Pfam Annotation in Wikipedia¶
The Pfam consortium coordinates the annotation of Pfam families via Wikipedia. This is some background on the process.
A new approach to annotation¶
Pfam families have traditionally been annotated by our curators as they were added into the Pfam database, but the annotation step has become by far the most time-consuming part of building a Pfam family. As we adapt the Pfam model to cope with the dramatic increases in sequence data that are on the horizon, we have had to consider ways to make this step quicker and more efficient. We are also striving constantly to improve the quality and depth of our annotations, and to this end we have now adopted the Wikipedia model of annotation that was pioneered by the Rfam resource.
In this approach we will gradually reduce the prominence of our traditional, curator-produced family annotations, replacing them with Wikipedia articles. Starting from Pfam release 25.0, you will see that some family pages in the Pfam website show Wikipedia content rather than our own annotations. Ultimately we hope to be able to assign a detailed, high-quality Wikipedia article in Pfam, but we need the help of the Pfam and Wikipedia communities to make this happen.
Wikipedia content in the Pfam website¶
When we build a new Pfam family, we try to find a Wikipedia article that describes the family and provides what we feel to be a valuable annotation for it. If we can’t find a suitable article we will, in many cases, generate a new Wikipedia article ourselves. Hence, most new families will be assigned a Wikipedia article as soon as they are created.
Where a Wikipedia article has been assigned to a family, the main summary tab of the family page will show the content of the article, rather than the Pfam annotation. You can still see the old Pfam annotation, along with the Interpro annotation text, in adjacent tabs. Note that we will no longer be updating Pfam annotation text for any family that has a Wikipedia article. Instead we will try to make improvements or corrections to the article itself and will encourage our users to make improvements and corrections themselves.
Unfortunately, while new Pfam families will have Wikipedia articles assigned when they are created, we simply do not have the resources to be able to revisit older, pre-existing Pfam families. The family pages for these families still continue to show the Pfam annotation, but we hope to replace this with Wikipedia content wherever possible.
You can now contribute to the improvement of Pfam annotations in several ways. First and foremost, if you come across a family that does not yet have a Wikipedia article assigned to it, we would really like to add one. If you know of an article that would provide a useful description of a family, please let us know via our annotation submission form (click the “Add annotation” button on the family page) or by email. You can find our email address at the bottom of every page.
One of the advantages of using Wikipedia to provide our annotations is that any user can now contribute to that annotation text. In many cases, families that do not yet have a Wikipedia article can be assigned an article that already exists. In some cases, however, no suitable article exists, and in that case we would encourage you to consider adding one to Wikipedia yourself.
Editing Wikipedia articles¶
You can see these notes on every family page by clicking “More” on the Wikipedia content tab.
Before you edit for the first time¶
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded¶
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the “Edit Wikipedia article” button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer’s IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of ‘vandalism’) your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
Does Pfam agree with the content of the Wikipedia entry?¶
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.