Function-process links Conclusions of the electron transport working group.

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

Lysine biosynthesis pathways

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)

Where do pathways start and end?

A B C D

process 1

process 2

process 3

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



Function

Process

Gene products

?

has_part

has_function



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.

So what can we do?

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.

We can mine the other links from pathway databases and make non-curated sometimes_part_of links.

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

http://www.treehugger.com/

Part_of

Car

car wheel

part_of?

http://www.classicnation.com/pictures/images/car_shows/goodguys_columbus/goodguys-columbus-car-show-047.jpg

http://www.classicnation.com/pictures/images/

has_part

car

wheel

has_part

http://www.aa1car.com/library/wheel_missing.jpg

Process:

Travel from New York to California

(by car)

Process: Travel from New York to California via Minnesota

(Google maps)

Process: Travel from New York to California via Oklahoma

Process: Travel from New York to California via Iowa


Travel from New York to California via

Minnesota


Iowa


Oklahoma

is_ais_ais_a



via Minnesota


via Iowa


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

Do the sub-process share any functions?

Function: get in the car.

http://www.ozbadge.com/sitebuildercontent/sitebuilderpictures/wapol1911ford.jpg



via Minnesota


via Iowa


via Oklahoma

is_ais_a is_a

Process

Function

Get in car

has_part

has_part

has_part



via Minnesota


via Iowa


via Oklahoma

is_ais_a is_a

Process

Function

Any part_of children?

Photosynthetic electron transport chain

http://genomics.energy.gov/gallery/gtl/originals/422.jpg

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

http://thumbs.dreamstime.com/

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

- No annotations for function

- no photosynthetic functions

But…

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

carbamoyl-phosphate synthase activityCatalysis of a reaction that results in

the formation of carbamoyl phosphate.

Urea cycle andmetabolism ofamino groups

Glutamate

metabolism

Arginine

and proline

metabolism

Nitrogen

metabolism

Function

Processhp hp hp hp

Function-process links Conclusions of the electron transport working group.

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