CZ:Proposals/Create a page for all notable genes in the human genome

This proposal has not yet been assigned to any decisionmaking group or decisionmaker(s).
The Proposals Manager will do so soon if and when the proposal or issue is "well formed" (including having a driver).
For now, the proposal record can be found in the new proposals queue.

Driver: Andrew Su

Complete explanation

This proposal was previously discussed on the forum in late 2007, so please read that thread for context. (If there are questions which are not addressed there, please let me know and I will expand here.) The proposal was tabled at that time due to uncertainty around the licensing of CZ content.

Past discussions:

• Forum: [1]
• Mailing list: [2] (all seem to be confined to September 2007 as linked here)

Previously-raised issues:

• License solved...
• Does the existence of similar WP pages reduce (or increase) enthusiasm?
• Does creation of up to 10k pages render the "Random page" link useless (or at least horribly biased)?
• Are there enough biologists and geneticists so that this effort won't stagnate?
• The driver is employed by a pharma company, so is impartiality a concern?
• Would this effort be sufficiently different from the array of other "gene portals" out there?

Reasoning

This would be a relatively unique tool in biology. All existing gene portals are "top-down" from centralized "gene annotation authorities". Of course, those authorities are a bottleneck for sharing new findings in a gene-centric web database. Looking several years down the road, I hope each of these stubs evolves into a gene-specific review article on every gene in the human genome.

I say relatively unique since one version of this project is now nearing completion at WP. Approximately 9500 pages are currently in existence (listed here: [3]). Some CZ users previously expressed concern about whether CZ should embark on this project given the similar/parallel WP effort , and that certainly should be discussed again below. (But note that this rationale was not the reason we did not move forward previously.)

Implementation

As I see it:

1. Discuss to decide if this project is appropriate for CZ. (If no, end here.)
2. Finalize a format, perhaps continuing the use of APP as the model.
3. Find a willing programmer (ideally an undergrad or master's student interested in a cool project).
4. Make the pages.

Assuming Step 3 doesn't drag on too long, I'd estimate that the whole project take approximately six months.

Discussion

A discussion section, to which anyone may contribute.

I am in no way knowledgeable in this area, but two things come to my mind after reading this. First, the Recent Changes issue. I agree with Larry Sanger that we should have some sort of exclusion code to prevent these from showing up. The whole purpose of the link (to me at least) is to get an interesting page on a different topic than one would normally read.

The second idea question is whether this would be better suited for a catalog. I know that would be a lot of pages, but having a central area to pick out what gene you want to look at doesn't seem like such a bad idea.

Well, there's my opinion on the matter. John Dvorak 16:08, 16 April 2008 (CDT)

I have the same arguments against this as previously.

1. Almost nothing is known about most genes, so most pages will essentially be blank.
2. People are much more interested in gene products, proteins, than the gene.

For example, one might look up insulin, but who knows what the name of the gene is for making it? How do you write an article about a gene? Gene so and so makes the protein TNF-alpha, then what? You might say it is upregulated or suppressed by other proteins, but what else? I will, however, admit that my interests and work may have clouded my thinking into one that is protein-centric. To me it seems natural to write articles about proteins, and add a link to GeneBank or another gene bank data set, much like we have been doing with the drug articles where we add links to DrugBank, MedMaster and an FDA site. David E. Volk 14:44, 17 April 2008 (CDT)

See the wikipedia version of the insulin gene. While proteins are the functional unit biologists often consider when thinking about physiology and biochemistry, if you're a developmental biologist or interested in human disease then the regulation of genes, and the various different alleles of a particular gene are of great interest. Bear in mind too that this project can be tailored to our needs.

While I agree that many of the articles will initially have minimal content will this not serve as a nucleus for content related to human biology? Also, i would imagine that most articles on proteins will not be specific to humans. Possibly these human gene articles could be more and have protein information specific to human diseases and physiology too, while directing readers to our articles that discuss the broader picture for a given protein. Chris Day 15:15, 17 April 2008 (CDT)

Regarding David's first comment, let me provide a few links to pages at WP as they were created by our bot, just to give people an idea of the range of stub content. Obviously, we can set the bar wherever we want here at CZ:

• http://en.wikipedia.org/wiki/PMM2 -- brief summary, protein structure
• http://en.wikipedia.org/wiki/WASF1 -- brief summary, no protein structure
• http://en.wikipedia.org/wiki/POLQ -- no summary, no protein structure

Regarding David's second comment, it's pretty rare over at WP to have separate pages about proteins and the genes that encode them. For example, consider this page. I would be happy to change all references from the "gene wiki" to "protein wiki"  ;) and/or incorporate any more protein-centric content that can be systematically harvested. As Chris alludes to, we are completely open to modifying the format according to what the CZ community feels is appropriate. Cheers, Andrew Su 15:45, 17 April 2008 (CDT)

Those articles are great examples of why I am against this proposal in general. It seems very odd to have a 1-3 sentence articles with 30 references listed. It looks and feels like an automated fact picker, but not an encyclopedia article. Most of the information in Gene Ontology in fact refers to what the protein does. Same for the Biological Process parts. The few things that can be said regarding up/down regulation could easily be put in a "Gene" subsection of the protein article. Finally, I notice that WP does not italicize genes like they should. Thus, the MutY protein is made by the MutY gene. David E. Volk 16:14, 17 April 2008 (CDT)

As I said above the articles could/should be about the human proteins and the gene. Re: MutY/MutY, does it matter what wikipedia does wrong with respect to our own proposal? Another thing to consider is that much of this information can be distributed into different subpages so potentially the creation of subpage content is the desired goal? Do we need an article to start a subpage? I ask this in all seriousness as we do have some subpages that exist without an article (related articles pages to date). Possibly this is a model to work with? Chris Day 16:22, 17 April 2008 (CDT)

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