Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2012/Section 83/Group 83B

Group 83B
This is the Wikipedia page for 410.602 Molecular Biology, 2012, group 83B. This group will be working on the Nucleotide excision repair article.

Use the talk page here to collaborate as a group, when learning to use and navigate Wikipedia, assessing articles, or for any other topic.

Use this page (not the talk page) for article assessments (optional, see Unit 5); rationale for selecting an article (Unit 6); progress reports (Units 9 and 12); and the final report (Unit 14). Please create a new section here for each of those assignments.

Unit 6: Article Selection Rationale (Nucleotide Excision Repair)
MCB WikiProject rates the nucleotide excision repair article as a mid-important start class article. No major edits were made in 2012, and the talk page consists of one non-substantive entry (the user added two links). We hope to increase the quality rating of this article to GA, and provide a better foundation for article discussion in the future. Our reasons for choosing this particular article are twofold:
 * 1) The article is rated mid-importance. This means it could serve as a useful resource for many students in upper-level college courses or entry-level graduate classes. Molecular Biology and Cell Biology classes often cover nucleotide excision repair; editing this article hopefully helps a large audience.
 * 2) The article is a start class article. By having more content than a stub article, it gives us an idea of how to format and organize information about nucleotide excision repair. We can see how other Wikipedia contributors think about article arrangement and build off their work while adding useful content and improving article flow and accessibility.

The article needs multiple non-substantive edits; list formatting, logic flow, and grammar are some things that immediately come to mind. The article also lacks diagrams and figures. There is currently one on the page but it lacks a caption. We hope to provide more relevant figures that are informative and help the reader understand material in the text. Finally, the article only utilizes 6 sources, 3 of which are specifically cited in the text. Increasing the breadth of supporting material will provide greater credibility and lead to a better article.

To increase the relevancy of this article to current research, we will add a section highlighting the role of nucleotide excision repair in cancer progression. Several recent publications have investigated the state and impact of nucleotide excision repair in colorectal and breast carcinomas. As we learn more about the topic, we hope to widen the scope of our substantive additions.

Unit 9: Progress Report
Our recent efforts to improve the nucleotide excision repair (NER) article fall in 3 main categories: (1) identifying relevant sources and journal articles, (2) proposing a new NER article outline, and (3) familiarizing ourselves with copyright issues. We focused on laying the groundwork for substantial edits and restructuring; we will be making these changes over the next two weeks. In addition, we suggested merging an NER subpathway (transcription-coupled repair) into our NER article; we hope to discuss this merger with more Wikipedia editors. Chris helped us navigate through the procedure for merging; we sincerely appreciate his direction and feedback.

As of November 6th, we have identified 18 articles useful for NER. Most of these articles are not only highly relevant to our topic, but are also high impact articles (as identified by the Science Citation Index via Web of Knowledge.) We compiled these articles in a Google Drive so we could easily access and annotate the articles together. We used the content of the articles to develop a new article outline: this outline comprises the bulk of our “To Do” list for the rest of the semester.

In addition to journal articles, we refined our outline using the DNA repair article as a guide. This Featured Article (FA) is extremely relevant to our topic: NER is a mechanism of DNA repair. In addition, DNA repair has multiple features that caught our attention. For example, the use of numbered lists and bulleting throughout the article provides a potential solution to the long list of mentioned proteins in the NER article. The section detailing repair disorders is especially useful. We were unsure of how to approach diseases related to transcription coupled repair and global genomic repair (two subpathways of NER) without providing unnecessary detail. The DNA repair disorder section solved this problem by crosslinking disease names and only providing a few symptoms of the disease in the article itself.

Our last area of progress was in understanding copyrights. We compiled a short list of useful links relating to image copyrights, and will use these guidelines for collecting published figures. If we cannot find an image we need, we must generate those figures or request them. We will assemble a list of pictures we need by November 15th. Copyright issues remain a concern for us despite our vigilance, but we trust any error on our part will be identified by other Wikipedia editors.

At the current time, we do not have a set “To Do” list outside of the image list above and writing the article as per our proposed outline. Once this work is done, we will have a better idea of specific things that need to be edited, referenced, crosslinked, diagramed, put in tables/lists, etc. Our deadline for writing the full first draft of the article is the same as our image list: November 15th.

Unit 12: Progress Report
Our goals from the previous report consisted of two major items: (1) a list of usable images (implemented and ), and (2) a draft of all substantial edits for our article. We have finished the majority of these items, but loose ends remain. Our reviewer group pointed out a few of these issues recently; we will be addressing these issues within the next few weeks. We sincerely thank Group 83A for taking the time to provide a thorough critique, and we look forward to their thoughtful feedback in the future. We commented individually on Group 83C's progress on their Amplicon article; we thought multiple perspectives might be helpful. Our feedback and interactions with the group can be found here, here, and here. They are working diligently on their article, and we are more than happy to provide more feedback as they continue their work.

We included most elements of our original article outline, but changed the order of a few sections. An expansion, merger, and addition were made respectively to the Eukaryotic NER, TC-NER, and NER and Cancer sections; we addressed the long list of NER associated proteins by using a table. We still need to tackle GG-NER and Prokaryotic NER. Addressing GG-NER will be fairly straightforward during the coming week, but we are still debating how to approach Prokaryotic NER.

The main enzyme involved in this process is UvrABC endonuclease; it is NER exclusive. A lot of information is available about the UvrABC complex, but detailing Prokaryotic NER will involve explaining UvrABC thoroughly. This would cause an excessive overlap of information between the two articles. If the articles were merged, it is possible that it would create an unnecessary level of detail on UvrABC endonuclease on the NER page. However, the detail may be appropriate since UvrABC is exclusive to NER.

The alternative to merging is adding extensive crosslinks between the articles, but this would lead to excessive overlap between the two articles. Another possibility is deleting the prokaryotic section entirely on the NER page and relying on the UvrABC page exclusively, or including a small introductory paragraph on the NER page and noting the 'Main Article' or 'Further Information' for the section as UvrABC. (The DNA article employs this strategy many times to avoid an excessively long article.) These are a few of the issues we are still discussing. We recently proposed a merger for this section; we hope additional Wikipedia contributors will provide some guidance on this issue.

An anonymous Wikipedia contributor posted a critique of our outline, but we believe the issue is a result of incorrect classification. The individual said DNA mismatch repair (MMR) is a subpathway of NER, but it is not: MMR is a separate excision repair pathway. We updated the DNA repair template to reflect this classification and noted the differences in our.

Over the next two weeks, our "To-Do" list consists of many small edits and a few substantial edits.
 * 1) Grammar/syntax edits
 * 2) Flow/general consistency of terms
 * 3) Crosslink to other articles
 * 4) Whittling down our references list
 * 5) Consistent/appropriate references throughout (ie no primary references)
 * 6) Pending Prokaryotic NER/UvrABC merge issue: write section + all of the above
 * 7) Expand GG-NER section
 * 8) Picture captions
 * 9) Consistent abbreviations
 * 10) Expand "See Also" and "External Links" sections

We remain committed to our original goal: improving our article's classification. With the content additions and upcoming edits, we hope to achieve this goal by the end of the semester.

Unit 14: Summary
During this project, our group made a significant improvement to the nucleotide excision repair (NER) article. We expanded the initial article outline to include more granular subsections, added new sections, merged with another article, included crosslinks and expanded the content in the article.

Nearly double the original length, the NER article now contains a glossary of NER asociated proteins, four new schematics detailing NER processes, and a new section detailing some of the implications NER has for cancer biology. We also expanded the Further Reading section to include three new sources, and the Reference list now contains a more useful index of relevant NER materials.

We also interacted significantly with other editors; we responded to questions and critiques regarding our work on the NER page, and also posting feedback on other groups’ progress. We received very helpful feedback from Group 83A on our work and attempted to respond to their posts as effectively as possible. We also received some anonymous feedback, and responded to that critique after investigating their concerns. We detailed this in the Unit 12 Progress Report.

In all, our group is satisfied with our work. We believe that we were very successful in accomplishing our initial goals and improving the NER article.