC)

Molecular and Cellular Biology WikiProject

Hi there! Thanks for the welcome to the group and for the helpful information! Currently, I'm working with two other grad students at Hopkins, adding to the Helicase page, and am looking forward to using my experience on this project to continue working with Wikipedia and contributing! Thanks again! Jennifergr (talk) 18:34, 3 November 2012 (UTC)

I look forward to your contributions to the Helicase article. If you have any questions, don't hesitate to ask. Cheers. Boghog (talk) 19:34, 3 November 2012 (UTC)

SFRP4

Thank you for cleaning up my edit of SFRP4. I'm wondering, are you automatically notified when changes are made to any of the gene pages, or did you just happen to land on SFRP4? jwclymer — Preceding unsigned comment added by Jwclymer (talk • contribs) 21:32, 8 November 2012 (UTC)

Hi. And thank you for your additions to the SFRP4 page. In answer to your question, I routinely monitor change in Gene Wiki articles and I am very happy when editors like yourself add content. Cheers. Boghog (talk) 06:41, 9 November 2012 (UTC)

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Reference formatting

Hi Boghog, what's the current best tool for reference formatting? I've been pointing new users (like Tselroy [3]) to the "Cite" option under the fancy new edit bar, but as your follow on edit showed that feature is not perfect. Is there better tool that we should be pointing new users to? Cheers, AndrewGNF (talk) 19:18, 30 November 2012 (UTC)

Hi Andrew. Per WP:CITEVAR, it very much depends on whether a predominate citation style has already been established for a particular article. In the case of Mir-155, a Vancouver system had already been established. Hence in this case Diberri template filler would be the most appropriate choice. Boghog (talk) 19:41, 30 November 2012 (UTC)

Great! Cheers, AndrewGNF (talk) 19:51, 30 November 2012 (UTC)

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NER Article

Hello! Thank you so much for helping format the references we added for the nucleotide excision repair page. Our semester is ending next week, and our group would like to finish adding as much as we can as one of the Hopkins groups. Is there anything in particular that we could do to improve the article within this week? We have a small list of things we would like to accomplish this week, but would love feedback, if you have any. Thank you for your time! Db4an (talk) 06:49, 9 December 2012 (UTC)

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Primary sources notification for Seratrodast

Hi Boghog, thank you for the notification. I am new to putting content on Wikipedia. For the comment that I received on 15th Dec 2012, I would like to state that currently there are no review articles on Seratrodast. Most of the articles are primary sources and there are no secondary or tertiary sources available, except for some information in books like Martindale where the information on the molecule is yet to be updated. The content in "Clinical Experience" of Seratrodast is just a gist of the results that were obtained in various clinical studies (primary sources). None of its content is my interpretation of the primary sources. The article in Wikipedia would be the first tertiary source of Seratrodast. This would enable people to have a brief understanding of the molecule, considering that there is no other tertiary source available. Thanks, Raghuram.chimata (talk) —Preceding undated comment added 04:18, 17 December 2012 (UTC)

SRGAP2

Hi looks like we both are interested in SRGAP2. Current version of the article SRGAP2 is giving conflicting information about the number of duplications. SRGAP2 was duplicated three times and not two times. Preetikapoor0 (talk) 18:58, 29 December 2012 (UTC)

Hi. I checked the source (PMID 22559943) and you are right, the gene was duplicated three time, not twice. I have corrected the text accordingly. It appears however that only SRGAP2C has significant expression while SRGAP2A, SRGAP2B, and SRGAP2D appear to be pseudo genes. Also Ensembl lists SRGAP2C as a pseudo gene.

In case you haven't seen this yet, please check out User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article. This tool can save you a lot of work and ensure that the citations are displayed in a consistent manner. Cheers. Boghog (talk) 19:19, 29 December 2012 (UTC)

Thanks for the awesome tip! It will save a ton of time!! Although for unclear reasons it is listed as a suspicious website on WOT Services. (http://www.mywot.com/en/scorecard/diberri.crabdance.com%7CPreetikapoor0]] (talk) 20:04, 29 December 2012 (UTC)

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