Transcript of "Lab Service Wiki: a wiki-based data management solution for laboratories production services"
Lab Service Wiki: a wiki-based data management solution for laboratories production services <ul>Antoni Hermoso Pulido , Michela Bertero, Silvia Speroni, Miriam Alloza and Guglielmo Roma <li>[email_address]
Bioinformatics Core Facility, Protein Service - CRG
<ul>Protein Service & Biocore @ CRG </ul>CRG @ PRBB (Barcelona) International-based research center in PRBB Biopark Protein Service Internal CRG service that produces and purifies proteins for researchers in CRG. Other analyses in the future, such as mutagenesis . Bioinformatics Core Facility Provide researchers at CRG, PRBB, and other external institutions with services of consultation, data analysis and management, software development, and access to computing resources.
<ul>Elements of a protein service laboratory </ul>Images from commons.wikimedia.org PCR HPLC Gel electrophoresis
Multiple files in multiple disks – not easily linked </li></ul><ul><li>Notetaking and reports (lab notebook, wordprocessors and spreadsheets) </li></ul><ul>Tasks before the wiki </ul>
Allows efficient collaboration between different users Group roles specific permissions Researchers , lab members, lab managers, administrators Well-know interface. All people should have edited Wikipedia once! Notetaking in wiki for future consultation <ul>Why Semantic MediaWiki? </ul>
Users can be both humans and robot script applications Refined and specific queries Possibility of logic connection with other semantic empowered software Easy set up of new environments (high level programming) <ul><li>Wiki templates, properties and forms vs coding and database design </li></ul><ul>Why Semantic MediaWiki? </ul>
Users roles S ubmit requests to the service using pre-defined templates, view the status of his/her requests at any time, and retrieve the study reports when experiments are complete Can add, edit experimental data, cannot create or delete experiments. Can create, edit, delete new experiments, associated to submitted requests, using pre-defined templates C reation of new templates, users management and their training
<ul>Simplified workflow of a laboratory service </ul>
<ul>Workflow of a laboratory service </ul><ul></ul><ul>Create study </ul><ul>Accept </ul><ul>Lab Member </ul><ul>Researcher </ul><ul>Access web interface </ul><ul>Fill form </ul><ul>Submit request </ul><ul>Reject </ul><ul>Review scientific info </ul><ul>Review study </ul><ul>Accept </ul><ul>Reject </ul><ul>Reject </ul><ul>Lab Manager </ul><ul>Assign study to core members </ul><ul>Finance Controller (ORDER MANAGEMENT SYSTEM) </ul><ul>Review financial Info? </ul><ul>Accept </ul><ul>Open study </ul><ul>Retrieve SOP </ul><ul>Perform all study steps </ul><ul>( quotation ) </ul><ul>Review study results </ul><ul>Reject </ul><ul>Sign-off (?) </ul><ul>Request review </ul><ul>Prepare report </ul><ul>( order number ) </ul><ul>Send results/report </ul><ul>( communication ) </ul><ul>// </ul><ul>Retrieve results/report </ul><ul>Sign-off (?) </ul><ul>Accept </ul><ul>Meeting </ul><ul>Meeting </ul><ul>Meeting </ul><ul>Meeting </ul><ul>Meeting </ul><ul>Meeting </ul><ul>// ? </ul><ul>// </ul><ul>// ? </ul><ul>Receive invoice </ul>Design: Guglielmo Roma
Permissions & security Login & role permissions. Done automatically or via administrator Namespaces specific permissions: Experiment:: (only lab members/managers) Template:: (only administrators) Page specific permissions By using user and parse functions extensions with Semantic properties MediaWiki Image authorization Network, LDAP, etc.
Request Form Thanks to Extension:Semantic Forms
Experiment form – fine-grained control Emailing linked to change of properties. Modified Semantic Tasks extension .
Experiment form - restrictions Logical input Restrictions. Data Type linked
<ul>Conditional syntax </ul>Enable certain experiment sections if asked by the researcher or lab manager Input value restriction at the form level Example: Only nucleotides allowed in Primer sequences. Regular expressions.
<ul>User Panel </ul>Template(s) created when the user first registers. Modified NewUserMessage extension
<ul>Current and upcoming development – May 2010 </ul>Better look and feel for the wiki Detailed image (semantic) annotation To study: http://commons.wikimedia.org/wiki/Help:Gadget-ImageAnnotator Semantic properties coupled to image permissions http://www.mediawiki.org/wiki/Manual:Image_Authorization Integration with popular biological services Study or search for a common ontology for laboratory services Import biological ontologies (e.g. Gene Ontology)