Combechem Jeremy G. Frey, David De Roure, Kieron Taylor, Jonathan Essex, Hugo Mills, and Ed Zaluska. Electronics and Computer Science / School of Chemistry University of Southampton Provenance, Annotation and the Semantic Web

The experimental process Plan Perform Ponder Publish

Chemistry Provenance Laboratory work What was planned? What actually happened? What was the environment like? Data management What is known about a compound? Where did that data come from? Link back to experiment(s)

Workflow Enactment Engine

KeyKey ProcessProcess InputInput LiteralLiteral O b s e r v a ti o n p l a n - t o - h e a t _ t e a _ i n _ w a t e r plan-to- add_tea_to_ water Add tea to hot waterwater He at te a for 5minutes5minutes Filt er off te a leavesleaves File: combechem/proces s/tea.rdf Ontology: combechem/process/process- record.rdfs 13:41:3613:41:36 14 Jul y © 2004 University of Southampton S t e p s P l a n P r o c e s s R e c o r d planned- weight_of_te a_leaves 5 planne d_tea_l eaves plan-to- weigh_tea_l eaves processed -by-iv material- observed-by produces- observation has-unithas-unit valuevalue p r o d u c e s - s u b s t a n c e p l a n - t o - f i l t e r _ t e a p r o d u c e s - s u b s t a n c e has-unithas-unit valuevalue processed -by-iv material- observed-by planned _some_ water plan-to- measure_som e_water produces- observation planned- volume_of_so me_water p r o c e s s e d - b y p r o c e s s e d - b y ne xt - st ep h e a t _ t e a _ i n _ w a t e r add_t ea_to _wate r weight _of_te a_leav es tea_leavestea_leaves weighin g_tea_l eaves processed -by-iv material- observed-by produces- observation has-unithas-unit valuevalue p r o d u c e s - s u b s t a n c e f i l t e r _ t e a p r o d u c e s - s u b s t a n c e &cec;volu meunit- millilitre has-unithas-unit valuevalue processed -by-iv material- observed-by some_watersome_water measuring _some_wa ter produces- observation volume_ of_som e_water p r o c e s s e d - b y p r o c e s s e d - b y p l a n - t o - t e a _ i n _ w a t e r p l a n - t o - h o t _ t e a t e a _ i n _ w a t e r h o t _ t e a st ep - te xt experiment- pretty-name The basic teaThe basic tea experimentexperiment experiment- description Ad d tea lea ves to hot water, refluxi ng, filt eri ng, dri nki ng (maybe)(maybe) exper iment er s t a r t i n g - p r o c e s s MakingTeaMakingTea s.soton.ac.uk / info/#p erson p r o c e s s - r e c o r d - o f m a t e r i a l - r e c o r d - o f p r o c e s s - r e c o r d - o f p r o d u c e s - s u b s t a n c e p l a n - t o - f i n i s h e d _ t e a p r o d u c e s - s u b s t a n c e f i n i s h e d _ t e a <tablet<tablet scribble>scribble> valuevalue process- observed-by watch ing_te a_boil produces- observation heat_tea_notesheat_tea_notes &cec;mas sunit- gramme &cec;volu meunit- millilitre &cec;mas sunit- gramme Smart tea.or g Mak ing Tea Na me spa ces rdfrdf /22-rdf-syntax-ns# rdfsrdfs 0/01/rdf-schema# xsdxsd 01/XMLSchema# aktakt /ontology/portal# cmlcml cml.org/schema/cml2/co re ceccec ology/process/0.1# stst marttea.org/# p a r t - o f - s t e p p a r t - o f - s t e p p a r t - o f - s t e p step1step1 step2step2 step3step3 experimen t-goal material-is- ingredient-of m a t e r i a l - i s - i n g r e d i e n t - o f m a t e r i a l - r e c o r d - o f p r o c e s s - r e c o r d - o f p r o c e s s - r e c o r d - o f p r o c e s s - r e c o r d - o f m a t e r i a l - r e c o r d - o f m a t e r i a l - r e c o r d - o f s t a r t i n g - s t e p

Environmental Provenance Data streams recording: Air temperature + aircon Sample temperature Humidity Vibration Motion sensors Door interlocks Equipment state Mains power...

Chemical information RDF triple store 60m asserted triples 24m inferred triples Multiple data sources Diverse schemas Inconsistent data Need to store provenance for each property

InChI: International Chemical Identifier Describes compounds Multiple layers of description Handles isomerism, stereochemistry, isotopes,... Guaranteed unique Algorithmically generated Can be turned into a URI (with some effort) Still some problems with inorganics

Tying it together Analytic Processes Synthetic Lab Chemical Properties Data analysis

More Information Dave De Roure, Jeremy Frey, Hugo Mills, Jamie Robinson, Kieron Taylor, Georgina Hallworth