Scientific Data Management

scientific information management Alberto Labarga, Feb 13th 2009

LIMS: Laboratory Information Management System ELN: Electronic Laboratory Notebook SDMS: Scientific Data Management System

ideal Your system should …

users manage your

instruments manage your

store manage your biological

Samples Cell lines Tissues

experiments manage your

requests schedule execute results collaborative analysis

Workflows: protein identification Gel Liquid Spots sample Picking Digestion and Digestion and deposition concentation MALDI LC-MS 2LC-MS .wiff .wiff Data processing (MASCOT, SEQUEST)

standards Support

CONTENT: Minimal/Core Information -> MIBBI (http://www.mibbi.org) SEMANTIC: Terminology used, ontologies -> OBI (http://obi-ontology.org) SYNTAX: Data Model, Data Exchange ->Fuge (http://fuge.sourceforge.net/)

MIBBI: Standard Content

OBO: Ontologies and controlled vocabulart

any device Be accessible from

other software be accessible from

Your LIMS goes here

external resources integrate

submission curation ws ws ws ws ws dataflow workflow

paper labboks support your

infrastructure integrate with your

architecture a pluggeable

functional genomics platform web application document management system Service Provider Interface LDAP iggLIMS BASE GEMS

protocols reports publications requests raw data

visualization

data analysis

further, it should But going a little bit

life cycle cover the full of information

collaboration support

co-creation

ideation

visualization

documents mine your

knowledge Help to generate new

Antileukoproteinase, Secretory leukocyte protease inhibitor, P03973 uniprot: http://www.uniprot.org/uniprot/P03973 genecards: http://www.genecards.org/cgi-bin/carddisp.pl?id=P03973 dasty: http://www.ebi.ac.uk/dasty/client/ebi.php?q=P03973 >sp|P03973|SLPI_HUMAN Antileukoproteinase OS=Homo sapiens GN=SLPI MKSSGLFPFLVLLALGTLAPWAVEGSGKSFKAGVCPPKKSAQCLRYKKPECQSDWQCPGK KRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLMLNPPNFCEMDGQCKRDLKCCMG MCGKSCVSPVKA

performance evaluate your

Scientific overviews (institutions, groups) Citation analysis Scientific impact and excellence assessment Measurement of the impact of funding and programs on scientific production Identification of scientific experts for conferences, workshops and peer panels organizations.

data deluge! And be prepared for the

Illumina / Solexa Genetic Analyzer Applied Biosystems Roche / 454 Applied Biosystems Genome Sequencer SOLiD ABI 3730XL 3000 Mb/run 100 Mb/run 1 Mb/day

In 2010 available scientific information will double every 72 hours

http://scienceroll.com	101
http://www.webicina.com	30
http://www.slideshare.net	11
http://limslivewire.blogspot.com	3
http://veltsos.gotdns.com	2
http://feedproxy.google.com	1
http://www.netvibes.com	1

Scientific Data Management

by Alberto Labarga on Feb 28, 2009

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Scientific Data Management — Presentation Transcript