Function-process links Conclusions of the electron transport working

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

biosynthetic UDP-glucose process metabolic process galactose carbohydrate metabolic catabolic response process to desiccation glucose metabolic process Process hp hp hp UTP: glucose-1 -phosphate uridylyltransferase activity α-D-glucose 1 -phosphate + UTP -> UDP-D-glucose + diphosphate Function colanic acid biosynthetic process hp

Lysine biosynthesis pathways

Process lysine biosynthesis is_a lysine biosynthesis 1 Function is_a lysine biosynthesis 7? is_a lysine biosynthesis 3 5 lysine biosynthesis 4 2 6

Process Lysine Biosynthesis = has_part Function Shared function? new GO term Non-shared function existing GO term

Process Lysine Biosynthesis Process B = has_part Function Shared function? new GO term Non-shared function existing GO term

Process Lysine Biosynthesis Process B Process C = has_part Function Shared function? new GO term Non-shared function existing GO term

Process B Function Lysine Biosynthesis Relationship explosion (or Editorial office explosion) Process C

Where do pathways start and end? process 2 A B C process 1 process 3 D

Use cases • Can we slim from function up to process? • Can we infer annotations to process from those to function?

has_part Process polyamine biosynthesis urea cycle has_function Function arginosuccinate synthase activity has_function but only as part_of urea cycle has_function but only as part_of polyamine biosynthesis Gene product x Gene product y

has_part Process polyamine biosynthesis urea cycle has_function Function ? Gene products Gene product x Gene product y

has_part Process polyamine biosynthesis urea cycle has_function Function No has_part cannot be used for slimming. Gene products Gene product x Gene product y

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?

Process phosphorylation part_of Function kinase activity We can make relationships between single step processes and their respective functions.

Process glucose transport part_of Function glucose transporter activity 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. reactome 2 go. We write the mining scripts.

Acknowledgements Michelle Gwinn-Giglio Debbie Siegele Ingrid Keseler Harold Drabkin Jennifer Deegan Chris Mungall Peifen Zhang

Part_of Car part_of? http: //www. treehugger. com/ e-zip-2008 -trailz-hybrid-electric-bike. jpg wheel

Part_of Car part_of? car wheel http: //www. classicnation. com/pictures/images/ car_shows/goodguys_columbus/ goodguys-columbus-car-show-047. jpg

has_part wheel has_part car http: //www. aa 1 car. 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 is_a Travel from New York to California via Iowa Travel from New York to California via Minnesota Travel from New York to California via Oklahoma

Travel from New York to California Process is_a Travel from New York to California via Minnesota sometimes _has_part is_a Travel from New York to California via Iowa sometimes _has_part Travel from Wisconsin to Minnesota Travel from Iowa to Nebraska Function is_a Travel from New York to California via Oklahoma sometimes _has_part Travel from Missouri to Oklahoma

Do the sub-process share any functions?

Function: get in the car. http: //www. ozbadge. com/sitebuildercontent/sitebuilderpictures/wapol 1911 ford. jpg

Travel from New York to California Process is_a Travel from New York to California via Minnesota is_a Travel from New York to California via Iowa has_part Get in car Function is_a Travel from New York to California via Oklahoma has_part

Travel from New York to California Process is_a Travel from New York to California via Minnesota is_a Travel from New York to California via Iowa Any part_of children? Function is_a Travel from New York to California via Oklahoma

Photosynthetic electron transport chain http: //genomics. energy. gov/gallery/gtl/originals/422. jpg

http: //thumbs. dreamstime. com/ thumb_55/1145821933432 C 7 c. jpg Green plants + Algae + Cyanobacteria http: //www. emc. maricopa. edu/faculty/farabee/BIOBK/84150 f. jpg Other photosynthetic bacteria Anoxygenic Oxygenic http: //genomicsgtl. energy. gov/benefits/hfromh 2 o. shtml

process terms photosynthetic electron transport chain (psth) is_a anoxygenic psth part_of has part H 2 O -> O 2 + NADPH Function terms lightharvesting part_of H 2 S -> NADPH +S Option 1

process terms photosynthetic electron transport chain (psth) part_of H 2 O -> O 2 + NADPH Function terms part_of lightharvesting part_of H 2 S -> NADPH +S Option 2

- No annotations for function - no photosynthetic functions But…

arginine biosynthetic process urea cycle hp hp polyamine biosynthesis hp Process arginosuccinate synthase activity Catalysis of the reaction: ATP + L-citrulline + L-aspartate = AMP +diphosphate + (N(omega)-L-arginino)succinate Function

Urea cycle and metabolism of amino groups Process Arginine and proline metabolism hp hp Glutamate metabolism Nitrogen metabolism hp hp carbamoyl-phosphate synthase activity Catalysis of a reaction that results in the formation of carbamoyl phosphate. Function