Cross-Product Status in GO
Cross Products
Cross products are logical definitions of
GO terms that use ‘simpler’ terms in
combination to define a more complex
term
Why Cross-Products?
• Cross-products can be expressed in OWL
– Allows for automated checking of ontology logic
– Allows for the use TermGenie to automatically
place terms in the ontology
• Cross-products are necessary to integrate the
ontology with annotation extension data.
• Cross-products with external ontologies allow
us to leverage external expertise (ChEBI).
Cross-Products
[Term]
id: GO:0000018
name: regulation of DNA recombination
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA
recombination, a DNA metabolic process in which a new genotype is formed
by reassortment of genes resulting in gene combinations different from those
that were present in the parents." [GOC:go_curators, ISBN:0198506732]
subset: gosubset_prok
is_a: GO:0051052 {is_inferred="true"} ! regulation of DNA metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006310 ! DNA recombination
relationship: regulates GO:0006310 ! DNA recombination
Cross-Products Come in 2 Flavours
• Internal Cross Products
– Cross products that consist of terms that are in GO
(MF, BP, CC).
• External Cross Products
– Cross products that consist of a term from GO and
a term from another ontology
Internal Cross Products
In the gene_ontology_write.obo
• Regulation
– Regulates: 2584
– Positively regulates: 2176
– Negatively regulates: 2200
• Part of: 1465
• Occurs in: 114
• Results in: 122
Regulates
[Term]
id: GO:0000018
name: regulation of DNA recombination
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA
recombination, a DNA metabolic process in which a new genotype is formed
by reassortment of genes resulting in gene combinations different from those
that were present in the parents." [GOC:go_curators, ISBN:0198506732]
subset: gosubset_prok
is_a: GO:0051052 {is_inferred="true"} ! regulation of DNA metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006310 ! DNA recombination
relationship: regulates GO:0006310 ! DNA recombination
Part of
[Term]
id: GO:0000022
name: mitotic spindle elongation
namespace: biological_process
def: "Lengthening of the distance between poles of the
mitotic spindle." [GOC:mah]
synonym: "spindle elongation during mitosis" EXACT []
is_a: GO:0051231 {is_inferred="true"} ! spindle elongation
intersection_of: GO:0051231 ! spindle elongation
intersection_of: part_of GO:0000278 ! mitotic cell cycle
relationship: part_of GO:0007052 ! mitotic spindle
organization
Occurs in
[Term]
id: GO:0000957
name: mitochondrial RNA catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown
of RNA transcribed from the mitochondrial genome and occurring in
the mitochondrion." [GOC:krc, GOC:mah]
is_a: GO:0000959 {is_inferred="true"} ! mitochondrial RNA metabolic
process
is_a: GO:0006401 {is_inferred="true"} ! RNA catabolic process
intersection_of: GO:0006401 ! RNA catabolic process
intersection_of: occurs_in GO:0005739 ! mitochondrion
Results in
[Term]
id: GO:0001559
name: regulation of cell growth by detection of nuclear:cytoplasmic ratio
namespace: biological_process
def: "Any process in which the size of the nucleus with respect to the cytoplasm
modulates the frequency, rate or extent of cell growth, the irreversible increase in size
of a cell over time." [GOC:dph]
synonym: "detection of nuclear:cytoplasmic ratio to regulate cell growth" EXACT []
synonym: "interpretation of nuclear:cytoplasmic ratio to regulate cell growth" EXACT
[]
synonym: "regulation of cell growth by nuclear:cytoplasmic ratio" EXACT []
synonym: "regulation of cell growth by sensing of nuclear:cytoplasmic ratio" EXACT []
is_a: GO:0016475 {is_inferred="true"} ! detection of nuclear:cytoplasmic ratio
is_a: GO:0061387 ! regulation of extent of cell growth
intersection_of: GO:0016475 ! detection of nuclear:cytoplasmic ratio
intersection_of: results_in GO:0001558 ! regulation of cell growth
Internal Cross Products
In gene_ontology_xp_write.obo
results_in_distribution_of
7
results_in_assembly_of
125
has_target_end_location
97
transports_or_maintains_localization_of
50
results_in_transport_to_from_or_in
12
results_in_organization_of
112
results_in_fission_of
3
results_in_disassembly_of
24
results_in_fusion_of:
22
has_target_start_location:
29
results_in_morphogenesis_of
10
occurs_in
6
Part_of
1
results_in_growth_of
1
results_in_maturation_of
1
results_in_remodeling_of
8
results_in_transport_across
5
results_in_transport_along
7
results_in_transport_to_from_or_mediated_by
1
Results_in_distribution_of
7
Internal Cross Products
in gene_ontology_xp_write.obo
[Term]
id: GO:0001675 ! acrosome assembly
intersection_of: GO:0022607 ! cellular component assembly
intersection_of: results_in_assembly_of GO:0001669 ! acrosomal vesicle
[Term]
id: GO:0006997 ! nucleus organization
intersection_of: GO:0016043 ! cellular component organization
intersection_of: results_in_organization_of GO:0005634 ! nucleus
[Term]
id: GO:0032989 ! cellular component morphogenesis
intersection_of: GO:0009653 ! anatomical structure morphogenesis
intersection_of: results_in_morphogenesis_of GO:0005575 ! cellular_component
External Cross Products
in gene_ontology_xp_write.obo
• Currently implemented with ChEBI
• Cross-products with the cell ontology
• Cross-products with anatomy
External Cross Products
In gene_ontology_xp_write.obo
Exports
15
Has_input
1858
Has_intermediate
56
Has_output
1154
Has_participant
1194
imports
50
Regulates_level_of
53
Transports_or_maintains_localization_of
876
External Cross Products
in gene_ontology_xp_write.obo
[Term]
id: GO:0000017 ! alpha-glucoside transport
intersection_of: GO:0006810 ! transport
intersection_of: transports_or_maintains_localization_of CHEBI:60979 ! alpha-glucoside
[Term]
id: GO:0000035 ! acyl binding
intersection_of: GO:0005488 ! binding
intersection_of: has_input CHEBI:22221 ! acyl group
[Term]
id: GO:0000951 ! methionine catabolic process to 3-methylthiopropanol
intersection_of: GO:0009056 ! catabolic process
intersection_of: has_input CHEBI:32644 ! methioninate
intersection_of: has_output CHEBI:49019 ! 3-methylthiopropanol
[Term]
id: GO:0001504 ! neurotransmitter uptake
intersection_of: GO:0006810 ! transport
intersection_of: imports CHEBI:25512 ! Neurotransmitter
Next step: Cell Ontology
• The cell ontology is already being used in
annotation extensions
• It is critical that we also incorporate cell
information into GO logical definitions.
Column 16 Data
Future of Cellular terms in GO
[Term]
id: GO:0002070
name: epithelial cell maturation
namespace: biological_process
def: "The developmental process, independent of morphogenetic
(shape) change, that is required for an epithelial cell to attain its fully
functional state. An epithelial cell is a cell usually found in a twodimensional sheet with a free surface." [GOC:dph]
is_a: GO:0048469 ! cell maturation
relationship: part_of GO:0002064 ! epithelial cell development
intersection_of: GO:0021700 ! developmental maturation
intersection_of: results_in_maturation_of CL:0000066 ! epithelial cell
In the Pipeline
• Cross-products with the plant ontology: 150
(Tanya)
• Cross-products for complexes that are capable
of some function: 700 (Harold)
• Hand editing non-parsable/incomplete terms.