GO Software Group 2006

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GO Software Group2006
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Regulation terms

• Regulation DAGs are COMPLEX and TANGLED!

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Regulation of B cell receptor signaling pathway
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Redundant link (asserted)
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Implied link (from reasoner)
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This entire DAG can be computed automatically
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How does the oboedit reasoner do this??
Reasoner requires logical definitions (aka
cross-products)
Decomposition of term into constituent terms
GO0050855 has computable definition A
regulatory process (ie regulation of biological
process), which regulates a B cell receptor
signaling pathway
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Term id GO0050855 name regulation of B cell
receptor signaling pathway namespace
biological_process def "Any process that
modulates the frequency, rate or extent of
signaling pathways initiated by the
cross-linking of an antigen receptor on a B
cell." GOCai is_a GO0050789 ! regulation of
biological process relationship regulates
GO0050853 ! B cell receptor signaling
pathway intersection_of GO0050789 ! regulation
of biological process intersection_of regulates
GO0050853 ! B cell receptor signaling pathway
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go.obo
go-xp.obo
Mini-obol
go-xp with implied links saved.obo
(nightly)
Obo-edit
Obo-edit
Reasoner
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Mini-obol parse heuristic IF labelregulation
of X THEN genus biological regulation differ
entia regulates X (when X is a
biological_process) Oboedit reasoner rule
(simplified) IF genus(A) (or is_a) genus(B)
differentium(A) is_a differentium(B) THEN A
is_a B
Regulation of B cell receptor signaling
pathway is_a Regulation of antigen
receptor-mediated signaling pathway Because B
cell receptor signaling pathway is_a antigen
receptor-mediated signaling pathway
go.obo
go-xp.obo
Mini-obol
(nightly)
Obo-edit
Obo-edit
Reasoner
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B cell receptor signaling pathway
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immune response-activating signal
transduction The cascade of processes by which a
signal interacts with a receptor, causing a
change in the level or activity of a second
messenger or other downstream target, and
ultimately leading to activation or perpetuation
of an immune response
immune response-regulating cell surface receptor
signaling pathway A series of molecular signals
initiated by the binding of an extracellular
ligand to a receptor on the surface of the target
cell capable of activating, perpetuating, or
inhibiting an immune response
disjoint_from
immune response-activating cell surface receptor
signaling pathway The cascade of processes by
which a signal interacts with a receptor, causing
a change in the level or activity of a second
messenger or other downstream target, and
ultimately leading to activation or perpetuation
of an immune response
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Next steps regulation terms

• Add logical definitions directly to go_edit.obo
• Remove dependency on heuristic obol term parsing
• Curators actively maintain logical definitions
• Win
• Maintenance of regulation DAG automated
• Potential problems
• Reasoner slows oboedit down
• Actively being addressed

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Logical definitions in other parts of GO

• Sequence Ontology
• 156 Logical definitions
• Automates a lot of DAG maintenance
• GO terms that refer to types of cell
• In progress
• Go live with regulation cross-products first
• Others
• Regulation of qualities (PATO)
• CC x CC
• Chemical
• Anatomy

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SWUG Progress Highlights 2006

• Applications
• Amigo1
• Amigo2
• OBO-Edit
• Database and perl tools
• Subsets/slims
• GO.xrf_abs
• Go-db-perl released to CPAN
• Term enrichment added to API
• Ontology development support
• Obo-format 1.2
• Logical definitions (regulation, cell, SO)

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SO x GO

• What kinds of entities to SO terms represent?
• Molecules?
• Physical sequences?
• Abstract sequences?

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Pre- and post- composition in GO

• Pre-composition
• Terms such as oocyte growth are present with IDs
  in GO
• Ideally the term is decomposed into a
  genus-differentia (cross-product) definition
  which is also stored in gene_ontology_edit.obo
• Post-composition
• Terms such as cholesterol transport in the liver
  are dynamically composed at annotation time
• Composed term need not be in GO
• But constituent terms (cholesterol transport,
  liver) should be in GO or other ontologies

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Implementing post-composition

• The two approaches are complementary
• We should extend the annotation format to allow
  denoting more specific classes
• e.g.
• cholesterol transport in liver
• advanced applications can query this
• standard applications suffer no loss
• extended annotations can be used to help seed new
  terms in the ontology
• This is already being done (MGI,Dicty)
• we just want to capture this in interopeable way

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Post-composition in gene association files

• New column in file format

Gene Product Term ID Slots
AABC1 GO0030301 (cholesterol transport) located_inMAliver
XYZZ1 GO0048663 (neuron fate development) has_central_participantFBbtY_neuron
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Important note on post-composition

• This is not an either-or situation
• We will retain pre-composed terms
• terms will continue to be created for real
  biological types
• Annotation post-composition can be used to
  further refine existing pre-composed terms
• if the post-composed term is later created in the
  GO, the annotation can be automatically migrated
• Tools can ignore post-composition for small loss
  in specificity
• defaults to the current paradigm