Guidelines for GO textual definitions: Difference between revisions

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In some cases, it is appropriate to add to the core definition to improve the comprehensibility. This can include further explanations of the genus and/or differentia or examples of the term usage.  
In some cases, it is appropriate to add to the core definition to improve the comprehensibility. This can include further explanations of the genus and/or differentia or examples of the term usage.  
===Use of standard definitions===
NOT YET REVIEWED
Wherever a 'standard' definition exists for a group of related terms, it should be used; please see the ontology guides for standard definitions used in each ontology. If you find yourself repeatedly using the same text string in a series of definitions, please add to the standard definitions:
   
   
   Link to http://geneontology.org/page/ontology-documentation
   Link to http://geneontology.org/page/ontology-documentation
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; ''xxx'' distribution  
; ''xxx'' distribution  
: Any process that establishes the spatial arrangement of ''xxx''.
: Any process that establishes the spatial arrangement of ''xxx''.
===Redefining terms===
NOT YET REVIEWED
A GO ID is really associated with a definition rather than with the term name. If we change the wording but not the meaning of a term, the GO ID stays the same; a new meaning requires a new GO ID, even if the text string doesn't change. Here's a trivial example that illustrates when we do and don't change GO IDs:
Assume that we have a term mouse, GO ID GO:0000123, in an ontology; it is defined as a small furry mammal.
We decide to change the term wording to Mus musculus, keeping the definition the same. In this case we merely update the text; the GO ID stays the same because the meaning stays the same. We may choose to keep "mouse" as a synonym, but there would still only be one ID associated with the term.
We decide that the term "mouse" should instead mean a piece of computer equipment. In this case, the old term and ID are moved to the obsolete category, and "mouse", as newly defined, gets a new GO ID, GO:0000456. The old GO ID and definitions are saved for posterity in case we ever need to know what happened to them.




[[Category:Curator_Guides]][[Category:Ontology]]
[[Category:Curator_Guides]][[Category:Ontology]]

Revision as of 15:21, 27 June 2018

  BEING REVIEWED

General points about definitions of GO terms

  • All terms require a definition and a definition cross-reference.
  • Definitions should explain clearly to the reader what is meant by a particular term.
  • They should be concise, full sentences (they should begin with an upper-case letter and end with a period).
  • As with term names, avoid using abbreviations that may be ambiguous (e.g. "ER" can mean "endoplasmic reticulum" or "estrogen receptor").


Use Aristotelian definitions

Ideally, definitions should follow the genus-differentia ("Aristotelian") pattern: they should take the form of a genus (generic term, an is_a parent) and differentia (discriminating characteristics which mark instances of the specific term as being different from is_a sibling terms).

For example, a spindle microtubule is defined as "Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole."

  • Genus: Any microtubule
  • Differentia: part of a mitotic or meiotic spindle; anchored at one spindle pole

The genus and differentia should make the definition necessary and sufficient such that all terms that are subclasses of that term satisfy the definition of the term, and any term that is not a subclass of the term does not satisfy the definition.

In some cases, it is appropriate to add to the core definition to improve the comprehensibility. This can include further explanations of the genus and/or differentia or examples of the term usage.

Use of standard definitions

NOT YET REVIEWED 

Wherever a 'standard' definition exists for a group of related terms, it should be used; please see the ontology guides for standard definitions used in each ontology. If you find yourself repeatedly using the same text string in a series of definitions, please add to the standard definitions:

 Link to http://geneontology.org/page/ontology-documentation
 Link to https://github.com/geneontology/go-ontology/tree/master/src/design_patterns
 Look for any other pages in the wiki such as http://wiki.geneontology.org/index.php/Transporter_terms_standard_definitions


membrane fusion
The joining of the lipid bilayer membrane around X to the lipid bilayer membrane around Y.
cellular component organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cellular component.
cellular component biogenesis
The process by which a cellular component is synthesized, aggregates, and bonds together.
macromolecular complex assembly
The aggregation, arrangement and bonding together of a set of components to form a macromolecular complex.
xxx distribution
Any process that establishes the spatial arrangement of xxx.


Redefining terms

NOT YET REVIEWED 

A GO ID is really associated with a definition rather than with the term name. If we change the wording but not the meaning of a term, the GO ID stays the same; a new meaning requires a new GO ID, even if the text string doesn't change. Here's a trivial example that illustrates when we do and don't change GO IDs:

Assume that we have a term mouse, GO ID GO:0000123, in an ontology; it is defined as a small furry mammal.

We decide to change the term wording to Mus musculus, keeping the definition the same. In this case we merely update the text; the GO ID stays the same because the meaning stays the same. We may choose to keep "mouse" as a synonym, but there would still only be one ID associated with the term.

We decide that the term "mouse" should instead mean a piece of computer equipment. In this case, the old term and ID are moved to the obsolete category, and "mouse", as newly defined, gets a new GO ID, GO:0000456. The old GO ID and definitions are saved for posterity in case we ever need to know what happened to them.