Wikipedia talk:WikiProject Molecular and Cellular Biology

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Other Notes

Identifier templates?[edit]

Hi,

I remember using PDB ID templates before to link to specific structures, i.e. PDB 1dan. I'd like to start building links to sequences in ENA/GCA/etc. is there a page within MCB that lists all the different recommended 'identifier' templates?

Many thanks, --Dan Bolser (talk) 12:03, 27 May 2014 (UTC)

I am not sure this is complete, but this link may help: Category:Biology_external_link_templates. Boghog (talk) 19:23, 2 June 2014 (UTC)
Thanks @Boghog:! BTW, did I do that right?
@Dan Bolser: Your welcome. If you want to alert someone to a reply, {{ping|user name}} is a good way to do it. Boghog (talk) 19:21, 24 June 2014 (UTC)

Here is my first attempt at an ENA linking template (based on the RefSeq linking template, e.g. ENA FN595246. This lets you link to anything in ENA, including GCAs, for example. i.e. ENA GCA_000003745. Should we also create an INSDC template to link to NCBI, ENA and DDBJ? Also, any value in making explicit templates for sample, gca, etc.? --Dan Bolser (talk) 11:39, 10 June 2014 (UTC)

BTW, seems the Template:NCBI should be moved to Template:NCBI Taxonomy (or similar). Should I be bold? --Dan Bolser (talk) 11:45, 10 June 2014 (UTC)

The {{NCBI taxonomy}} template was already taken, so I moved it to {{NCBI taxid}} (note that 'taxid' is the term used by the NCBI in their URLs). The template redirect is working fine. --Dan Bolser (talk) 11:57, 24 June 2014 (UTC)
Looks good (both the name and the link). I agree that the {{NCBI taxonomy}} template is probably misnamed. In analogy to Wikipedia:Medical disclaimer, {{NCBI taxonomy}} should probably be renamed to {{NCBI taxonomy disclaimer}} or something similar. The disclaimer itself looks a bit over the top, but I am not a taxonomist. Boghog (talk) 19:21, 24 June 2014 (UTC)
If you need a template, create it. That is the only justification required. Boghog (talk) 19:47, 24 June 2014 (UTC)

AfC submission - 02/06[edit]

Draft:Family with Sequence Similarity 163 Member B. FoCuSandLeArN (talk) 17:17, 2 June 2014 (UTC)

Non-notable (no sources that are specifically about this gene). Draft contains largely original research. On that basis, the submission should be rejected. Boghog (talk) 20:02, 2 June 2014 (UTC)
What is this page? --Dan Bolser (talk) 11:17, 24 June 2014 (UTC)
The draft page is about a human gene with unknown function. The link I provided above is to PubMed citations about this gene. Boghog (talk) 22:12, 4 July 2014 (UTC)

EC numbers, "synonyms" , and readability[edit]

I am not a biochemist. I looked up cellulase and found a previous version of the article that began this way:

Cellulase (EC 3.2.1.4, endo-1,4-beta-D-glucanase, beta-1,4-glucanase, beta-1,4-endoglucan hydrolase, celluase A, cellulosin AP, endoglucanase D, alkali cellulase, cellulase A 3, celludextrinase, 9.5 cellulase, avicelase, pancellase SS, 1,4-(1,3, 1,4)-beta-D-glucan 4-glucanohydrolase) refers to a suite of enzymes produced chiefly by fungi, bacteria, and protozoans that catalyze cellulolysis (i.e. the hydrolysis of cellulose). However, there are also ...
Reaction: ...

I saw several problems with this text:

  • The EC number in the text is superfluous, since it is also given in the infobox. Moreove, the "EC number" template links to a database that may be important to specialists, but is quite unhelpful to the interested non-specialists. Since Wikipedia is meant for the latter, the link does not deserve so much evidence.
  • That database has its own division of the "enzyme space" into pages (EC numbers), which surely will not and should not be the division of Wikipedia articles. That is to say, one should not assume a one-to-one correspondence of WP articles and EC numbers. This is another reason for not giving such prominence the EC number. (The Cellulase article may be a case in point: to reduce the reader's confusion, perhaps it should be split in two: one about "Cellulase" as a generic enzyme name, and another about "cellulase complex".)
  • The multi-line list of names within parenthesis breaks the sentence and makes the text completely unreadable. The first line of an article should be a readable definition of the article's topic, in good English, as clear and concise as possible, and accessible to the interested non-specialist. One or two synonyms in parentheses (in boldface, not italics) are acceptable, but beyond that the synonyms should be placed in a separate sentence, later in the head section.
  • That list of "synonyms" is taken verbatim from the EC database page, and apparently contains not only synonyms, but also subclasses and specific enzymes, related molecules, and maybe even commercial names. That indiscriminate list may be appropriate for the EC database, but is not for Wikipedia. Synonyms should be distinguished from other related but non-synonymous terms, and the latter shuld be given as links in the text or in the "See slso" section.
  • Boldface in the head section should be used only for synonyms of the topic, not for related terms or for titles of pseudo-subsections.

Some of these same problems were present in the article Glucan 1,4-beta-glucosidase, presumably they occur in many other articles. I tried to improve the cellulase article, but I am unable to sort out the list of "synonyms"; it would require some specialized help. Thanks... --Jorge Stolfi (talk) 20:21, 4 July 2014 (UTC)

Point #1: Agreed that in-line link to EC number should not appear in the text.
Point #2: "which surely will not and should not be the division of Wikipedia articles" – You must be kidding. Per WP:V, Wikipedia articles must be based on reliable sources. Enzyme Commission number database is the definitive way of classifying enzymes. There is no question that Wikipedia enzyme articles should mirror this classification system. What alternative classification system would you propose?
Point #3: "indiscriminate list may be appropriate for the EC database, but is not for Wikipedia" – not an indiscriminate list per point #2.
Point #4: "The multi-line list of names within parenthesis breaks the sentence and makes the text completely unreadable" – agreed. This sentence should be split out as a separate nomenclature section and converted into a bulleted list minus the bolding.
Boghog (talk) 21:21, 4 July 2014 (UTC)
First, many nodes in the EC system are clearly classes of enzymes, not individal enzymes. But it would make sense for Wikipedia to have separate articles for certain individual enzymes, since the articles contain more information than the EC pages, and it will often be confusing to write about different enzymes in the same article. The cellulase is an example -- the EC class is a mixed bag of several enzymes and enzyme suites, that should be sorted out in WIkipedia. Conversely, some mid-level nodes in the EC system may not be worth separate articles in Wikipedia. Second, in such a rapidly evolving field any classification scheme will be perpetually inadequate, since changing its classes to reflect scientific progress would be extremely disruptive to users (think of all papers out there that refer to EC numbers). Wikipedia does not have this problem, its articles can be updated, split, merged, and renamed according to the most current knowledge and understanding. Organizing its articles on enzymes by the EC criteria would be as inappropriate as organizing other areas by the Dewey classification used in libraries. Third, the EC system may be an important 'reliable source', and it may be used to generate a starting set of articles; but it is not the ONLY reliable source. There must be thousands of quality articles and books that can be used to legitimize Wikipedia articles that do not correspond to a unique EC class. (The same happens in chemistry, for example: not every substance that readers may look up in Wikipedia and is supported by reliable publications has a number in the Chemical Abstracts database; but this is no excuse for excluding a Wikipedia article on it.) Fourth, the EC classification was defined to be useful for specialists; but Wikipedia is primarily directed to a very different public, for which that classification may hinder more than help.
As for the name list in the EC pages being "indiscriminate", I stand by that claim: that list is obviously a keyword list, placed there so that people who search for any of those "names" will find that page. It is a search trick used in many other scientific databases, e.g. of chemical substances, living species, etc.. The keyword list is obviously not meant to be an authoritative or systematic list of synonyms or class members; lists of different classes may overlap, and the list may include obsolete or deprecated names (e.g. a database for living species may list "bear" as a keyword on the Koala page.) Finally, it has been clearly stated since day one that "Wikipedia is not a database", so its articles should not be mechanically derived from a database, not forced to mirror it. All the best, --Jorge Stolfi (talk) 03:10, 6 July 2014 (UTC)
As discussed here and here, there is consensus within the MCB project to create enzyme articles based on EC numbers. I strongly support that consensus.
The EC system is more than a database, it is a system of enzyme nomenclature. Strictly speaking, a terminal EC node refers not to a class of enzymes but rather to a specific type of chemical reaction that is catalyzed by enzymes. While there are a few other classification systems (e.g., MEROPS), the EC system is by far the most comprehensive and widely used. In addition, while there have been updates to the EC system, these changes occur slowly and the rate of change has slowed down. Most changes involve addition of new EC nodes. Furthermore most individual EC nodes have not changed since they were first introduced. The system as a whole is relatively stable. Wikipedia conforms to the long tail with a hierarchy of articles from the most general (e.g., enzyme) that would be of interest to a wide audience to very specific ones like glucan 1,4-beta-glucosidase that would likely be of interest only to specialists. The only requirement for creation of a Wikipedia article is if there are sufficient reliable sources to establish the notability of the subject, not how wide of interest a subject may be. There are sufficient reliable sources to establish the notability of most if not all EC nodes.
not every substance that readers may look up in Wikipedia and is supported by reliable publications has a number in the Chemical Abstracts databaseFalse. CAS and Beilstein work diligently in registering and indexing chemicals that are described in the chemical, patent, and related literature. If a chemical does not have a CAS or Beilstein number, it probably is not notable.
Wikipedia aims to provide "the sum of all human knowledge". The types of reactions that are catalyzed by enzymes as reflected in the EC nomenclature system is part of that knowledge hence having a series of Wikipedia articles that capture that knowledge is appropriate. Boghog (talk) 08:48, 6 July 2014 (UTC)
One additional point. As illustrated in {{Infobox enzyme}}, links to IntEnz, BRENDA, ExPASy, KEGG, PRIAM, PDB, and PubMed are all based on the EC number. The EC number is not only used by the Enzyme Commission database, but these other seven databases as well. One cannot have a comprehensive article about an enzyme without mentioning its EC number. Boghog (talk) 18:20, 7 July 2014 (UTC)

image feedback - addiction cascade[edit]

I'm still undecided on whether or not to use this image outside ΔFosB, but if anyone has any feedback - technical, cosmetic or otherwise - for improving this, I'd appreciate it. This is probably the most apt wikiproject to ask for technical feedback, so chime in if you have any. Face-smile.svgSeppi333 (Insert  | Maintained) 06:24, 20 July 2014 (UTC)

Featured picture nominations for technical diagrams[edit]

Cross-posted on WT:MED, WT:PHARM, WT:MCB, and WT:NEURO

I nominated two technical diagrams (the signaling cascade involved in psychostimulant addiction and amphetamine pharmacodynamics in dopamine neurons) for featured picture.
I spent about 30 hours making the ΔFosB diagram alone, so I'd really appreciate it if anyone is willing to contribute an image review!

Regards, Seppi333 (Insert  | Maintained) 21:28, 21 August 2014 (UTC)

Nagalase[edit]

Nagalase previously linked to the Alpha-N-acetylgalactosaminidase article, which contained substantial amounts of uncited material, and what appeared to be a three-paragraph copyvio from an abstract. Given the recent controversy regarding nagalase research (for example, this article retraction, we should be very careful about ensuring all statements on this subject are both adequately cited, and that a retraction search has been performed on the cited papers. -- The Anome (talk) 16:29, 27 July 2014 (UTC)