Wikipedia:WikiProject Molecular and Cellular Biology/Style guidelines

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This page will eventually contain a series of style guidelines for the Wikipedia:WikiProject Molecular and Cellular Biology.

It still has a long way to go.

Diagram guide

The guidelines for creating diagrams for the project can be found in the Molecular and Cellular Biology Diagram Guide.

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).

Naming

Genes

The abbreviations of genes are according to HUGO Gene Nomenclature Committee and written in italic font style (the full names are also written in italic). It is recommended that we use abbreviations instead of the full name. Human gene names are written in capitals, for example ALDOA, INS, etc. For orthologs of human genes in other species, only the initial letter is capitalised, for example 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 not in italics. Thus human proteins are written like "THIS", whilst their orthologs in other species are written like "This". -- Boris 15:32, 29 December 2005 (UTC)

Templates

Infoboxes

Template:Protbox function Template:Protbox location Template:Protbox other

Myoglobin
Myoglobin.png
Model of helical domains in myoglobin.
Gene code: HUGO code: MB
Structure: molecular structure
Recent publications: role in human pathologies, gene knockout

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:

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. You'll find these very useful when citing your sources.

Template Name Usage Renders As
Human genetics for a protein/gene: {{OMIM|160000}} Online Mendelian Inheritance in Man (OMIM) 160000
Digital object identifier
{{Doi|10.1038/437794a}}
doi:10.1038/437794a
Enzyme number:
{{EC number|4.1.1.39}}
EC 4.1.1.39
Template for Protein Data Bank citations: {{Protein Data Bank|9RUB}} Template:Protein Data Bank
Template for PubMed Central full text articles
{{PMC|137841}} PMC 137841
Template for Entrez PubMed citations
{{Entrez Pubmed|10336462}} Entrez PubMed 10336462
Template for Entrez gene citations
{{EntrezGene|2695}} EntrezGene 2695
Template for RefSeq citations
{{RefSeq|NM_004123}} RefSeq NM_004123
Template for UniProt citations
{{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}}

45px DNA structure research at King's College London 1947-1959
Rosalind Franklin | Raymond Gosling | John Randall | Alec Stokes | Maurice Wilkins | Herbert Wilson

What is a subtemplate?

{{Infobox Molecular and Cellular Biology }}


Stub templates


Add to existing categories

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

Project banner template

{{Wikiproject MCB}} – A simple project banner template to mark articles that are part of this project. It serves, in part, as advertising for the project. It is to placed on the talk page of any articles of interest to this wikiproject.

Template:Wikiproject MCB

Collaboration of the Month templates

Template What it makes Where it goes
{{MCBnom}} Template:MCBnom The talk pages of articles nominated for the MCB Collaboration of the Month.
{{MCBcur}} Template:MCBcur The talk pages of articles that are currently the MCB Collaboration of the Month.
{{MCBprev | month=MONTH}} Template:MCBprev The talk pages of articles that were previously an MCB Collaboration of the Month.

Protein structure templates

{{Protein quaternary structure}} under construction; suggestions welcome!

{{Protein tertiary structure}}

{{Protein structure determination}}

{{Protein secondary structure}}

Protein secondary structure
Helices: α-helix | 310 helix | π-helix | β-helix | Polyproline helix | Collagen helix
Extended: β-strand | Turn | Beta hairpin | Beta bulge | α-strand
Supersecondary: Coiled coil | Helix-turn-helix | EF hand
Secondary structure propensities of amino acids
Helix-favoring: Methionine | Alanine | Leucine | Glutamic acid | Glutamine | Lysine
Extended-favoring: Threonine | Isoleucine | Valine | Phenylalanine | Tyrosine | Tryptophan
Disorder-favoring: Glycine | Serine | Proline | Asparagine | Aspartic acid
No preference: Cysteine | Histidine | Arginine
←Primary structure Tertiary structure→

{{Protein primary structure}}

{{Amino acids}}

Templates for major families of biochemicals

{{Biochemical families}} under construction, overview template, fast cross-link

Major families of biochemicalsPeptides | Amino acids | Nucleic acids | Carbohydrates | Nucleotide sugars | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | GlycosidesAnalogues of nucleic acids: Analogues of nucleic acids:

{{AminoAcids}} under construction

v  d  e
Major families of biochemicals
Peptides | Amino acids | Nucleic acids | Carbohydrates | Nucleotide sugars | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | Glycosides
Analogues of nucleic acids:The 20 Common Amino Acids ("dp" = data page)Analogues of nucleic acids:
Alanine (dp) | Arginine (dp) | Asparagine (dp) | Aspartic acid (dp) | Cysteine (dp) | Glutamic acid (dp) | Glutamine (dp) | Glycine (dp) | Histidine (dp) | Isoleucine (dp) | Leucine (dp) | Lysine (dp) | Methionine (dp) | Phenylalanine (dp) | Proline (dp) | Serine (dp) | Threonine (dp) | Tryptophan (dp) | Tyrosine (dp) | Valine (dp)

{{Nucleic acids}} under construction

v  d  e
Major families of biochemicals
Peptides | Amino acids | Nucleic acids | Carbohydrates | Nucleotide sugars | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | Glycosides
Analogues of nucleic acids:Types of Nucleic AcidsAnalogues of nucleic acids:
Nucleobases: Purine (Adenine, Guanine) | Pyrimidine (Uracil, Thymine, Cytosine)
Nucleosides: Adenosine/Deoxyadenosine | Guanosine/Deoxyguanosine | Uridine | Thymidine | Cytidine/Deoxycytidine
Nucleotides: monophosphates (AMP, GMP, UMP, CMP) | diphosphates (ADP, GDP, UDP, CDP) | triphosphates (ATP, GTP, UTP, CTP) | cyclic (cAMP, cGMP, cADPR)
Deoxynucleotides: monophosphates (dAMP, dGMP, TMP, dCMP) | diphosphates (dADP, dGDP, TDP, dCDP) | triphosphates (dATP, dGTP, TTP, dCTP)
Ribonucleic acids: RNA | mRNA | tRNA | rRNA | gRNA | miRNA | ncRNA | piRNA | shRNA | siRNA | snRNA | snoRNA
Deoxyribonucleic acids: DNA | mtDNA | cDNA
Nucleic acid analogues: GNA | LNA | PNA | TNA | morpholino
Cloning vectors: plasmid | cosmid | fosmid | phagemid | BAC | YAC | HAC


{{Carbohydrates}} under construction

{{Lipids}} under construction

{{Terpenoids}} under construction

{{Carotenoids}} under construction

{{Tetrapyrroles}} under construction

{{Enzyme cofactors}} under construction

{{Steroids}} under construction

{{Flavonoids}} under construction

{{Alkaloids}} under construction

{{Polyketides}} under construction

{{Peptides}} under construction, completing cycle of biochemicals


Other templates

Circulatory system

{{Blood}}

Human chromosomes

{{Chromosomes}}

Vitamin-specific template

{{Vitamin}}

Endocrinology template (hormones and glands)

{{hormones}}


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