Function-process links Conclusions of the electron transport working group.
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Transcript of Function-process links Conclusions of the electron transport working group.
UTP:glucose-1-phosphate uridylyltransferase activity α-D-glucose 1-phosphate + UTP ->
UDP-D-glucose + diphosphate
glucose metabolic process
UDP-glucosemetabolicprocess galactose
metabolic process
biosyntheticprocess
colanic acidbiosyntheticprocess
responseto desiccation
carbohydrate catabolic process
Function
Processhp hp
hphp hp
hp hp
lysinebiosynthesis
lysinebiosynthesis1
lysinebiosynthesis3
lysinebiosynthesis2
lysinebiosynthesis4
lysinebiosynthesis5
lysinebiosynthesis6
Function
Process
is_a
is_ais_a is_a is_a
is_a
lysinebiosynthesis 7?
is_a
Process
Function
Lysine Biosynthesis
Shared function?
= has_part
Non-shared function
new GO term
existing GO term
Process
Function
Lysine Biosynthesis
Process B
Shared function?
= has_part
Non-shared function
new GO term
existing GO term
Process
Function
Lysine Biosynthesis
Process B Process C
Shared function?
= has_part
Non-shared function
new GO term
existing GO term
Process
Function
Lysine Biosynthesis
Process B Process CRelationship explosion
(or Editorial office explosion)
Use cases
• Can we slim from function up to process?
• Can we infer annotations to process from those to function?
has_part
has_function
has_function but only as part_of polyamine biosynthesis
has_function but only as part_of urea cycle
urea cyclepolyamine biosynthesis
arginosuccinate synthase activity
Gene product x Gene product y
Function
Process
Gene products
has_part
has_function
urea cyclepolyamine biosynthesis
Gene product x Gene product y
Function
Process
Gene products
?
has_part
has_function
urea cyclepolyamine biosynthesis
Gene product x Gene product y
Function
Process
Gene products
No
has_partcannot beused for slimming.
Can we infer annotations to process from those to function?
• No. There is too much variation in process details, and too many functions are shared.
phosphorylation
kinase activity
Function
Process
part_of
We can make relationships between single step processes and their respective functions.
glucose transport
glucose transporter activity
Function
Process
part_of
We can make any obvious relationship where part_of holds, and this will allow useful slimming.
sometimes_part_of
What does this buy us?
Very full coverage of function-process links.No manual link curation.
What work does it involve?
We maintain the mapping files e.g. reactome2go.We write the mining scripts.
Acknowledgements
Michelle Gwinn-GiglioDebbie SiegeleIngrid KeselerHarold DrabkinJennifer DeeganChris MungallPeifen Zhang
Part_of
Car
wheel
part_of?
http://www.treehugger.com/e-zip-2008-trailz-hybrid-electric-bike.jpg
Part_of
Car
car wheel
part_of?
http://www.classicnation.com/pictures/images/car_shows/goodguys_columbus/goodguys-columbus-car-show-047.jpg
Travel from New York to California
Travel from New York to California via
Minnesota
Travel from New York to California via
Iowa
Travel from New York to California via
Oklahoma
is_ais_ais_a
Travel from New York to California
Travel from New York to California
via Minnesota
Travel from New York to California
via Iowa
Travel from New York to California
via Oklahoma
is_ais_a is_a
Process
Function
Travel from Iowa to Nebraska
Travel from Missouri to Oklahoma
Travel from Wisconsin to Minnesota
sometimes_has_part
sometimes_has_part sometimes
_has_part
Function: get in the car.
http://www.ozbadge.com/sitebuildercontent/sitebuilderpictures/wapol1911ford.jpg
Travel from New York to California
Travel from New York to California
via Minnesota
Travel from New York to California
via Iowa
Travel from New York to California
via Oklahoma
is_ais_a is_a
Process
Function
Get in car
has_part
has_part
has_part
Travel from New York to California
Travel from New York to California
via Minnesota
Travel from New York to California
via Iowa
Travel from New York to California
via Oklahoma
is_ais_a is_a
Process
Function
Any part_of children?
http://genomicsgtl.energy.gov/benefits/hfromh2o.shtml
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/84150f.jpg
http://thumbs.dreamstime.com/thumb_55/1145821933432C7c.jpg
Other photosyntheticbacteria
Green plants
+
Algae
+
CyanobacteriaAnoxygenic
Oxygenic
photosynthetic electron transport chain (psth)
oxygenic psth anoxygenic psth
is_a is_a
light-harvesting
H2S -> NADPH + S
H2O -> O2 + NADPH
processterms
Functionterms
Option 1
part_of has part
haspart
part_of
photosynthetic electron transport chain (psth)
light-harvesting
H2S -> NADPH + S
H2O -> O2 + NADPH
processterms
Functionterms
Option 2
part_of part_of part_of
ureacycle
arginosuccinate synthase activity Catalysis of the reaction: ATP + L-citrulline + L-aspartate = AMP
+diphosphate + (N(omega)-L-arginino)succinate
arginine
biosynthetic
process
polyamine biosynthesis
Function
Process
hp hp hp