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. |
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Gene Wiki – Discussion |
Hi! Should File:PBB GE MYH6 204737 s at fs.png and File:PBB GE MYH7 204737 s at fs.png be duplicates? And File:PBB GE PSG3 209738 x at fs.png and File:PBB GE PSG6 209738 x at fs.png? -- MGA73 ( talk) 19:27, 5 March 2010 (UTC)
Just found my way to Template:PDB Gallery, um the description there could do with some expansion! Was wandering if I could I add it to huntingtin for example? Lee∴V (talk • contribs) 01:01, 23 March 2010 (UTC)
I thought I'd point out that the gallery generated by this Template is broken on the Thrombin page. Not sure if it's a problem with the template itself or with the way it was implemented, but it produces a mess of code on the page (though fortunately hidden until you expand the section). I'm going to comment out the template but leave it there for someone to fix. GiftigerWunsch [TALK] 13:06, 17 May 2010 (UTC)
In the current implementation, the GO sub-box contains links to the individual GO terms, but not to the protein itself. Would it be possible to add this link? E.g. Aurora A kinase should link here. MichaK ( talk) 09:50, 27 May 2010 (UTC)
While we are at it, I would like to propose that the available structure section of the {{ GNF_Protein_box}} be made collapsible. The list PDB links can be very long (see HBA1 for example) and can overwhelm the rest of the content in the infobox. I have edited the sandbox in this change. The code is a bit messy, but it seems to work (see prototype). Does this look OK? Boghog ( talk) 08:19, 29 May 2010 (UTC)
Hi all, the work you are doing here is amazing. I am a PhD student in Bioinformatics, as well as a Wikipedia-administrator-on-retirement, and I'm very much interested in the details on how you've designed bots to create the gene records, and where the data is coming from. Who should I talk to about this topic? :-) Cheers, Venullian ( talk) 14:04, 8 June 2010 (UTC)
I started List of biological wikis, but it needs improvements if anyone is interested. Biophys ( talk) 17:00, 13 July 2010 (UTC)
Is there template that provides a infobox/link to the Gene Wiki portal project? I was just noticing that from a gene's article or discussion page there's no way to navigate to the main Gene Wiki portal page. Such a thing would help spread the word about the project and attract potential contributors. I'm imagining something like {{Wikiproject Gene|class=Stub|importance=Low}} which would expand to a box stating something like "This article is within the scope of the Gene WikiProject. To participate, visit the WikiProject for more information...". I'd recommend something like this appear at the bottom of every gene's page as well as at the top of the gene's discussion page. Kudos++ on this project, btw! SteveChervitzTrutane ( talk) 02:17, 21 August 2010 (UTC)
A pilot project for integrating semantic wikilinks (SWLs) into gene articles, listed at User:ProteinBoxBot/Ideas, seems interesting. The first two bullet points suggest finding some facts about a set of genes and encoding them with SWLs. There are several database from which such information could be gathered en masse, including MIPS, IntAct, BioGRID and others.
However the quality of these datasets has been brought into question -- see for example Literature-curated protein interaction datasets, 2009. The maintainers of the MINT repository have done some work to address concerns about reliability by introducing a scoring system for interaction confidence ( MINT, the molecular interaction database: 2009 update). Would MINT be the most promising dataset to use for encoding semantic wikilinks? Given concerns about protein interaction datasetes, what should be the threshold for reliability for encoding a SWL? Would the SWLs only consider interactions between human proteins? Emw ( talk) 03:28, 24 August 2010 (UTC)
There is a few thousand unused File:PBB Protein xxxx image.jpg and as suggested on User_talk:AndrewGNF/Archive2#To_Commons it should be safe to delete them. Before we start a DR I would like to hear if other users think that thy should not be deleted (and why). AndrewGNF has a lot of things to do so there is still some files in use that should be replaced if someone has some time to help. -- MGA73 ( talk) 21:12, 26 August 2010 (UTC)
Some protein names have multiple single quotes, like PPP2R3A: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha. This normally initiated an italic section. I've manually added the nowiki tag around the '' in the page title, but it's still there in the sections edited by PBB. Could you please check the bot to add nowiki tags when necessary? Thanks, MichaK ( talk) 12:10, 7 September 2010 (UTC)
So the warnings "The PBB_Summary template is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates." are more or less obsolete now? In this cases I'd suggest to remove them (and the PBB_Summary template?), as editors (like me) then refrain to edit the summaries. I know that it is possible to tell PBB not to edit the summary, but if I have the impression that PBB is going to update the summaries regularly, then I'm reluctant to disable this. MichaK ( talk) 08:46, 30 September 2010 (UTC)
According to various sources, the guanylate cyclase-C receptor is the target of the drug linaclotide. Any idea what this receptor is? Do we have a page about it/its gene? Thanks, ἀνυπόδητος ( talk) 14:59, 28 September 2010 (UTC)
The article Selectin has an infobox containing the sushi domain, which isn't mentioned anywhere in the article. Then again, the section "Examples" lists "Human genes encoding proteins containing this domain" (without explaining what "this" domain is). Some list entries definitely contain sushi. Could someone clarify this? Thanks -- ἀνυπόδητος ( talk) 18:58, 11 October 2010 (UTC)
As part of an unrelated task, I've accidentally generated a list of unused PDB Galleries. Posted here in case it's of use:
10395 - 11166 - 1401 - 1454 - 1471 - 156 - 1742 - 2919 - 335 - 336 - 344 - 350 - 367 - 3952 - 4179 - 462 - 5176 - 5447 - 5617 - 596 - 627 - 6310 - 633 - 637 - 6426 - 6658 - 7143 - 718 - 728358 - 7293 - 835 - 847 - 8654 - 9370 - _26002
We have got ITIH1, ITIH2, ITIH3, and ITIH4, but we seem to be lacking an article on the inter-alpha-trypsin inhibitor itself. Or did I miss anything? -- ἀνυπόδητος ( talk) 16:07, 6 December 2010 (UTC)
FYI, I have started translating the German article on Kunitz domains. It focuses on the pharmaceutical use, so any material on its biological functions would be welcome. -- ἀνυπόδητος ( talk) 17:13, 6 December 2010 (UTC)
Glucocerebrosidase (GBA) lists "glucosylceramidase" and "β-glucosidase" as synonyms, while Glucosylceramidase (EC 3.2.1.45) seems to imply that GBA is a type of glucosylceramidase (and the only one listed). Beta-glucosidase has EC 3.2.1.21 and contains a box names "glucosidase, beta; acid (includes glucosylceramidase)". Perhaps I'm being silly, but I don't get the relationship between these terms. Can someone enlighten me? -- ἀνυπόδητος ( talk) 17:52, 30 December 2010 (UTC)
This is out of my field, but it appears that EC 3.2.1.21 and EC 3.2.1.45 are two very closely related enzymes with similar substrate specificity and therefore similar names:
Enzyme | Enzyme commission number | Human genes | Aliases |
---|---|---|---|
Beta-glucosidase | EC 3.2.1.21 | GBA3 | amygdalase, beta-D-glucoside glucohydrolase, cellobiase, gentobiase |
Glucosylceramidase | EC 3.2.1.45 | GBA, GBA2 | acid beta-glucosidase, beta-glucocerebrosidase, D-glucosyl-N-acylsphingosine glucohydrolase |
I hope this helps. Cheers. Boghog ( talk) 21:31, 30 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 |
Gene Wiki – Discussion |
Hi! Should File:PBB GE MYH6 204737 s at fs.png and File:PBB GE MYH7 204737 s at fs.png be duplicates? And File:PBB GE PSG3 209738 x at fs.png and File:PBB GE PSG6 209738 x at fs.png? -- MGA73 ( talk) 19:27, 5 March 2010 (UTC)
Just found my way to Template:PDB Gallery, um the description there could do with some expansion! Was wandering if I could I add it to huntingtin for example? Lee∴V (talk • contribs) 01:01, 23 March 2010 (UTC)
I thought I'd point out that the gallery generated by this Template is broken on the Thrombin page. Not sure if it's a problem with the template itself or with the way it was implemented, but it produces a mess of code on the page (though fortunately hidden until you expand the section). I'm going to comment out the template but leave it there for someone to fix. GiftigerWunsch [TALK] 13:06, 17 May 2010 (UTC)
In the current implementation, the GO sub-box contains links to the individual GO terms, but not to the protein itself. Would it be possible to add this link? E.g. Aurora A kinase should link here. MichaK ( talk) 09:50, 27 May 2010 (UTC)
While we are at it, I would like to propose that the available structure section of the {{ GNF_Protein_box}} be made collapsible. The list PDB links can be very long (see HBA1 for example) and can overwhelm the rest of the content in the infobox. I have edited the sandbox in this change. The code is a bit messy, but it seems to work (see prototype). Does this look OK? Boghog ( talk) 08:19, 29 May 2010 (UTC)
Hi all, the work you are doing here is amazing. I am a PhD student in Bioinformatics, as well as a Wikipedia-administrator-on-retirement, and I'm very much interested in the details on how you've designed bots to create the gene records, and where the data is coming from. Who should I talk to about this topic? :-) Cheers, Venullian ( talk) 14:04, 8 June 2010 (UTC)
I started List of biological wikis, but it needs improvements if anyone is interested. Biophys ( talk) 17:00, 13 July 2010 (UTC)
Is there template that provides a infobox/link to the Gene Wiki portal project? I was just noticing that from a gene's article or discussion page there's no way to navigate to the main Gene Wiki portal page. Such a thing would help spread the word about the project and attract potential contributors. I'm imagining something like {{Wikiproject Gene|class=Stub|importance=Low}} which would expand to a box stating something like "This article is within the scope of the Gene WikiProject. To participate, visit the WikiProject for more information...". I'd recommend something like this appear at the bottom of every gene's page as well as at the top of the gene's discussion page. Kudos++ on this project, btw! SteveChervitzTrutane ( talk) 02:17, 21 August 2010 (UTC)
A pilot project for integrating semantic wikilinks (SWLs) into gene articles, listed at User:ProteinBoxBot/Ideas, seems interesting. The first two bullet points suggest finding some facts about a set of genes and encoding them with SWLs. There are several database from which such information could be gathered en masse, including MIPS, IntAct, BioGRID and others.
However the quality of these datasets has been brought into question -- see for example Literature-curated protein interaction datasets, 2009. The maintainers of the MINT repository have done some work to address concerns about reliability by introducing a scoring system for interaction confidence ( MINT, the molecular interaction database: 2009 update). Would MINT be the most promising dataset to use for encoding semantic wikilinks? Given concerns about protein interaction datasetes, what should be the threshold for reliability for encoding a SWL? Would the SWLs only consider interactions between human proteins? Emw ( talk) 03:28, 24 August 2010 (UTC)
There is a few thousand unused File:PBB Protein xxxx image.jpg and as suggested on User_talk:AndrewGNF/Archive2#To_Commons it should be safe to delete them. Before we start a DR I would like to hear if other users think that thy should not be deleted (and why). AndrewGNF has a lot of things to do so there is still some files in use that should be replaced if someone has some time to help. -- MGA73 ( talk) 21:12, 26 August 2010 (UTC)
Some protein names have multiple single quotes, like PPP2R3A: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha. This normally initiated an italic section. I've manually added the nowiki tag around the '' in the page title, but it's still there in the sections edited by PBB. Could you please check the bot to add nowiki tags when necessary? Thanks, MichaK ( talk) 12:10, 7 September 2010 (UTC)
So the warnings "The PBB_Summary template is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates." are more or less obsolete now? In this cases I'd suggest to remove them (and the PBB_Summary template?), as editors (like me) then refrain to edit the summaries. I know that it is possible to tell PBB not to edit the summary, but if I have the impression that PBB is going to update the summaries regularly, then I'm reluctant to disable this. MichaK ( talk) 08:46, 30 September 2010 (UTC)
According to various sources, the guanylate cyclase-C receptor is the target of the drug linaclotide. Any idea what this receptor is? Do we have a page about it/its gene? Thanks, ἀνυπόδητος ( talk) 14:59, 28 September 2010 (UTC)
The article Selectin has an infobox containing the sushi domain, which isn't mentioned anywhere in the article. Then again, the section "Examples" lists "Human genes encoding proteins containing this domain" (without explaining what "this" domain is). Some list entries definitely contain sushi. Could someone clarify this? Thanks -- ἀνυπόδητος ( talk) 18:58, 11 October 2010 (UTC)
As part of an unrelated task, I've accidentally generated a list of unused PDB Galleries. Posted here in case it's of use:
10395 - 11166 - 1401 - 1454 - 1471 - 156 - 1742 - 2919 - 335 - 336 - 344 - 350 - 367 - 3952 - 4179 - 462 - 5176 - 5447 - 5617 - 596 - 627 - 6310 - 633 - 637 - 6426 - 6658 - 7143 - 718 - 728358 - 7293 - 835 - 847 - 8654 - 9370 - _26002
We have got ITIH1, ITIH2, ITIH3, and ITIH4, but we seem to be lacking an article on the inter-alpha-trypsin inhibitor itself. Or did I miss anything? -- ἀνυπόδητος ( talk) 16:07, 6 December 2010 (UTC)
FYI, I have started translating the German article on Kunitz domains. It focuses on the pharmaceutical use, so any material on its biological functions would be welcome. -- ἀνυπόδητος ( talk) 17:13, 6 December 2010 (UTC)
Glucocerebrosidase (GBA) lists "glucosylceramidase" and "β-glucosidase" as synonyms, while Glucosylceramidase (EC 3.2.1.45) seems to imply that GBA is a type of glucosylceramidase (and the only one listed). Beta-glucosidase has EC 3.2.1.21 and contains a box names "glucosidase, beta; acid (includes glucosylceramidase)". Perhaps I'm being silly, but I don't get the relationship between these terms. Can someone enlighten me? -- ἀνυπόδητος ( talk) 17:52, 30 December 2010 (UTC)
This is out of my field, but it appears that EC 3.2.1.21 and EC 3.2.1.45 are two very closely related enzymes with similar substrate specificity and therefore similar names:
Enzyme | Enzyme commission number | Human genes | Aliases |
---|---|---|---|
Beta-glucosidase | EC 3.2.1.21 | GBA3 | amygdalase, beta-D-glucoside glucohydrolase, cellobiase, gentobiase |
Glucosylceramidase | EC 3.2.1.45 | GBA, GBA2 | acid beta-glucosidase, beta-glucocerebrosidase, D-glucosyl-N-acylsphingosine glucohydrolase |
I hope this helps. Cheers. Boghog ( talk) 21:31, 30 December 2010 (UTC)