Guidelines for equivalence axioms

From GO Wiki
Jump to: navigation, search
  In progress

Moved from the GO website: TO REVIEW

Cross-Products and Logical Definitions To be maximally useful, the Gene Ontology should 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 the genus, the broader class to which the term belongs, and the differentia, the properties that distinguish the term from other members of the class. For example:

mitochondrial DNA replication is DNA replication that occurs in a mitochondrion

DNA replication is the genus and the differentia is occurs in a mitochondrion.

lysosomal membrane is the membrane that surrounds a lysosome

membrane is the genus and the differentia is surrounds a lysosome.

If we use ontology terms in the genus and the differentia, we can see that these logical definitions take the general form

term = term that relation term

For example:

mitochondrial DNA replication is DNA replication that occurs in a mitochondrion

lysosomal membrane is a membrane that surrounds a lysosome

These definitions of terms created by combining other terms with relations are called cross-products in GO parlance. In the OBO 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
       def: "The process whereby new strands of DNA are synthesized in the mitochondrion." [source: GOC:ai]
       intersection_of: GO:0006260 ! DNA replication
       intersection_of: OBO_REL:occurs_in GO:0005739 ! mitochondrion
       [Term]
       id: GO:0005765
       name: lysosomal membrane
       def: "The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm." [source: GOC:ai]
       intersection_of: GO:0016020 ! membrane
       intersection_of: 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.


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'