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 |
Dear MCB group,
I am involved in the informatics of two high-throughput gene-knockout projects conducted in part by Team87 at the Wellcome Trust Sanger Institute. These are the eucomm project ( http://www.eucomm.org) and the KOMP project ( http://www.knockoutmouse.org). These projects have been running for approximately three years, and between them aim to create a library of mutant mouse ES cells with targeted knockouts for about half the genes in the mouse genome. Currently the mutant ES cell archive has about 2000 mouse genes knocked out with targeted, conditional mutations. The distribution of vectors and ES cell lines arising from these efforts is done on a cost-recovery basis to serve the international research community.
The information for these resources has been publicly visible for over two years (see www.knockoutmouse.org or www.eucomm.org). The experimental techniques and resources have some supporting published material (see Brief Funct Genomic Proteomic. 2007 Sep;6(3):180-5. Epub 2007 Oct 29 for EUCOMM or Nat Genet. 2004 Sep;36(9):921-4 for KOMP) but the main publication for the experimental technique is to be submitted to Nature Genetics within a couple of weeks. In addition, there are a large number of existing 'random' knockouts for about 10,000 mouse genes, best catalogued at http://www.genetrap.org, which have been in the public eye for a while (Nucleic Acids Res. 2006 Jan 1;34). The 'knockout mouse' wiki page ( http://en.wikipedia.org/wiki/Knockout_mouse) does point to some of these resources already.
I would like to propose that where a mouse gene has an available mutant ES cell generated by these programs, that the corresponding mammalian gene entry is appended with a 'box' similar in vision to the protein box on the mammalian gene pages.
An example of a mammalian gene page is this: http://en.wikipedia.org/wiki/ART4. The 'mutabox' box would give a pointer to further information on all existing mutant alleles for the gene, as well as providing a picture of the molecular structure of a single mutant. Here is a simple straw-man for the Art4 mutabox:
Would you support the addition of external links on the relevant individual Gene pages to the GeneGo pathways? There are many pathways available in the free portion of the GeneGo site. This would be a parallel resource to the existing GeneCards and OMIM links. -- Kariohlsen ( talk) 01:54, 17 January 2010 (UTC)
As part of an independent effort called WikiPathways, we are managing the curation of hundreds of biological pathways. This is a 100% free, open source and open access effort. We recently produced imagemaps of these pathway diagrams that include links to wikipedia articles for every gene, protein and metabolite in the pathway, or a link to "start a new article" in cases where one does not exist. We believe these pathway diagrams will not only enrich existing protein and pathways articles, but also enhance the connections across related articles. We've prepared a demonstration using a TCA Cycle pathway template on the following pages:
Notice how the imagemap links to protein and metabolite articles. There are template variables to highlight a particular protein and to control the map size per usage.
I've done my homework and coordinated with Gene Wiki folks in preparing this demo and I've read up on the Metabolic Pathways Task Force, Talk pages and External_links#Links_normally_to_be_avoided, etc. I'm eager for feedback on this proposal. Thanks! AlexanderPico ( talk) 01:29, 1 August 2010 (UTC)
Click on genes, proteins and metabolites below to link to respective articles. [§ 1]
Thanks for all the feedback! We were also concerned about the size of the maps. Here are possible solutions:
I also looked into CSS Sprites, but again, the problem is how to link from the sprited (or cropped) view to the full view containing useful links to all the related GeneWiki articles. Overall, #1 is the easiest and most flexible. #2 could probably be improved upon if encouraged. I'm concerned that #3 would defeat the purpose. Your continued feedback and ideas would be appreciated! AlexanderPico ( talk) 18:46, 4 August 2010 (UTC)
I was unaware of this thread until I just got a message about it at my talk. Being unaware of it, I had (sorry!) reverted some of the additions of these pathways to pages that I watch (mostly dopamine-related). But I feel flexible about it. I will repeat here part of what I said about it at my talk:
That's what I said by way of concerns at my talk. But I see that this is a work in progress being discussed here, and as I said, I feel flexible about it. I'll watch this discussion now. -- Tryptofish ( talk) 22:13, 3 September 2010 (UTC)
Could this be used to create an interactive claddogram navigation tool for taxoboxes? I mean, could there be in a taxobox a picture of the position of the branch of the tree of life of the refferent? And then could the user click on the claddogram and zoom in and out and click on taxa and be sent to articles? Have you seen how they do it at the hall of vertibrates at the American Museum of Natural History in Manhattan? There's a big claddogram at the front and then each hall is laid out to follow the clades, and a cladogram is there at each exhibit so you can see where the animal fits onto the tree of life? Could we do something like that using this tool? I hope I've said enough for you to understand the kind of thing I'm driving at, but if not but if I've piqued your interest and want me to describe this idea in more detail, please ask and I'll try to flesh it out more, but for the moment I don't want to go on too long. Chrisrus ( talk) 04:50, 22 October 2010 (UTC)
I would like to know if we could include a possible relation of protein gap-43 with autism, as stated on this scientific article:
http://www.jneurosci.org/cgi/content/abstract/30/44/14595
And this:
http://blog.autismspeaks.org/2010/11/11/what-lies-beneath-brain-connections/#comment-9286
The page I think should be modified is this:
http://en.wikipedia.org/wiki/Gap-43_protein
{{
cite journal}}
: Unknown parameter |laysource=
ignored (
help); Unknown parameter |laysummary=
ignored (
help)Hi all, the latest Database Issue of NAR has just been published and I wonder if it would be worth to create an infobox biodatabase. For each database I would write an article with this infobox. The fields would be:
I plan to use a XSLT stylesheet to quiclky write a WP article from a pubmed abstract. -- Plindenbaum ( talk) 14:59, 5 January 2011 (UTC)
OK, I started here: Template:Infobox_biodatabase-- Plindenbaum ( talk) 18:17, 5 January 2011 (UTC)
This is a timely suggestion. Recently a paper has been published about something called BioDBCore. This initiative aims to define a set of minimal information requirements about a database. In fact it is very much like what we would want for an infobox. BioDBCore currently define 17 different fields of information, including the resources Wikipedia entry! It would make sense that as far as possible we try to mirror that set up. If it does become a widely adopted standard it will make it easier for us to keep these boxes up to date in the future. The paper includes an excel file with some examples from some well known databases.
The paper is here: http://www.ncbi.nlm.nih.gov/pubmed/21097465 The field description is in the excel file in the supp. materials: http://nar.oxfordjournals.org/content/early/2010/11/17/nar.gkq1173/suppl/DC1
Here is the list of their fields:
Thanks for starting this! Alexbateman ( talk) 08:28, 6 January 2011 (UTC)
Content | |
---|---|
Description | Comparative genomics of Fusarium strains, |
Contact | |
Primary citation | PMID 21087991 |
Access | |
Website | http://www.fusarium.org |
-- Plindenbaum ( talk) 13:10, 6 January 2011 (UTC)
I wrote a Xslt stylesheet to transform a Pubmed article to wikipedia. See Template:Infobox_biodatabase/doc for a demo. And here are a two pages I created with this stylesheet : PlasmoDB and Rebase. I also created the template Template:Biodatabase-stub -- Plindenbaum ( talk) 21:19, 6 January 2011 (UTC)
FYI the data from Template:Infobox_biodatabase have now been integrated into DBPedia 3.7. See:
those data can now be searched through a SPARQL query -- Plindenbaum ( talk) 09:56, 11 September 2011 (UTC)
I believe it would be informative as well as useful to create a stub on the ribosyl group. I submitted an article for review, albeit, more of a definition, and it was promptly rejected. So I concluded that joining the project and hearing some opinions on whether it is important enough to have its own article, or if the ribose article could be edited to include its radical and its subsequent presence in proteins and enzymes. Let me know what you think. Dissonase 02:12, 17 February 2011 (UTC)
Discuss. Blahdenoma ( talk) 05:59, 30 April 2011 (UTC)
Mouse Mutant Alleles for Art4 | ||
---|---|---|
Marker Symbol for Mouse Gene. This symbol is assigned to the genomic locus by the MGI | Art4 | |
Mutant Mouse Embryonic Stem Cell Clones. These are the known targeted mutations for this gene in a mouse. | Art4tm1aWTSI(KOMP) | |
Example structure of targeted conditional mutant allele for this gene | ||
These Mutant ES Cells can be studied directly or used to generate mice with this gene knocked out. Study of these mice can shed light on the function of Art4 see Knockout mouse |
I envision the mutabox updates to the gene pages will be made by a robot ('mutabot', still to be proposed & written) which scans the known high-throughput mutations at www.knockoutmouse.org and applies the changes to a template in each mammalian gene entry. Also note that all mutabox entries would point back to the existing wiki page Knockout mouse], which explains further why these mutants are scientifically interesting (they help the study of gene function), and gives more links.
I would like to get opinions (and hopefully consensus) from the MCB group for this proposal.
Regards,
Vivek Iyer
High Throughput Gene Targeting
Wellcome Trust Sanger Institute
I'd propose a channel on freenode.net (just like #wikipedia has)... my suggestion would be the following channel irc://irc.freenode.net/#wikipedia-mcb
There are a bunch of people in irc://irc.freenode.net/#bioinformatics for example... I'm sure you could recruit some of them if you had an irc presence... also I'd just quite like to chat to some of you guys some time ;-)
-- Dan| (talk) 18:35, 14 April 2009 (UTC)
I made a suggestion over at the cell signaling wikiproject (see here [1]) to consider merging into this project as a task force. I noticed above there has been suggestions to make a few task forces but not sure whether they went ahead as planned? Anyone here happen to have any suggestions/comments they would like to make re: merging cell signalling wikiproject as a task force here? Cheers. Calaka ( talk) 11:13, 5 May 2009 (UTC)
I think a photosynthesis taskforce should be a great idea. A couple of months ago I tried to make a wikiproject about this subject, but a taskforce should be better. At the moment the most important articles about this subject (Photosynthesis, Light Reactions, Dark reactions, Chloroplast) are not anything near FA-status. (Altough, I have put a lot time in the light reactions article). And all the other articles of this subject are mostly stubs.
I think the photosynthesis article itself is one of the examples of what happens if you have to many authors. One of the three guys that have ever posted something on the wikiproject photosynthesis wrote this about it:
"In my opinion, this article is one of the worst on WikiPedia. There is a heck of a lot of good information on this page, but it is obtuse, chaotic and so badly written that is absolutely useless. The only people who can understand it are the people who already know it; a solid case of preaching to the choir, if I've ever seen one."
And I think he is totally right...
So what do you guys think? Kasper90 ( talk) 16:42, 26 May 2009 (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 |
Dear MCB group,
I am involved in the informatics of two high-throughput gene-knockout projects conducted in part by Team87 at the Wellcome Trust Sanger Institute. These are the eucomm project ( http://www.eucomm.org) and the KOMP project ( http://www.knockoutmouse.org). These projects have been running for approximately three years, and between them aim to create a library of mutant mouse ES cells with targeted knockouts for about half the genes in the mouse genome. Currently the mutant ES cell archive has about 2000 mouse genes knocked out with targeted, conditional mutations. The distribution of vectors and ES cell lines arising from these efforts is done on a cost-recovery basis to serve the international research community.
The information for these resources has been publicly visible for over two years (see www.knockoutmouse.org or www.eucomm.org). The experimental techniques and resources have some supporting published material (see Brief Funct Genomic Proteomic. 2007 Sep;6(3):180-5. Epub 2007 Oct 29 for EUCOMM or Nat Genet. 2004 Sep;36(9):921-4 for KOMP) but the main publication for the experimental technique is to be submitted to Nature Genetics within a couple of weeks. In addition, there are a large number of existing 'random' knockouts for about 10,000 mouse genes, best catalogued at http://www.genetrap.org, which have been in the public eye for a while (Nucleic Acids Res. 2006 Jan 1;34). The 'knockout mouse' wiki page ( http://en.wikipedia.org/wiki/Knockout_mouse) does point to some of these resources already.
I would like to propose that where a mouse gene has an available mutant ES cell generated by these programs, that the corresponding mammalian gene entry is appended with a 'box' similar in vision to the protein box on the mammalian gene pages.
An example of a mammalian gene page is this: http://en.wikipedia.org/wiki/ART4. The 'mutabox' box would give a pointer to further information on all existing mutant alleles for the gene, as well as providing a picture of the molecular structure of a single mutant. Here is a simple straw-man for the Art4 mutabox:
Would you support the addition of external links on the relevant individual Gene pages to the GeneGo pathways? There are many pathways available in the free portion of the GeneGo site. This would be a parallel resource to the existing GeneCards and OMIM links. -- Kariohlsen ( talk) 01:54, 17 January 2010 (UTC)
As part of an independent effort called WikiPathways, we are managing the curation of hundreds of biological pathways. This is a 100% free, open source and open access effort. We recently produced imagemaps of these pathway diagrams that include links to wikipedia articles for every gene, protein and metabolite in the pathway, or a link to "start a new article" in cases where one does not exist. We believe these pathway diagrams will not only enrich existing protein and pathways articles, but also enhance the connections across related articles. We've prepared a demonstration using a TCA Cycle pathway template on the following pages:
Notice how the imagemap links to protein and metabolite articles. There are template variables to highlight a particular protein and to control the map size per usage.
I've done my homework and coordinated with Gene Wiki folks in preparing this demo and I've read up on the Metabolic Pathways Task Force, Talk pages and External_links#Links_normally_to_be_avoided, etc. I'm eager for feedback on this proposal. Thanks! AlexanderPico ( talk) 01:29, 1 August 2010 (UTC)
Click on genes, proteins and metabolites below to link to respective articles. [§ 1]
Thanks for all the feedback! We were also concerned about the size of the maps. Here are possible solutions:
I also looked into CSS Sprites, but again, the problem is how to link from the sprited (or cropped) view to the full view containing useful links to all the related GeneWiki articles. Overall, #1 is the easiest and most flexible. #2 could probably be improved upon if encouraged. I'm concerned that #3 would defeat the purpose. Your continued feedback and ideas would be appreciated! AlexanderPico ( talk) 18:46, 4 August 2010 (UTC)
I was unaware of this thread until I just got a message about it at my talk. Being unaware of it, I had (sorry!) reverted some of the additions of these pathways to pages that I watch (mostly dopamine-related). But I feel flexible about it. I will repeat here part of what I said about it at my talk:
That's what I said by way of concerns at my talk. But I see that this is a work in progress being discussed here, and as I said, I feel flexible about it. I'll watch this discussion now. -- Tryptofish ( talk) 22:13, 3 September 2010 (UTC)
Could this be used to create an interactive claddogram navigation tool for taxoboxes? I mean, could there be in a taxobox a picture of the position of the branch of the tree of life of the refferent? And then could the user click on the claddogram and zoom in and out and click on taxa and be sent to articles? Have you seen how they do it at the hall of vertibrates at the American Museum of Natural History in Manhattan? There's a big claddogram at the front and then each hall is laid out to follow the clades, and a cladogram is there at each exhibit so you can see where the animal fits onto the tree of life? Could we do something like that using this tool? I hope I've said enough for you to understand the kind of thing I'm driving at, but if not but if I've piqued your interest and want me to describe this idea in more detail, please ask and I'll try to flesh it out more, but for the moment I don't want to go on too long. Chrisrus ( talk) 04:50, 22 October 2010 (UTC)
I would like to know if we could include a possible relation of protein gap-43 with autism, as stated on this scientific article:
http://www.jneurosci.org/cgi/content/abstract/30/44/14595
And this:
http://blog.autismspeaks.org/2010/11/11/what-lies-beneath-brain-connections/#comment-9286
The page I think should be modified is this:
http://en.wikipedia.org/wiki/Gap-43_protein
{{
cite journal}}
: Unknown parameter |laysource=
ignored (
help); Unknown parameter |laysummary=
ignored (
help)Hi all, the latest Database Issue of NAR has just been published and I wonder if it would be worth to create an infobox biodatabase. For each database I would write an article with this infobox. The fields would be:
I plan to use a XSLT stylesheet to quiclky write a WP article from a pubmed abstract. -- Plindenbaum ( talk) 14:59, 5 January 2011 (UTC)
OK, I started here: Template:Infobox_biodatabase-- Plindenbaum ( talk) 18:17, 5 January 2011 (UTC)
This is a timely suggestion. Recently a paper has been published about something called BioDBCore. This initiative aims to define a set of minimal information requirements about a database. In fact it is very much like what we would want for an infobox. BioDBCore currently define 17 different fields of information, including the resources Wikipedia entry! It would make sense that as far as possible we try to mirror that set up. If it does become a widely adopted standard it will make it easier for us to keep these boxes up to date in the future. The paper includes an excel file with some examples from some well known databases.
The paper is here: http://www.ncbi.nlm.nih.gov/pubmed/21097465 The field description is in the excel file in the supp. materials: http://nar.oxfordjournals.org/content/early/2010/11/17/nar.gkq1173/suppl/DC1
Here is the list of their fields:
Thanks for starting this! Alexbateman ( talk) 08:28, 6 January 2011 (UTC)
Content | |
---|---|
Description | Comparative genomics of Fusarium strains, |
Contact | |
Primary citation | PMID 21087991 |
Access | |
Website | http://www.fusarium.org |
-- Plindenbaum ( talk) 13:10, 6 January 2011 (UTC)
I wrote a Xslt stylesheet to transform a Pubmed article to wikipedia. See Template:Infobox_biodatabase/doc for a demo. And here are a two pages I created with this stylesheet : PlasmoDB and Rebase. I also created the template Template:Biodatabase-stub -- Plindenbaum ( talk) 21:19, 6 January 2011 (UTC)
FYI the data from Template:Infobox_biodatabase have now been integrated into DBPedia 3.7. See:
those data can now be searched through a SPARQL query -- Plindenbaum ( talk) 09:56, 11 September 2011 (UTC)
I believe it would be informative as well as useful to create a stub on the ribosyl group. I submitted an article for review, albeit, more of a definition, and it was promptly rejected. So I concluded that joining the project and hearing some opinions on whether it is important enough to have its own article, or if the ribose article could be edited to include its radical and its subsequent presence in proteins and enzymes. Let me know what you think. Dissonase 02:12, 17 February 2011 (UTC)
Discuss. Blahdenoma ( talk) 05:59, 30 April 2011 (UTC)
Mouse Mutant Alleles for Art4 | ||
---|---|---|
Marker Symbol for Mouse Gene. This symbol is assigned to the genomic locus by the MGI | Art4 | |
Mutant Mouse Embryonic Stem Cell Clones. These are the known targeted mutations for this gene in a mouse. | Art4tm1aWTSI(KOMP) | |
Example structure of targeted conditional mutant allele for this gene | ||
These Mutant ES Cells can be studied directly or used to generate mice with this gene knocked out. Study of these mice can shed light on the function of Art4 see Knockout mouse |
I envision the mutabox updates to the gene pages will be made by a robot ('mutabot', still to be proposed & written) which scans the known high-throughput mutations at www.knockoutmouse.org and applies the changes to a template in each mammalian gene entry. Also note that all mutabox entries would point back to the existing wiki page Knockout mouse], which explains further why these mutants are scientifically interesting (they help the study of gene function), and gives more links.
I would like to get opinions (and hopefully consensus) from the MCB group for this proposal.
Regards,
Vivek Iyer
High Throughput Gene Targeting
Wellcome Trust Sanger Institute
I'd propose a channel on freenode.net (just like #wikipedia has)... my suggestion would be the following channel irc://irc.freenode.net/#wikipedia-mcb
There are a bunch of people in irc://irc.freenode.net/#bioinformatics for example... I'm sure you could recruit some of them if you had an irc presence... also I'd just quite like to chat to some of you guys some time ;-)
-- Dan| (talk) 18:35, 14 April 2009 (UTC)
I made a suggestion over at the cell signaling wikiproject (see here [1]) to consider merging into this project as a task force. I noticed above there has been suggestions to make a few task forces but not sure whether they went ahead as planned? Anyone here happen to have any suggestions/comments they would like to make re: merging cell signalling wikiproject as a task force here? Cheers. Calaka ( talk) 11:13, 5 May 2009 (UTC)
I think a photosynthesis taskforce should be a great idea. A couple of months ago I tried to make a wikiproject about this subject, but a taskforce should be better. At the moment the most important articles about this subject (Photosynthesis, Light Reactions, Dark reactions, Chloroplast) are not anything near FA-status. (Altough, I have put a lot time in the light reactions article). And all the other articles of this subject are mostly stubs.
I think the photosynthesis article itself is one of the examples of what happens if you have to many authors. One of the three guys that have ever posted something on the wikiproject photosynthesis wrote this about it:
"In my opinion, this article is one of the worst on WikiPedia. There is a heck of a lot of good information on this page, but it is obtuse, chaotic and so badly written that is absolutely useless. The only people who can understand it are the people who already know it; a solid case of preaching to the choir, if I've ever seen one."
And I think he is totally right...
So what do you guys think? Kasper90 ( talk) 16:42, 26 May 2009 (UTC)