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

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

3000x

In 2010
available
scientific
information
will double
every 72 hours