The Chemtools LaBLog

The Chemtools LaBLog Recording research in the real world Cameron Neylon Contributions from Jeremy Frey, Andrew Milsted, Steve Wilson, Simon Coles, Mark Borkum, Jenny Hale, and others

Goals
A complete and useable record for the researcher and research team
Enable a human reader to fully reproduce all experiments and replicate all data analysis in detail
New functionality (video, search, communication, links, visualisation)
Enable machine reading for automated aggregation and analysis

A small challenge… Can anyone name or identify a paper in which it is possible to completely and precisely replicate the data analysis, including availability of raw data, full details of tools, version, and parameters for data analysis, and version (or date) of any databases used in the analysis.

A blog as the lab book http://chemtools.chem.soton.ac.uk/projects/blog / “Bio Blogs” http://blogs.openwetware.org/scienceintheopen Discussion

One item – one post (1I-1P) system

1I-1P gives every sample a URI

1I-1P relationships between posts An rdf dump of posts and links between them rendered using Welkin (simile.mit.edu/welkin)

1I-1P relationships between posts

What about semantics?
System is semantically unaware
Arbitrary key-value pairs stored as XML
Complete freedom to add or modify metadata
Complete freedom to muck it up

Templates provide ease of use and consistent metadata [table] [row] Lane[col]Sample[col]ul [/row] … [row] 4[col] [[Dna:%]] [col] [[box]] [/row] … [/table] [[Section>Procedure]] [[Procedure_Type>electrophoresis_agarose]] [[Sandpit_group>DrexelDemo]]

System to date
Our main laboratory notebook system
Around 4000 posts, 800 Gb of data
Used for biochemistry, synthetic chemistry, biophysics
Also used as a collaboration and management tool in other projects
Currently rolling out onto other sites

Goals
Enable a human reader to fully reproduce all experiments and replicate all data analysis in detail

Versioning and provenance for analysis using workflows and API
Workflow enacted online (MyExperiment)
Pull down data from lab book and process
Write results and record back to blog
Provenance of workflow, versioning, and sharing via MyExp
Record of enactment in LaBLog

Automatic Blogging by Machines

Automatic Blogging by Sensors
Continuous log of ‘environmental’ conditions in a laboratory
Instant detection of erroneous events
Correlate with inconsistencies in datasets

Goals
Enable a human reader to fully reproduce all experiments and verify all data analysis in detail

Visualisations and communication

Pictorial commenting
Annotation tools allow comments and foster collaboration and / or communication
Need for more advanced Blog tools / technology around data

Goals
Enable a human reader to fully reproduce all experiments and verify all data analysis in detail
?

RDF to ‘real’ RDF?
Currently just links and post titles
Include metadata
Infer a vocabulary (probably human driven process)
Refactor to generate a rich rdf version

Linking it all up Unstructured Unfiltered Arbitrary vocabulary Structured Filtered Controlled vocab Primary lab book Autoblogging instrument Published paper Database entry Personal journal Raw data Data processing

What could it look like? GO Ontology Browser Raw SANS Data - D22 run #29483 from D22 at the Institut Laue-Langevin Raw SANS Data - D22 run #29483 from D22 at the Institut Laue-Langevin

The Chemtools LaBLog

by Cameron Neylon on Aug 06, 2008

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