The curation curation of laboratory experimental of laboratory - PowerPoint PPT Presentation

The curation curation of laboratory experimental of laboratory experimental The data as part of the overall data data as part of the overall data lifecycle lifecycle Jeremy G.Frey G.Frey Jeremy School of Chemistry, University of School of Chemistry, University of Southampton, UK Southampton, UK 21 Nov 2006 21 Nov 2006 DCC Conference, Glasgow DCC Conference, Glasgow Jeremy G. Frey Jeremy G. Frey DCC Conference Glasgow 21 Nov 2006 21 Nov 2006 University of Southampton University of Southampton

If you do things right at the start then all the following processes are much easier! Exponentially growing amount of data - the future overwhelms the past 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

e Chem Comb e The Comb Chem Project Project The  End to End linking of data and End to End linking of data and  information information  Publication@Source Publication@Source   So collect data with regard to how it So collect data with regard to how it  could eventually be used could eventually be used  Make sure the metadata is of high quality Make sure the metadata is of high quality   Record properly at source in Digital Form Record properly at source in Digital Form   The Chemistry Lab The Chemistry Lab   People & Machines working together People & Machines working together  21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

Combechem E-Malaria Smart Lab R4L e-Bank Instruments on the Grid Statistics BioSimGrid 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

The concept of Publication @ Source The concept of Publication @ Source Goal Knowledge Literature Smart Dissemination Smart Laboratory Report not just one laboratory Plan & but many co-laboratories COSHH working together Information Integration Smart HCI Digital Model Analysis Smart Workflow Smart Storage Synthesis 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

If only I knew exactly how she did this experiments I wish I had recorded things at the start the way I do now….. I know all this supplementary information could be useful but will people really remember the I wish I could get format? Is it worth all the the numbers from hassle? this graph - the pdf Typical Laboratory is not much use. 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

Need to make the data available Need to be able to find it But how to expose it? First, they do an online search 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

I am sure we collected that information a few years ago… The details should be in her thesis….. Can you read what he says here….? Can you find the file of data that were used to make the plot? Some of these problems are due to the lack of information recorded at the time. Others are due to loss of information over time. 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

What are the people up to? What are the people up to?  Capture Data and Context  Capture Data and Context  People People   Process Process   Environment Environment  21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

Permanent, documented and primary record of laboratory observations 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

Observations are never collected on note pads, filter paper or other temporary paper for later transfer into a notebook If you are caught using the “scrap of paper” technique, your improperly recorded data may be confiscated by your TA 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

COSHH COSHH L everage off things we already L everage off things we already have to do – – “ “We have a cunning We have a cunning have to do plan” ” plan 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

List To D Ingredient List Dissolve 4- Add K2CO3 Heat at reflux Cool and add Heat at Cool and add Extract with Combine organics, Remove Fuse compound to silica & flourinated powder for 1.5 hours Br11OCB reflux until water (30ml) DCM dry over MgSO4 & solvent in column in ether/petrol Fluorinated biphenyl 0.9 g biphenyl in completion (3x40ml) filter vacuo Br11OCB 1.59 g butanone Potassium Carbonate 2.07 g Butanone 40 ml Plan Add Cool Add Reflux Remove Column Liquid- Add Reflux Cool Add Dry Filter Fuse liquid Solvent Chromatography by Rotary extraction Evaporation 0.9031 grammes g excess Inorganics dissolve 2 3 of 40 ml layers. Added brine ~20ml. text Ether/ image Petrol Weigh Process Measure Silica Ratio Record Measure Sample of 4- Butanone dried via silica column and flourinated measured into 100ml RB flask. biphenyl Used 1ml extra solvent to wash out Annotate DCM MgSO4 container. Annotate 1 1 2 2 1 3 1 4 3 5 2 6 2 7 4 8 9 10 11 12 13 14 Add Cool Add Reflux Remove Column Add Reflux Cool Add Liquid- Dry Filter Fuse Solvent Chromatography liquid (Buchner) text Sample of Annotate by Rotary Butanone extraction Br11OCB Sample of Evaporation Water Annotate Annotate K2CO3 Measure Powder Measure Weigh Weigh text Started reflux at 13.30. (Had to change heater stirrer) Only reflux text text Washed MgSO4 with 40 ml for 45min, next step 14:15. Organics are yellow DCM ~ 50ml solution 30 ml 2.0719 g g 1.5918 Key Observation Types Future Questions Process weight - grammes Whether to have many subclasses of processes or fewer with annotations measure - ml, drops Combechem How to depict destructive processes Input annotate - text 30 January 2004 Literal How to depict taking lots of samples ° C gvh, hrm, gms temperature - K, What is the observation/process boundary? e.g. MRI scan Observation 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

Ingredient List Dissolve 4- Add K2CO3 Heat at reflux flourinated powder for 1.5 hours Fluorinated biphenyl 0.9 g biphenyl in Br11OCB 1.59 g butanone Potassium Carbonate 2.07 g Butanone 40 ml Add Add Reflux grammes 0.9031 Weigh Sample of 4- Butanone dried via silica column and flourinated measured into 100ml RB flask. biphenyl Used 1ml extra solvent to wash out container. Annotate 1 1 2 2 1 3 Add Add Reflux text Annotate Butanone Sample of K2CO3 Powder Measure Weigh text Started reflux at 13.30. (Had to change heater stirrer) Only reflux 40 ml for 45min, next step 14:15. 2.0719 g 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

Pub-Sub systems provide the flexible & extensible approach to distribution of real time laboratory monitoring & archiving Smart Laboratory Spaces

But what about the laboratory environment? “I just realized, Howard, that everything in this apartment is more sophisticated than we are” 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

Semantic DataGrid DataGrid Semantic  CombeChem  CombeChem used, tested & used, tested & strained the Semantic Web strained the Semantic Web for for  Enhanced (annotated) Enhanced (annotated)  DataGrid over multiple diverse over multiple diverse DataGrid stores stores  Storage of Provenance Storage of Provenance  Information Information  Some Data Storage Some Data Storage   Annotated multimedia streams Annotated multimedia streams   Units & Units & Propoerties Propoerties Ontology Ontology   Multiple Triple Stores Multiple Triple Stores 

Laboratory “ “Blogs Blogs” ” Laboratory  Laboratory notebook is a  Laboratory notebook is a Blog Blog  Encourage and facilitate collaboration  Encourage and facilitate collaboration  Need a data repository behind the  Need a data repository behind the B Blog log  R4L R4L   E-Bank E-Bank   Flexible  Flexible  Service oriented approach Service oriented approach being developed being developed   A VRE  A VRE 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton

Instrument Blog ‘Blog-jects’ 21 Nov 2006 21 Nov 2006 Jeremy G. Frey Jeremy G. Frey DCC Conference 2006 University of Southampton University of Southampton