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"it is recomended that we use the ABR instead of the full name form" <-- Use of abbreviations for gene and protein names should follow the rules for jargon. -- JWSchmidt 16:04, 29 December 2005 (UTC)
No, it is better to be consitent: either use the abbreviation or don't in all the articles no matter how long the name of the protein is. We all have a different opinions about how long is too long. I agree, writing the full name once followed with abreviation in betwenn bracketts and then using the abrevation in the rest of the article is a good way to make an article clear and concise. It's also possible to add an index containing all the abreviations used at the top of the article. Do not place the index at the end, as the reader won't know it is there before he reaches the bottom of the paper.
The abreviations (ABR) of the genes are according to HUGO Gene Nomenclature Committee and written in ITALIC font style (the full names are also written in italic), it is recomended that we use the ABR instead of the full name form. The human gene names are in all big caps (correct me if i haven't written it well), example - ALDOA, INS, etc. Human homologous of genes in other species start with a big cap and the rest of the letters are small caps - mouse Aldoa, bovine Ins, etc. When we write about the genes this is correct - "the ALDOA gene is regulated...", "the rat gene for Aldoa is regulated..." or "ALDOA is regulated...", while this should not be allowed - "the gene ALDOA is regulated", b/c it's redundant. And if anyone starts arguing with you about it, say "Sorry, but we have a standard to follow" and redirect them to this section. -- Boris 15:32, 29 December 2005 (UTC)
Below is an example of what i think we should attempt to do.
Type | Protein | Gene | Recessive allele | Dominant allele |
---|---|---|---|---|
mouse | ALDOA | ALDOA | aldoa | |
human | ||||
yeast | ||||
C. elegans | Aldoa | ALDOA | aldoa | |
dropsophila | ||||
zebra fish | ||||
arabidopsis | SHOOT MERISTEMLESS or STM | SHOOT MERISTEMLESS or STM | shoot meristemless or stm | shoot meristemless or stm |
maize | KNOTTED1 or KN1 | KNOTTED1 or KN1 | knotted1 or kn1 | Knotted1 or Kn1 |
The same as with the genes, but in NORMAL font style. -- Boris 15:32, 29 December 2005 (UTC)
Hi everyone. We have to decide whether - to use the abreviations (ABRs) for the objects (such as Glc for glucose) throughout the project's articles; use them in the object's article only ot not use them at all. I preffer to use them all the way, with one exception - in the introduction part of the article, so those who are not familiar to be able to understand, after that the text becomes high level anyway so we don't need to have the full names. There are many reasons for that but the main is that i want our articles to look very well done almost pro, so we can atract more and more scientist to join us in making the project because with their knowledge they can help us tremendously (i know some of you are, but we need more - hundreds, or thousands is even better), i want these people to take us seriously and not just as some sort of online-encyclopedia joke, i want that these people know that anytime they need a reliable and good writen info they can come here and find it easily. Boris 17:00, 18 December 2005 (UTC)
Archived Boris' ideas (long read)
Copied from User talk:Opabinia regalis:
...my experience at Photon has set me brooding. Do you think that we as a community could come up with a standard set of questions that should be considered to make a biochemistry article "complete", e.g.,
along with subquestions for each of these, such as
It might be useful to have some kind of checklist for editors to help gauge how complete an article is. What do you think? It's more of a thought for a thought. Willow 15:15, 31 August 2006 (UTC)
As a first step for this project, we can create a standardized system for presenting information about proteins and genes within wikipedia. A logical place to start is with a system for categorization of proteins, start here: Whole proteome analysis. (see also: EC number, protein nomenclature talk, talk about protein lists, Talk:List of proteins and discussion about a specific class of non-enzyme proteins).
For organismal biology evolutionary relatedness of organisms provides a way to categorize all organisms. For proteins, functional categories are probably best and that is what is emphasized at Whole proteome analysis.
moved to #Standardising_article_structure.
This topic is now being voted upon!
I think it would be nice to standardize the rendered images of proteins in some way to give the same look and feel for this kind of articles. Of course this might not be possible in all cases as there are far too many protein articles. Also there are some that have good illustrations already which should not be removed just for the sake of standardization. However for all those pictureless protein articles where an image might be useful it would be nice to use the same representation. What do you think?
I suggest to use the open source program PyMol to render the images. It is widely used, gives nice results and had cartoon representations of both proteins and nucleic acids. For some articles I am interested in I did some images: actin, Arp2/3 complex, MreB, Profilin, Zinc finger(Protein + DNA)
If you think this would be useful, I'd volunteer to render some images on request. Just leave a message on my talk page.
Any thoughts?--
Splette
Talk
12:16, 1 September 2006 (UTC)
It seems that others are also interested in what's used to make protein representation pictures. There's a discussion over on the help page about what tools everyone uses. I think it's a great idea that we standardize the rendered images. We should discuss the pro's and con's of the various imaging tools and vote on it. And then produce a tutorial to instruct new users of the program how to use it and a series of guidelines so that the images all share similar standards. GAThrawn22 22:53, 2 September 2006 (UTC)
I disagree with the original proposal that base representations should be standardized at the software/technical level. Because structure is intimately connected with function, the structural representation (which will be the first thing that people see, and the first thing they focus on) should be designed to immediately call attention to the primary function or defining characteristic of that protein. I'll admit this is not an easy thing to define, but I do feel it should be the general goal. The exact representation is secondary. My area of interest is certainly a special example, but it serves to illustrate the point: a viral protein which is relevant only as an assembled complex (>4 MegaDa) needs a much different representation than cyt-c.
In my opinion, a style guideline would be more useful. Colors, background, labels, etc. I personally take into consideration color blindness when using colors: avoid red/green distinctions for critical areas. Since I'm not that familiar with Wikipedia, are animated images appropriate? Are representations with multiple level-of-detail layers ok? These kinds of style guidelines would let the experts for each protein choose the best way to show them while retaining some standards for presentation.
On a different issue, I've added a software option to the visualization list. Unless you're really serious about this stuff, it's pretty much a novelty, but it does give choices and representations that just aren't available elsewhere. I've also changed some pros/cons regarding Chimera (source code is available, for example). TheTweaker 19:55, 20 October 2006 (UTC)
Re. Wikipedia:WikiProject Molecular and Cellular Biology/Collaboration of the Month/History - could the table perhaps have include links to the article before and after. Also, I'm not sure how the table works, but the cell nucleus does have a review, a fact that should be included in the appropriate data-cell. ShaiM 11:48, 22 October 2006 (UTC)
It would be fun to have a few more MCB-specific barnstars, as suggested above, perhaps one for every major area? The DNA Barnstar is great. For proteins, Tup1 is a possibility, but it has seven blades, not five; maybe we should try another β-propellor such as 1gyh? IgM is another five-fold possibility. Willow 11:15, 24 October 2006 (UTC)
Like the title says... every barnstar should have a name, so what do we call it? – Clockwork Soul 18:27, 3 November 2006 (UTC)
Might as well use the vote page... shall we vote on name and which image to use? - Zephyris Talk 13:27, 7 November 2006 (UTC)
There are a number of stub classes that relate to this project, but seem to relate to one another in a haphazard way, if they do at all. So far, I've found:
I would like to sort these stub categories by placing them in a hierarchy beneath - I'm thinking - Category:Molecular and Cellular Biology stubs. Any thoughts? – Clockwork Soul 17:10, 25 October 2006 (UTC)
Tim's recent efforts into improving influenza got me to wondering a simple thing: does it fit within the scope of out MCB project? If it does, then do all varieties of viruses and unicellular critters have a place on out worklist? Looking over several similar pages, none of them seem to be claimed by any particular project already. However, our project's collective plate is already pretty full. Does anybody have any thoughts on the matter? – Clockwork Soul 17:43, 25 October 2006 (UTC)
Well I'm not taking that project over. My plan is to get the "big three" diseases to FA (only malaria to go) and then go back to more biochem-type subjects. TimVickers 20:54, 25 October 2006 (UTC)
That sounds like an excellent plan. TimVickers 14:50, 26 October 2006 (UTC)
I think it might be a good idea to make external links to Uniprot for individual proteins, or to Pfam for groups of proteins described in Wikipedia articles. As for links to PDB, this is not so simple, because every protein can be represented by a large set of PDB entries. The references to SCOP are better (anyone has an idea why SCOP is so outdated?). Also, it would be better to refer to PDBsum instead of the PDB, because PDBsum provides a much better interface with other databases and a lot of structural parameters of proteins that can not be found in PDB. Biophys 19:27, 31 October 2006 (UTC)
Re. the image seen on the templates (as put up on talk pages) and also on the user box: How come they keep changing? I think we're onto our third one. Personally I liked the one before this one, the molecule image. I don't care much for the current one, the colour scheme isn't too atractive. Any chance of reverting? ShaiM 04:28, 1 November 2006 (UTC)
User:Splette volunteered to do protein pictures upon request, but if there are others willing to do this, it might make sense to add a page like Wikipedia:WikiProject Molecular and Cellular Biology/ProteinPictureRequests where "Protein Picture Hitpersons" could watch and field requests. Are there others willing to do this is? I'd be most happy, since I am terrible at rendering these things. ~Doc~ EquationDoc 16:33, 10 November 2006 (UTC)
DONE! See Wikipedia:WikiProject_Molecular_and_Cellular_Biology/Requested_proteins for protein image and pathway diagram requests--field a request or add one to the list! ~Doc~ EquationDoc 16:46, 11 November 2006 (UTC)
Does anyone else see a need for aliases/alternative names/etc in the protein info box? I know this sort of works against the important goal of standardization of gene/protein names, but the reality is you often can't find references (PubMed, google, etc) without them. Moreover, in most cases, it probably makes little sense to devote space to them in article content, so adding them to the template seems reasonable (to me). Anyone? ~Doc~ EquationDoc 16:52, 10 November 2006 (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 main page. |
Archive 1 | Archive 2 | Archive 3 | Archive 4 |
"it is recomended that we use the ABR instead of the full name form" <-- Use of abbreviations for gene and protein names should follow the rules for jargon. -- JWSchmidt 16:04, 29 December 2005 (UTC)
No, it is better to be consitent: either use the abbreviation or don't in all the articles no matter how long the name of the protein is. We all have a different opinions about how long is too long. I agree, writing the full name once followed with abreviation in betwenn bracketts and then using the abrevation in the rest of the article is a good way to make an article clear and concise. It's also possible to add an index containing all the abreviations used at the top of the article. Do not place the index at the end, as the reader won't know it is there before he reaches the bottom of the paper.
The abreviations (ABR) of the genes are according to HUGO Gene Nomenclature Committee and written in ITALIC font style (the full names are also written in italic), it is recomended that we use the ABR instead of the full name form. The human gene names are in all big caps (correct me if i haven't written it well), example - ALDOA, INS, etc. Human homologous of genes in other species start with a big cap and the rest of the letters are small caps - mouse Aldoa, bovine Ins, etc. When we write about the genes this is correct - "the ALDOA gene is regulated...", "the rat gene for Aldoa is regulated..." or "ALDOA is regulated...", while this should not be allowed - "the gene ALDOA is regulated", b/c it's redundant. And if anyone starts arguing with you about it, say "Sorry, but we have a standard to follow" and redirect them to this section. -- Boris 15:32, 29 December 2005 (UTC)
Below is an example of what i think we should attempt to do.
Type | Protein | Gene | Recessive allele | Dominant allele |
---|---|---|---|---|
mouse | ALDOA | ALDOA | aldoa | |
human | ||||
yeast | ||||
C. elegans | Aldoa | ALDOA | aldoa | |
dropsophila | ||||
zebra fish | ||||
arabidopsis | SHOOT MERISTEMLESS or STM | SHOOT MERISTEMLESS or STM | shoot meristemless or stm | shoot meristemless or stm |
maize | KNOTTED1 or KN1 | KNOTTED1 or KN1 | knotted1 or kn1 | Knotted1 or Kn1 |
The same as with the genes, but in NORMAL font style. -- Boris 15:32, 29 December 2005 (UTC)
Hi everyone. We have to decide whether - to use the abreviations (ABRs) for the objects (such as Glc for glucose) throughout the project's articles; use them in the object's article only ot not use them at all. I preffer to use them all the way, with one exception - in the introduction part of the article, so those who are not familiar to be able to understand, after that the text becomes high level anyway so we don't need to have the full names. There are many reasons for that but the main is that i want our articles to look very well done almost pro, so we can atract more and more scientist to join us in making the project because with their knowledge they can help us tremendously (i know some of you are, but we need more - hundreds, or thousands is even better), i want these people to take us seriously and not just as some sort of online-encyclopedia joke, i want that these people know that anytime they need a reliable and good writen info they can come here and find it easily. Boris 17:00, 18 December 2005 (UTC)
Archived Boris' ideas (long read)
Copied from User talk:Opabinia regalis:
...my experience at Photon has set me brooding. Do you think that we as a community could come up with a standard set of questions that should be considered to make a biochemistry article "complete", e.g.,
along with subquestions for each of these, such as
It might be useful to have some kind of checklist for editors to help gauge how complete an article is. What do you think? It's more of a thought for a thought. Willow 15:15, 31 August 2006 (UTC)
As a first step for this project, we can create a standardized system for presenting information about proteins and genes within wikipedia. A logical place to start is with a system for categorization of proteins, start here: Whole proteome analysis. (see also: EC number, protein nomenclature talk, talk about protein lists, Talk:List of proteins and discussion about a specific class of non-enzyme proteins).
For organismal biology evolutionary relatedness of organisms provides a way to categorize all organisms. For proteins, functional categories are probably best and that is what is emphasized at Whole proteome analysis.
moved to #Standardising_article_structure.
This topic is now being voted upon!
I think it would be nice to standardize the rendered images of proteins in some way to give the same look and feel for this kind of articles. Of course this might not be possible in all cases as there are far too many protein articles. Also there are some that have good illustrations already which should not be removed just for the sake of standardization. However for all those pictureless protein articles where an image might be useful it would be nice to use the same representation. What do you think?
I suggest to use the open source program PyMol to render the images. It is widely used, gives nice results and had cartoon representations of both proteins and nucleic acids. For some articles I am interested in I did some images: actin, Arp2/3 complex, MreB, Profilin, Zinc finger(Protein + DNA)
If you think this would be useful, I'd volunteer to render some images on request. Just leave a message on my talk page.
Any thoughts?--
Splette
Talk
12:16, 1 September 2006 (UTC)
It seems that others are also interested in what's used to make protein representation pictures. There's a discussion over on the help page about what tools everyone uses. I think it's a great idea that we standardize the rendered images. We should discuss the pro's and con's of the various imaging tools and vote on it. And then produce a tutorial to instruct new users of the program how to use it and a series of guidelines so that the images all share similar standards. GAThrawn22 22:53, 2 September 2006 (UTC)
I disagree with the original proposal that base representations should be standardized at the software/technical level. Because structure is intimately connected with function, the structural representation (which will be the first thing that people see, and the first thing they focus on) should be designed to immediately call attention to the primary function or defining characteristic of that protein. I'll admit this is not an easy thing to define, but I do feel it should be the general goal. The exact representation is secondary. My area of interest is certainly a special example, but it serves to illustrate the point: a viral protein which is relevant only as an assembled complex (>4 MegaDa) needs a much different representation than cyt-c.
In my opinion, a style guideline would be more useful. Colors, background, labels, etc. I personally take into consideration color blindness when using colors: avoid red/green distinctions for critical areas. Since I'm not that familiar with Wikipedia, are animated images appropriate? Are representations with multiple level-of-detail layers ok? These kinds of style guidelines would let the experts for each protein choose the best way to show them while retaining some standards for presentation.
On a different issue, I've added a software option to the visualization list. Unless you're really serious about this stuff, it's pretty much a novelty, but it does give choices and representations that just aren't available elsewhere. I've also changed some pros/cons regarding Chimera (source code is available, for example). TheTweaker 19:55, 20 October 2006 (UTC)
Re. Wikipedia:WikiProject Molecular and Cellular Biology/Collaboration of the Month/History - could the table perhaps have include links to the article before and after. Also, I'm not sure how the table works, but the cell nucleus does have a review, a fact that should be included in the appropriate data-cell. ShaiM 11:48, 22 October 2006 (UTC)
It would be fun to have a few more MCB-specific barnstars, as suggested above, perhaps one for every major area? The DNA Barnstar is great. For proteins, Tup1 is a possibility, but it has seven blades, not five; maybe we should try another β-propellor such as 1gyh? IgM is another five-fold possibility. Willow 11:15, 24 October 2006 (UTC)
Like the title says... every barnstar should have a name, so what do we call it? – Clockwork Soul 18:27, 3 November 2006 (UTC)
Might as well use the vote page... shall we vote on name and which image to use? - Zephyris Talk 13:27, 7 November 2006 (UTC)
There are a number of stub classes that relate to this project, but seem to relate to one another in a haphazard way, if they do at all. So far, I've found:
I would like to sort these stub categories by placing them in a hierarchy beneath - I'm thinking - Category:Molecular and Cellular Biology stubs. Any thoughts? – Clockwork Soul 17:10, 25 October 2006 (UTC)
Tim's recent efforts into improving influenza got me to wondering a simple thing: does it fit within the scope of out MCB project? If it does, then do all varieties of viruses and unicellular critters have a place on out worklist? Looking over several similar pages, none of them seem to be claimed by any particular project already. However, our project's collective plate is already pretty full. Does anybody have any thoughts on the matter? – Clockwork Soul 17:43, 25 October 2006 (UTC)
Well I'm not taking that project over. My plan is to get the "big three" diseases to FA (only malaria to go) and then go back to more biochem-type subjects. TimVickers 20:54, 25 October 2006 (UTC)
That sounds like an excellent plan. TimVickers 14:50, 26 October 2006 (UTC)
I think it might be a good idea to make external links to Uniprot for individual proteins, or to Pfam for groups of proteins described in Wikipedia articles. As for links to PDB, this is not so simple, because every protein can be represented by a large set of PDB entries. The references to SCOP are better (anyone has an idea why SCOP is so outdated?). Also, it would be better to refer to PDBsum instead of the PDB, because PDBsum provides a much better interface with other databases and a lot of structural parameters of proteins that can not be found in PDB. Biophys 19:27, 31 October 2006 (UTC)
Re. the image seen on the templates (as put up on talk pages) and also on the user box: How come they keep changing? I think we're onto our third one. Personally I liked the one before this one, the molecule image. I don't care much for the current one, the colour scheme isn't too atractive. Any chance of reverting? ShaiM 04:28, 1 November 2006 (UTC)
User:Splette volunteered to do protein pictures upon request, but if there are others willing to do this, it might make sense to add a page like Wikipedia:WikiProject Molecular and Cellular Biology/ProteinPictureRequests where "Protein Picture Hitpersons" could watch and field requests. Are there others willing to do this is? I'd be most happy, since I am terrible at rendering these things. ~Doc~ EquationDoc 16:33, 10 November 2006 (UTC)
DONE! See Wikipedia:WikiProject_Molecular_and_Cellular_Biology/Requested_proteins for protein image and pathway diagram requests--field a request or add one to the list! ~Doc~ EquationDoc 16:46, 11 November 2006 (UTC)
Does anyone else see a need for aliases/alternative names/etc in the protein info box? I know this sort of works against the important goal of standardization of gene/protein names, but the reality is you often can't find references (PubMed, google, etc) without them. Moreover, in most cases, it probably makes little sense to devote space to them in article content, so adding them to the template seems reasonable (to me). Anyone? ~Doc~ EquationDoc 16:52, 10 November 2006 (UTC)