Guidelines for logical definitions: Difference between revisions

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* in this case these are different functions, not some emerging function of the complex. We would capture a logical definition only if there is one overall function for the complex.  
* in this case these are different functions, not some emerging function of the complex. We would capture a logical definition only if there is one overall function for the complex.  


'''Note: Equivalence Axioms (or Logical Definitions) used to be referred to as 'cross-products', but we have largely abandonned this nomenclature. '''
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==Moved from the GO website: TO REVIEW==
==Equivalence Axioms (or Logical Definitions)==
Equivalence Axioms, also known as Logical Definitions (LD), are '''computable logical definitions''' that complement the existing text definitions. Equivalence Axioms enable tools to access the data and perform tasks and analyses that would be time-consuming and work intensive for humans. One aspect that can aid automated access to the ontology is creating


  See also http://wiki.geneontology.org/index.php/Logical_Definitions


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==Structure of Equivalence Axioms==  
 
Equivalence Axioms are in the '''genus-differentia form''', such that an equivalence axiom consists of:  
==Cross-Products and Logical Definition==
* a '''genus''': the broader class to which the term belongs, and  
To be maximally useful, the Gene Ontology aims to be accessible to computers as well as to human users, enabling tools to access the data and perform tasks and analyses that would be time-consuming and work intensive for humans. One aspect that can aid automated access to the ontology is creating '''computable logical definitions''' to complement the existing text definitions. These logical definitions are in the genus-differentia form: the definition consists of:  
* one or more '''differentia''':  the property/ies that distinguish the term from other members of the same class.  
* the '''genus''': the broader class to which the term belongs, and  
* the '''differentia''':  the property/ies that distinguish the term from other members of the same class.  


Examples:
Examples:

Revision as of 11:25, 7 January 2020

  In progress


 NEED TO DESCRIBE HOW TO DEFINE SPECIFIC TYPES OF TERMS: for example protein complex: 
  • Discussion GO editors 2019-05-06: We should only add 'capable of' MF when there is an emerging function
  • in this case these are different functions, not some emerging function of the complex. We would capture a logical definition only if there is one overall function for the complex.

Note: Equivalence Axioms (or Logical Definitions) used to be referred to as 'cross-products', but we have largely abandonned this nomenclature.


Equivalence Axioms (or Logical Definitions)

Equivalence Axioms, also known as Logical Definitions (LD), are computable logical definitions that complement the existing text definitions. Equivalence Axioms enable tools to access the data and perform tasks and analyses that would be time-consuming and work intensive for humans. One aspect that can aid automated access to the ontology is creating


Structure of Equivalence Axioms

Equivalence Axioms are in the genus-differentia form, such that an equivalence axiom consists of:

  • a genus: the broader class to which the term belongs, and
  • one or more differentia: the property/ies that distinguish the term from other members of the same class.

Examples:

  • mitochondrial DNA replication is DNA replication that occurs in a mitochondrion
    • genus: 'DNA replication'
    • differentia: 'occurs in' some mitochondrion
  • lysosomal membrane is the membrane that surrounds a lysosome
    • genus: 'whole membrane'
    • differentia: and 'bounding layer of' some lysosome
  IS THIS STILL RIGHT : 
 These definitions of terms created by combining other terms with relations are called cross-products in GO parlance. In the OBO 1.2 (NOTE: CURRENT VERSION is 1.4 ???? 1.4 according to GO website but GO-edit states 1.2) format file, the human-readable text definition is held in the def line, and the cross-product definition in the intersection_of lines of a stanza. The cross-products above would be represented as follows:


[Term]
id: GO:0006264
name: mitochondrial DNA replication
namespace: biological_process
def: "The process in which new strands of DNA are synthesized in the mitochondrion." [GOC:ai]
is_a: GO:0006261 ! DNA-dependent DNA replication
intersection_of: GO:0006260 ! DNA replication
intersection_of: occurs_in GO:0005739 ! mitochondrion
[Term]
id: GO:0005765
name: lysosomal membrane
namespace: cellular_component
def: "The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm." [GOC:ai]
is_a: GO:0005774 ! vacuolar membrane
intersection_of: GO:0098805 ! whole membrane
intersection_of: bounding_layer_of GO:0005764 ! lysosome
relationship: part_of GO:0005764 ! lysosome

Cross-Products with external ontologies

Cross-products need not be restricted to terms within GO; cross-products can also be created by combining GO terms with those from other ontologies. For example, by using the Cell Ontology, we can easily extract cell type information from GO terms. For example:

megasporocyte nucleus (GO:0043076) is a nucleus (GO:0005634) that is part of a megasporocyte (CL:0000320)

       [Term]
       id: GO:0043076
       name: megasporocyte nucleus
       def: "The nucleus of a megasporocyte, a diploid cell that undergoes meiosis to produce four megaspores, and its descendents."
       [source: GOC:jl, ISBN:0618254153]
       intersection_of: GO:0005634 ! nucleus
       intersection_of: part_of CL:0000320 ! megasporocyte

osteoblast development (GO:0002076) is cell development (GO:0048468) that results in the complete development of an osteoblast (CL:0000062)

       [Term]
       id: GO:0002076
       name: osteoblast development
       def: "The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone." [source: GOC:dph]
       intersection_of: GO:0048468 ! cell development
       intersection_of: OBO_REL:results_in_complete_development_of CL:0000062 ! osteoblast

Cross-products are currently being retrofitted to existing ontology terms and added to new terms. Eventually, the hope is that cross-products could be dynamically generated, rather than having be added manually each time a new term is required. This would obviate the need for some of highly specific terms in GO—for example, many of the terms referring to organism anatomy or chemical entities—and simplify ontology searches and browsing.

More information on the ongoing work on cross-products can be found in the cross-products category on the GO wiki.

Define 'necessary and sufficient'

Some relationships assert classification (a nucleolus is a class of organelle), others make statements about necessary conditions for being a member of a class (being part of a nucleus is a necessary condition of being in the class nucleolus). Other relationships specify both necessary and sufficient conditions for being a class member (any channel activity that transports ions is an ion channel activity). Along with reasoning software, we can use these to automate classification.

++ How can you tell that a term's equivalence axioms are necessary and sufficient?

Molecular function

Equivalent axioms for MF that include 'binding': use 'has_part' some binding (see https://github.com/geneontology/go-ontology/issues/14266)


Children of transcription regulator activity

For example: DNA-binding transcription factor activity

transcription regulator activity 'part of' some 'regulation of transcription, DNA-templated' 'has necessary component activity' some 'transcription regulatory region sequence-specific DNA binding'

Using the reasoner in Protégé

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