Wikipedia:WikiProject Molecular Biology/Molecular and Cell Biology

Some Wikipedians have formed a project to better organize information in articles related to Molecular and Cellular Biology. This page and its subpages contain their suggestions; it is hoped that this project will help to focus the efforts of other Wikipedians. If you would like to help, please inquire on the talk page and see the to-do list there. Also of interest is the Molecular and Cellular Biology Portal associated with this project.

For more information on WikiProjects, please see Wikipedia:WikiProjects and Wikipedia:WikiProject best practices.

Featured Molecular and Cellular Biology Illustration. Image:Calvin-cycle2.png by User:Adenosine

Title

WikiProject on Molecular and Cellular Biology

Scope

This project aims to improve coverage of molecular and cell biology at wikipedia. A major problem facing biology is organizing the vast amount of information that has been and continues to be collected about genomes, proteomes and cell function. Can wiki tools make a significant contribution to solving this problem? Can wikipedia provide an entry point for the world to the wealth of biological data that is currently hidden in obscure databases and journal articles?

As a first step for this project, we can create a standardized system for presenting information about proteins and genes within wikipedia. A logical place to start is with a system for categorization of proteins, start here: Whole proteome analysis. (see also: EC number, protein nomenclature talk, talk about protein lists, Talk:List of proteins and discussion about a specific class of non-enzyme proteins).

For organismal biology evolutionary relatedness of organisms provides a way to categorize all organisms. For proteins, functional categories are probably best and that is what is emphasized at Whole proteome analysis.

We can continue to develop the template for protein information boxes. Protein information boxes can be included in each wikipedia article about a particular protein. Eventually, there should also be an information box about cell types.

Similar WikiProjects

The list of active projects has sections for both Biology and Health sciences, but the most relevant seems to be the Medicine Project listed at the Biology Portal and the Medicine Portal. Listed within the Medicine Project, there is a Preclinical Medicine Project that is concerned with the kinds of basic science courses that medical students take, however, there is only minimal emphasis on the type of molecular and cell biology issues that are centered on fundamental concerns such as naming and categorizing genes, proteins and cell types.

Wikipedia articles about cellular and molecular biology topics can also be improved by making use of the Wikiversity Biomedical Research Project.

Daughter project

Wikipedia:WikiProject Cell Signaling

Participants

Alphabetically, please.

Name	Talk page	Special interests
Adenosine	Talk	We need more diagrams, they can convey more information in one image than two volumes of text
Alberrosidus	Talk	Membrane structure/function, protein synthesis/signaling
Alteripse	Talk
Arcadian	Talk
BerserkerBen	Talk	"Will draw any enzymatic reaction for food": If you feel an article can be improve with a picture of the protein or enzyme reaction/mechanism simply ask.
Biohacker	Talk
Blastwizard	Talk	Bioinformatics, Sequence analysis, Protein structure prediction, Metabolism, Cellular processes
BorisTM	Talk	Here: Primary - Inter and intra cell signaling, Metabolism, Regulation; Secondary - everything else. Outside this project - Neuroscience.
ClockworkSoul	Talk
Daen	Talk	Bioinformatics esp. sequence analysis, cheminformatics
David D.	Talk	Epigenetics, biochemistry and development, emphasis on plants
Diberri	Talk	template tools
GACGGT	Talk	Muscle Biology, Neuromuscular Junction, cell signaling, receptor tyrosine kinases, aging.
GAThrawn22	Talk	Developmental Biology - I would also like to see a wikipedia page for every human protein
Goldfinger820	Talk	RNA interference, RNA molecular biology
Hydkat	Talk	Bioinformatics, Sequence analysis, Microarray data analysis, Biodatabases.
Inositol	Talk
Johnalrd	Talk	understanding the Secrets of Life from the nanoscale up
Jfdwolff	Talk
JOK	Talk
JWSchmidt	Talk	I admit it; I want a Wikipedia article for every human protein.
Kjaergaard	Talk	Biophysical and structural aspects of proteins.
LasseFolkersen	Talk
MarcoTolo	Talk
Nitramrekcap	Talk
OldakQuill	Talk
Peregrine Falcon	Talk
Peter Znamenskiy	Talk	Cell culture and adult stem cells, developmental signalling pathways
WikipedianProlific	Talk	I make images, diagrams, cross sections etc. for scientific (biological mostly) wikipedia articles. Please feel free to contact me with a request if you need graphics. My gallery can be seen here.
Staranise	Talk
Stewartadcock	Talk
Tim Vickers	Talk	Enzymes, enzyme kinetics and enzyme inhibition
Tycho	Talk
Wlad	Talk	Structure-function. Biochemistry of neural development.
Zephyris	Talk
Rozzychan	Talk	I am trying to improve the organization of the major biochemical pathways in cell biology by adding templates and links. I am also hoping to improve readability of articles.

Structures

Proteins

1. Wikipedia articles about individual proteins or small protein families can be organized so as to look like Myoglobin, Gonadotropin-releasing hormone or Rubisco.
2. Wikipedia articles about individual proteins or small protein families can each have a protein information box (see Myoglobin for an example).
3. Each Wikipedia article about individual proteins or small protein families can be organized into one or more wikipedia category. See Whole proteome analysis for needed protein categories. See Cytoskeleton and Category:Cytoskeleton for an example.
4. The main articles in each wikipedia protein category can be put into a navigation box (see the bottom of Cytoskeleton for an example).

Hierarchy definition

No classification of this project has been defined.

Goals

1. Create a standard system for providing fundamental information about the proteins and cells that are mentioned and discussed in wikipedia articles.

Projects

1. Public relations/outreach. Ways need to be found to recruit more of the molecular and cell biologists of the world (and their students) to contribute to wikipedia.
2. Categorization of articles about proteins. See Whole proteome analysis.
3. Organizing and upgrading articles about proteins. See the section on infoboxes, below.
4. Requested articles. List new wikipedia pages that are needed:

Requested Articles

• New wikipedia pages for granulysin and protocadherin are needed at Common chimpanzee.
• New wikipedia pages for RuBisCO activase and CA1P-phosphatase are needed at RuBisCO.
• New wikipedia pages for plakoglobin, desmoplakin, desmogleins and desmocollins are needed at Intermediate filament.
• New wikipedia pages for ParM and Crescentin are needed at Cytoskeleton.
• New wikipedia pages for Prestin and bacterial MotA, MotB, FliG, FliM, and FliN motor components are needed at Motor protein.
• New wikipedia pages for more protein domains at Structural domain.
• Wikipedia page is needed for basic term carrier protein, carrier-protein or carrier (protein).
• New wikipedia page for TATA Binding Protein for RNA polymerase I, RNA polymerase II and RNA polymerase III.
• New wikipedia pages for Histone H1, Histone H2A, Histone H2B, Histone H3 and Histone H4 for Histone.

More ways to "get the red out"

• List of molecular biology topics <-- start articles for topics in red.

Tasks

Example of a GFDL image that can be used to illustrate protein structure.

1. Put links to this project in all of the correct places within wikipedia. This includes existing short articles about specific proteins and new stubs (see #Stub templates) for other proteins that are currently only mentioned in other wikipedia articles. Note on finding existing articles about proteins and mentioned proteins: search wikipedia for "protein"; many proteins are mentioned in this sort of context: "the protein X", "a protein called Y" etc. On 8/30/05 I (User:JWSchmidt) went through the first 50 Google hits for "protein" in wikipedia, placing some stub templates (see below) and adding to List of proteins. See also: requested protein articles. Note: many enzymes can be found in the wikipedia enzymes category.
2. expand stubs Molecular and cellular biology stubs
   It seems a reasonable goal to have each wikipedia article that is about a particular protein include a paragraph that expands on each item in the corresponding protein information box. In other words, the protein information box can serve as a standard-format summary of many of the key topics in the full article.
3. As protein information boxes are added to pages about specific proteins, be sure to add them to the List of proteins.
4. There are also pages dealing with protein structural domains such as Homeobox. Maybe there should be an optional infobox template just for protein structural domains.
5. Images. The Homeobox article is a good example of a page that contains an image that is for non-commercial use. The Oxytocin article contains a similar image that may also be a problem. I suggest that all such images that were derived from images that were archived at the PDB website (and were covered by their non-commercial uses disclaimer) be replaced by molecular model images generated by wikipedia users themselves from the raw structural data in the Protein Data Base. The image to the right is an example of such an image. The Protein Data Bank says, "The contents of PDB are in the public domain. Online and printed resources are welcome to include PDB data and images from the Structure Explorer pages, as long as they are not for sale as commercial items themselves, and their corresponding citations are included." (source) Also see: Category:Protein images.
6. Protein-containing macromolecular complexes like ribosome should also be organized.
7. Make sure that all articles about proteins are placed in the Proteins category or lower level categories that are subcategories of the Proteins category. Additional categories: Whole proteome analysis.

Adopt an article

Similar to the Collaboration of the week, but on a smaller scale, you might want to "adopt" an article. This would involve doing the research, writing, and picture-taking (if possible) for either a non-existent article or a stub. Of course, everyone else can still edit an adopted article, and you can work on other things too, but the idea is to find a focus for a while, to try and build up the number of quality articles the Project has produced.

• Example article: User:Example

General strategy and discussion forums

• /General
• /Strategy

Other subpages

Guidelines for creating diagrams for the project can be found at: The Molecular and Cellular Biology Diagram Guide

Templates

Infoboxes

Protein info box

Info box example for the protein myoblobin (to right).
Note: only the first (start) and last (finish) template are required. The middle three templates (function, location, other) are options.

{{Protbox start}} template:

• preferred name of the protein
• image for protein (might be structural diagram, cell localization, etc)
• caption for image
• link to gene(s) in database, which gene(s) code for it?
• link to database entry for protein structural info
• links to recent articles at Entrez PubMed.

(To support proteins that do not have an image, this template has been broken down into three components: Template:Protbox header, Template:Protbox image, and Template:Protbox topfields. An alternative to the topfields section is provided in Template:Protbox codes, and a simplified version is at Template:Protein.)

{{Protbox function}} template:

• categorization of the protein; what type of protein is it?
• functions of the protein
• structural domains in the protein
• disease conditions involving the protein

{{Protbox location}} template:

• taxonomic range of expression (wide? restricted?)
• which types of cells express it?
• Subcellular localization.

{{Protbox other}} template:

• covalent modifications with functional significance
• all names that have been applied to the protein
• what other molecules interact with it?
• links to wikipedia pages that discuss the protein

{{Protbox enzyme}} template:

• What reaction it catalyses
• The cofactors involved in the reaction
• Method enzyme is regulated

{{Protbox receptor}} template:

• Receptor actions, e.g. vasoconstriction, neuronal excitation, etc.
• Agonists
• Antagonists

{{Protbox finish}} template:

• This template simply marks the end of a protein information box. (required)

Cell type info box

This will be an information box for displaying basic information about individual cell types.
List of distinct cell types in the adult human body

Some useful references:

• open source cell type ontology project
• http://www.bioeng.auckland.ac.nz/anatml/anatml/database/cells/cells/index.html
• Cell types from Dorland's Medical Dictionary

Basic info could be, name(s), functions, what taxonomic groups has the cell type, etc.
Tissue type(s) that contain the cell type
The major types of proteins that are expressed and that provide the specialized functions of the cell type

I suggest we pick one cell type as an example and get started. I propose skeletal muscle.

Database templates

Templates like this ({{OMIM}}) for the Protein databases, Enzyme Number and PubMed.

---

Human genetics for a protein/gene:
Example: {{OMIM|160000}}
Online Mendelian Inheritance in Man (OMIM): 160000

---

Digital object identifier
Example: {{Doi|10.1038/437794a}}
doi:10.1038/437794a

---

Enzyme number:
Example: {{EC number|4.1.1.39}}
EC 4.1.1.39

---

Template for Protein Data Bank citations. Example:

Example: {{Protein Data Bank|9RUB}}

PDB: 9RUB​

---

Template for PubMed Central full text articles
Example: {{PMC|137841}}

PMC 137841

---

Template for Entrez PubMed citations
Example:{{Entrez Pubmed|10336462}}

There is no need for that. Typing PMID with the code will render automatically as with ISBNs, like this - PMID 1234567890 JFW | T@lk 21:27, 31 August 2005 (UTC)

The Entrez Pubmed template is better because it does not subject the reader to an unexplained abbreviation (PMID) and it provides a link to a wikipedia page that talks about the database being linked to. --JWSchmidt 22:47, 31 August 2005 (UTC)

---

Template for Entrez gene citations
Example: {{EntrezGene|2695}}

EntrezGene 2695

---

Template for RefSeq citations
Example: {{RefSeq|NM_004123}}

RefSeq NM_004123

---

Template for UniProt citations
Example: {{UniProt|P09681}}

P09681

---

Protein topics navigation boxes

See User:Lilious for how to jazz up such navigation boxes.

Templates:

{{Protein topics}}

{{Protein methods}} Protein methods

{{Protein domains}}

{{Cytoskeletal Proteins}}

Research topic navigation boxes

Example: {{King's College DNA}}

What is a subtemplate?

• {{subst:template}}
• e.g.{{Infobox Molecular and Cellular Biology}}

{{Infobox Molecular and Cellular Biology }}

Stub templates

For new articles

{{Molcellbio-stub}}
Puts the new stub article in Category: Molecular and cellular biology stubs Template:Molcellbio-stub

Add to existing short articles

{{Molecular and Cellular Biology-stub}} Template:Molecular and Cellular Biology-stub

Other templates

Add to existing categories

{{Molecular and Cellular Biology-category}} Template:Molecular and Cellular Biology-category

Mark articles that are part of this project

{{templateMolecular and Cellular Biology}} Template:TemplateMolecular and Cellular Biology

Human chromosomes

{{Chromosomes}}

Categories

• Molecular and Cellular Biology
• Molecular and cellular biology stubs

Protein families

There needs to be a category for each protein family at the Whole proteome analysis article Also, a navigation bar template (see templates, above).

Cytoskeleton

This template: {{Template:Cytoskeletal Proteins}} marks articles as being in the Cytoskeleton category.

• Cytoskeleton category

Other categories

• Category:Motor proteins

Lists

• List of proteins
• List of biomolecules

Requests

• see #protein families
• see #Requested Articles

Archives

• #1

Naming

Genes

The abreviations (ABR) of the genes are according to HUGO Gene Nomenclature Committee and written in ITALIC font style (the full names are also written in italic), it is recomended that we use the ABR instead of the full name form. The human gene names are in all big caps (correct me if i haven't written it well), example - ALDOA, INS, etc. Human homologous of genes in other species start with a big cap and the rest of the letters are small caps - mouse Aldoa, bovine Ins, etc. When we write about the genes this is correct - "the ALDOA gene is regulated...", "the rat gene for Aldoa is regulated..." or "ALDOA is regulated...", while this should not be allowed - "the gene ALDOA is regulated", b/c it's redundant. And if anyone starts arguing with you about it, say "Sorry, but we have a standart to follow" and redirect them to this section. -- Boris 15:32, 29 December 2005 (UTC)

Proteins

The same as with the genes, but in NORMAL font style. -- Boris 15:32, 29 December 2005 (UTC)

Articles needing attention

• Biology pages needing attention (cleanup, expansion, wikification, expert needed, etc.)