Wikipedia:WikiProject Molecular Biology/Molecular and Cell Biology/Proposals

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Integrin subunit designations

It appears from a partial survery of pages which concern integrins that the most common formatting for subunit designations, including page titles, uses the strings "alpha" and "beta" for the subunits, e.g., Integrin alpha M and alpha-5 beta-1. Some close up the spacing before the specific number or letter; some don't.

I suggest standardizing our formatting of integrins with the use of the greek letters α and β followed (with no space) by the designation in-line, so that, e.g., "alphaMbeta2" would become αMβ2, whose beta subunit would be separately designated β2 (i.e., CD18).

Although MeSH uses the former format, a cursory examination of secondary sources (mainly literature surveys/reviews) demonstrates the precedence of the greek designations over their romanized names. I've looked to see if there has been any discussion of this formatting before, but have been unable to find any. apdshoe (talk) 20:46, 12 September 2011 (UTC)[reply]

Hear hear. Rich Farmbrough, 22:13, 16 September 2012 (UTC).[reply]

MalaCards - www.malacards.org

I'm Marilyn Safran, head of GeneCards suite development at the Weizmann Institute of Science in Israel. GeneCards and the Gene Wiki project have had cross links for some time now.

I'd like to introduce this forum to our MalaCards database of human diseases (see www.malacards.org) and recent publication Rappaport et al: MalaCards: an integrated compendium for diseases and their annotation, Database 2013; http://database.oxfordjournals.org/content/2013/bat018.full?%250Aijkey=MEtqc5V6fAKchaq&keytype=ref.

MalaCards now comprises ~17K entries consolidated from 44 sources, leveraging GeneCards and GeneDecks annotations, and including links to Wikipedia. The resource has gotten positive feedback, we continue to develop and improve it, and has motivated our PI Doron Lancet to organize and chair a special session on Human Disease Bioinformatics at ISMB 2013 in Berlin in July.

We feel that just as Gene Wiki has symbiotic cross-links to/from GeneCards, it would be beneficial to the community to have the right-hand-sidebar of relevant Wikipedia pages (e.g. Huntingtons_disease) link to the corresponding MalaCard (e.g.at http://malacards.org/card/huntingtons_disease).

Your comments on how to proceed would be very much appreciated.Marilyn Safran (talk) 14:02, 9 June 2013 (UTC)[reply]

Yes this proposal sounds good to me. The MalaCard link provides more immediately useful information to a reader than most of the other links in the disease infobox. Alexbateman (talk) 08:54, 10 September 2013 (UTC)[reply]

Seems like a reasonable suggestion. I note that Andrew Su (talk · contribs) is in the process of proposing a revamp of the disease infobox (see User:ProteinBoxBot/Phase 3) that would be bot maintained. They are currently discussing which data to include in the box, so I would suggest speaking to him about including a link to MalaCards. Rockpocket 09:34, 10 September 2013 (UTC)[reply]

I agree, this seems like a good idea. We'll definitely incorporate it into our planning... Cheers, Andrew Su (talk) 17:23, 17 September 2013 (UTC)[reply]

Has consensus been developed for this anywhere? Doc James (talk · contribs · email) (if I write on your page reply on mine) 11:08, 28 November 2013 (UTC)[reply]

MalaCards version 1.05 is out. We will supply mapping file to whoever interested in taking on updating the disease box. 132.76.50.5 (talk) 08:11, 3 April 2014 (UTC)[reply]

@Marilyn Safran: The best solution would be to add MalaCard IDs to Wikidata (making them also available to Wikipedias in other languages; and as open, linked data), then include them automatically in the infobox. Ditto other identifiers. @Andrew Su: I'm happy to work on this with you. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 10:44, 27 October 2014 (UTC)[reply]

I've made a proposal for a Wikidata property for this. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 12:12, 27 October 2014 (UTC)[reply]

Now in {{Infobox disease}}, as |MalaCard=; see this example edit. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 12:21, 27 October 2014 (UTC)[reply]

And now out again. Wiki CRUK John (talk) 21:33, 24 November 2014 (UTC)[reply]

Now in Wikidata, as P1583. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 16:44, 3 November 2014 (UTC)[reply]

On infobox design

(Copied from Wikidata): I support the property and the inclusion in Wikidata, but the inclusion in the disease-infobox on en-wiki is, and the same goes for all those cryptic identifiers, a sub-optimal usage of infoboxes. 99 % of readers will not read those codes, nor follow the links to the sites, which are usually intended to be consumed by experts. In my opinion the infobox should give basic information to basic questions a reader might have: "how can I get this disease?", "how do I know I have it?", "is it treatable?". Even if we simplify, what is a very complex multi-variate system, we can still offer a quick overview and link to the sections within the text, where we can place all the statistic information and the "and, or, if else" information. I would rather have some over-simplified information and guide the reader to the appropriate section than these codes which probably lead many people to give up reading the information in the first place. -Tobias1984 (talk) 16:34, 27 October 2014 (UTC)[reply]

Tobias1984 The answer to all those questions is usually "depends" and cannot be captured in a small infobox. That's why we use prose in the article. JFW | T@lk 20:33, 27 October 2014 (UTC)[reply]

External links to MBInfo

I would like to propose including external links to MBInfo, a wiki project that is being developed by the Mechanobiology Institute, Singapore (National University of Singapore).

Although the project incorporates community contribution, it differs considerably from wikipedia and would provide wikipedia users with supplementary information that addresses cell biology/molecular biology topics from a mechanobiology perspective.

Proteins, for example are discussed in relation to their function in a given process, while specific processes are discussed in relation to a wider cellular function.

For example Fascin is described in the Actin Filament Bundle Assembly, which is subsequently discussed in the Filopodia Assembly topic.

Along with alternative descriptions we also provide custom figures (schematic diagrams and microscopy images), and animations that are produced in house.

You can see some examples here: http://www.mechanobio.info/modules/go-0045010 (Actin Nucleation) http://www.mechanobio.info/topics/cytoskeleton-dynamics/go-0030175/go-0046847 (Filopodium Assembly) http://www.mechanobio.info/topics/synthesis/go-0006323 (DNA packaging)

As a bit more background on the website: MBInfo will feed directly into course work at NUS and is used for the production of other interactive material. Although the content may be written and amended by any user, the pages are reviewed by at least one expert in the field and this review attribution will be included in the next update of the site. This review is carried out to enable MBInfo to remain a reliable and citable resource. Contributors and editors are also given "authorship" of subsequent interactive material that may be published.

The project is still in its infancy, with the webiste you see now having been rolled out earlier this year. It is maintained by a fulltime team of writers, illustrators, animators and a data curator and our community editor base is slowly growing. It was established by Prof Michael P Sheetz, who now serves as the editor-in-chief.

Hopefully this gives you enough background on the resource to get an idea on how it can benefit Wikipedia readers. MBproj (talk)

Great illustrations and well writeup. Could you elaborate about licensing, especially figures? It is allowed to used in Wikipedia article? Do we need an explicit permission? Okisan (talk)

Thanks. The site has a Creative Commons attribution-noncommercial-ShareAlike 4.0 license however at the moment the copyright statement present on each image page takes priority. This means the images are copyright to MBI/NUS and permission is required to use images. This is usually granted to PhD students and lecturers wishing to use the images in their thesis or in presentations as long as attribution is given. We are planning to release a selection of images under the creative commons licence in the near future, however the bulk will continue to require explicit permission before being reused. MBproj (talk) 06:38, 10 March 2014 (UTC)[reply]