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Module 4

In Module 3 you learned how to upload images and add them to the article. In this module you will learn best practices of writing Wikipedia articles and will start your own page.

This module include:
Hints for creating a good Wikipedia entry for your gene/protein
Wikipedia article structure
Guidance for formatting a Wikipedia article on a gene/protein
Qualities of Wikipedia Pages on Genes/Proteins
Module 4 Assignment

Hints for creating a good Wikipedia entry for your gene/protein

Wikipedia is a dynamic self-regulated online resource where traditions, policies, self-appointed guardians, and random, sometimes opinionated and/or ignorant individuals come together to create something that is better than an autocratically produced encyclopedia or an encyclopedia created from complete anarchy.

What this means for you is that what you produce may be ignored or set upon/edited/marked for deletion, in part due to chance and in part due to how professionally (and conforming to Wikipedia policy) you make your entry.

Here are some suggestions to help your work have the best chance of surviving the natural selection process that exists out there.

• Avoid saying that there is "no known function" for your gene/protein. That makes your gene/protein seem not-notable for some readers. Saying the gene/protein is "poorly understood" or better, "not yet well understood by the scientific community" might be safer wording.
• Carefully evaluate the significance of what you post: it is not likely to be interesting that your protein has 302 amino acids or that it has "no charge clusters". Molecular weight, pI, and what it does have, are much more interesting aspects if your protein to report.
• Be thorough and precise whenever you can: Don't say "it is conserved in mammals" when you could say (accurately) that orthologs have been found in eukaryotes, archaea, and bacteria. Don't just say it is highly conserved when you could say that no mammalian ortholog shows less than 90% identity with the human protein sequence.
• Don't repeat yourself, be redundant, or say effectively the same thing twice.
• Organize your entry sensibly with headers resembling other gene/protein entries and with a narrative that flows rather than feeling like you just put everything you knew into the entry without thought of how it all holds together. You are not aiming for a writing award, but you should still try to make it interesting and, well, encyclopedic.
• Cite whatever published literature and authoritative bioinformatics database/tool that supports your claims. A solidly cited article will help you overcome the objections of those who criticize the article for not identifying a clear function for the gene/protein, or who say you are just reporting your own research (not permitted by Wikipedia).
• Think about what your could include that would be interesting (existence or lack thereof of paralogs, for example) but haven't.
• Finally, check your entries "edits" page to see what people are doing with your entry. If someone deletes something, consider restoring it if you don't think it is a valid deletion, and making your explanation clear in the edits log.

Wikipedia article structure

Refer to this PDF for the Wikipedia article structure.

Guidance for formatting a Wikipedia article on a gene/protein

This is the reality of our situation. Selection of gene. A gene, even if it is human, may not meet Wikipedia notability requirements unless a function has determined for the protein. Most of the genes that have been selected by the class are pretty obscure. There are some well known gene families for which not all members have Wikipedia articles that might be a better choice (higher “notability”) since the function of these genes is generally known (see for example the red links in Solute_carrier_family#Families). Our class, however, is going to swim against the tide on this one, though. The truest test of your bioinformatic analysis abilities is your ability to find the most obscure information about your chosen gene.

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.

For consistency with other Gene Wiki articles, the {{GNF_Protein_box}} infobox should normally not be included directly in the article but rather transcluded using the {{PBB}} template. User:ProteinBoxBot is setup to maintain transcluded templates, but not templates directly contained in articles. The GeneWikiGenerator will automatically create both the template and the article that transcludes the template.

Concerning the lead sentence, as discussed here and here, we have tried to make clear that these Gene Wiki articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:

• <recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.
  The that in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human.
• Per WP:HEAD, sentence case should be used for section headings.
• Per WP:REFPUNC, punctuation before citations.

Qualities of Wikipedia Pages on Genes/Proteins

Qualities of the best ones (but not all of the following must be included)

• Concise with wording
• Headings that make sense and are in a good order (e.g. C4orf21)
• Graphics with good resolution and production value (resolution: 72 Mb)
• Annotated Allen Brain Atlas image, it you are including it
• Links to other Wikipedia pages
• Well-formatted references
• Diagram of chromosome itself might be nice (with gene marked)
• Microarray data if it contributes well to your story
• Insert picture box to the right because it takes less room
• Include figure legend with figure
• Lots of links to other Wikipedia pages (links to your page are valuable e.g. interacts with another protein)
• Divergence graph: reference sequences and species labels for dots
• Cite source of all data and most claims
• Some protein data that is not included in the table (not overly precise)
(acknowledge range for orthologs)

Some things to avoid

Red links (few and obscure if you must)
“a gene has an mRNA.. or has a protein”

“…is a human gene coding for a protein of unknown function.[1]”

Gene -> Expression -> Interactions -> Protein -> Clinical Significance (what’s wrong with this order?)

“It is well conserved in primates, rodents, zebra fish”

“… is located on the long arm of Chromosome 8 in humans on the anti-sense located at 24.23” -> “… in humans is located on the minus strand at 24q23”

“FAM135B is expressed in the brain, ear, eye, pancreas and testis.[2]” [ref 2 is Unigene EST]

“…has shown to interact with KAT5, a gene that encodes for a histone acetyltransferase[4] through yeast two-hybrid experimentation.”

“…has been shown to be expressed in individuals with extrapulmonary tuberculosis.[5]”

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End of Module 4

Congratulations! You’ve completed the Wikipedia tutorial. Now you have a better understanding on how to write and publish Wikipedia articles. Submit the screenshot of your article that you did so far to Wikipedia Training 4 dropbox.