www.infrafrontier.eu monterotondo cryopreservation course, october 20-24, 2014 infrafrontier-i3 cnr,...
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www.infrafrontier.eu Monterotondo Cryopreservation Course, October 20-24, 2014
INFRAFRONTIER-I3CNR, THE JACKSON LAB, EMMA
LABORATORY COURSE ONCRYOPRESERVATION OF MOUSE GERMPLASM
Databases for Cryopreservation
R. Matteoni
• Paper records (paper spreadsheets, index cards, etc.)very cheapfast data inputslow data query/retrieve/sorting/backupvery difficult complex queries (“multiple-key search”) very difficult multi-user access (“transactions”) no automatic connection among ‘DB components’ (“multidimensionality”)no automatic error checking (“data consistency”) require user training
• Desktop spreadsheets (“bidimensional”: ‘columns x rows’)relat. cheap (single user, also avail. open source)fast data inputslow data query/retrieve/sortingfast data backupdifficult complex queries/autom. connection among ‘DB components’difficult multi-user accessdifficult automatic error checkingrequire user training
•…
• Paper records (paper spreadsheets, index cards, etc.)very cheapfast data inputslow data query/retrieve/sorting/backupvery difficult complex queries (“multiple-key search”) very difficult multi-user access (“transactions”) no automatic connection among ‘DB components’ (“multidimensionality”)no automatic error checking (“data consistency”) require user training
• Desktop spreadsheets (“bidimensional”: ‘columns x rows’)relat. cheap (single user, also avail. open source)fast data inputslow data query/retrieve/sortingfast data backupdifficult complex queries/autom. connection among ‘DB components’difficult multi-user accessdifficult automatic error checkingrequire user training
•…
Mouse Mutant Strain Resource Database:different implementations (…)
• Commercial desktop DB applications (incl. dedicated animal/sample management software tools)
relat. cheap (single user) - or expensive (multi-user access) slower data inputfast data query/retrieve/sorting/backupallow complex queries/automatic connect. among ‘DB components’ automatic error checkingrequire user training (building/using input/query interfaces, etc.)
• Relational DB Management Systems (DBMS)very cheap (open source: mySQL …) - or expensive (commerc.: Oracle …) slower data inputvery fast data query/retrieve/sorting/backupvery fast complex queries/automatic connect. among ‘DB components’ built-in multi-user accessautomatic error checkingrequire dedicated programmer (building input/query interfaces, etc.) require user training (using input/query interf. and/or query language (SQL …)optimized for UNIX/Linux OS
• Commercial desktop DB applications (incl. dedicated animal/sample management software tools)
relat. cheap (single user) - or expensive (multi-user access) slower data inputfast data query/retrieve/sorting/backupallow complex queries/automatic connect. among ‘DB components’ automatic error checkingrequire user training (building/using input/query interfaces, etc.)
• Relational DB Management Systems (DBMS)very cheap (open source: mySQL …) - or expensive (commerc.: Oracle …) slower data inputvery fast data query/retrieve/sorting/backupvery fast complex queries/automatic connect. among ‘DB components’ built-in multi-user accessautomatic error checkingrequire dedicated programmer (building input/query interfaces, etc.) require user training (using input/query interf. and/or query language (SQL …)optimized for UNIX/Linux OS
Mouse Mutant Strain Resource Database:(…) different implementations
Mouse Mutant Strain Resource Database: packages
MutantStrain
Stock(live+cryo)
Shipping(import/export)
SanitaryControl
… (space for extension)
Mutant Strain Database: data flow
MUTANT STRAINS
DBautomatically
(from XMLor formattedExcel files)
Strain data input Strain data output
Manually(web interfaces)
• Interconnected "Strain" and "Stock” packages: Describe genetic and phenotypic properties of strains and the internal structure of the repository (live animals and frozen sample stocks).
• Strain model: Implementation-independent tool for the establishment and maintenance of biological strain resource databases.Classifies and describes strains with their single/multiple mutations and genetic and phenotypic characteristics.
• User-oriented access interfaces with appropriate protocols and standards facilitating data exchange, database querying and the dissemination of mutant strain resources.
• Interaction with reference databases (EMBL-EBI, Jackson Lab., etc) for assigning, curating up-to-date nomenclature/description of genes/alleles, strains, phenotypes, disease models - in accordance with internationally-accepted standards.
• Interconnected "Strain" and "Stock” packages: Describe genetic and phenotypic properties of strains and the internal structure of the repository (live animals and frozen sample stocks).
• Strain model: Implementation-independent tool for the establishment and maintenance of biological strain resource databases.Classifies and describes strains with their single/multiple mutations and genetic and phenotypic characteristics.
• User-oriented access interfaces with appropriate protocols and standards facilitating data exchange, database querying and the dissemination of mutant strain resources.
• Interaction with reference databases (EMBL-EBI, Jackson Lab., etc) for assigning, curating up-to-date nomenclature/description of genes/alleles, strains, phenotypes, disease models - in accordance with internationally-accepted standards.
Mouse Mutant Strain Resource Database:essential features
Mutant Strain Database: “Stock” model
STRAIN
Hardware/Operating SystemsSoftware tools
Testing and Production machines (CNR, EBI):Dell/LinuxSun/SunSolarisApple Macintosh/OS X (Unix)
DataBase Management System:MySQL 5.x (CNR, EBI)
Application software:Java JDBC (Java DataBase Connectivity), JDBC Drivers (DBMS specific)JSP (JavaServer Pages), PHP (Hypertext Preprocessor)SpringSource
CNR, Monterotondo (I) R. Matteoni, M. Massimi, R. Butler G. Tocchini-Valentini
EMBL-EBI, Hinxton (UK)T. Meehan, G. Koscielny, P. Wilkinson, C.-K. Chen H. Parkinson
CERBM-GIE ICS, Strasbourg, (F)
Helmholtz Zentrum-IEG, München (D)M. Hagn, S. Fessele M. Hrabé de Angelis
INFRAFRONTIER-EMMA Data Curation
INFRAFRONTIER-I3 is supported by the EU FP7 Capacities Specific Programme
MRC-MGU, Harwell (UK)M. Fray, S. Ball, J. Kenyon, A. Blake, A.-M. Mellon S. Brown
L. Vasseur Y. Hérault
DB integration: ENSEMBL (EMBL-EBI), BioMart server MGI-MGD, BioMart server IKMC, BioMart server EUROPHENOME, BioMart server IMSR (MMRRC, MRC, RIKEN, Jackson Lab., etc) IMPC …
other collaborations: INFRAFRONTIER Gmbh (ESFRI Roadmap) EUMODIC, EUCOMM, EUCOMMTools EU FP Projects CASIMIR, CREATE, InfraCOMP EU FP Coord. Actions FIMRE (Federation of Intern. Mouse Resources) OMIM (Human Disease Models, NIH-NCBI) …
EMMA-RDB: integration withInternational Mouse DB Resources
Mutant strain annotation:(some!) nomenclature rules…
Genes, alleles and strains names assigned and reviewed according to interntl. mouse genetic nomenclature rules:http://www.informatics.jax.org/mgihome/nomen
EM:00602 (“bim-/-”) EM:01139 (“CD4-cre”)B6.129S1-Bcl2l11tm1.1Ast/Kctt B6;D2-Tg(CD4-cre)1Cwi/Cnrm
Genetic background (abbrev. symbols):(129S1/Sv ES cells; chimera crossed to C57BL/6, then backcrossed, N≥5)
Genetic background (abbrev. symbols):(B6D2F2 fertil. eggs, backcr. to C57BL/6, N<5)
Transgene“CD4-cre transgene, insertion 1, Christopher B. Wilson”
Gene“BCL2-like prot.11(apoptosis facilitator)”Synonym: Bim (Bcl2-interact. mediator)
Allele“(knock-out)targeted mutation 1.1,Andreas Strasser”
current breeding facility“Cnrm”(CNR, M.rotondo)
UNIQUE DB strain ID UNIQUE DB strain ID
Mutant strain nomenclature assignment
STRAIN NOMENCLATURE APPROVAL BY NOMEN. COMMITTEE (MGD-MGI, IMSR)* Proposed full strain name (backgnd(s)-gene1<allele1> gene2<allele2>….) (eg: NOD/LtSz-Prkdcscid B2mtm1Unc)
* MGD gene symbol(s)/name(s): (eg: Prkdc: protein kinase, DNA activated, catalytic polyp.; B2m: beta-2 microglobulin)
* Allele name(s) (with original producer/laboratory ILAR code):(eg: B2mtm1Unc: targeted mutat. #1 of beta-2 microgl. gene made at Univ of North Carolina)
Search codes at Inst. for Laboratory Animal Research website : “http://dels.nas.edu/global/ilar/Lab-Codes”
* Strain category(ies):(targeted mutation/ transgenic/gene trap/chemically- or radiation- induced, etc.)
* Strain common names* References (Medline/PubMed_ID or other publication ref.) * Other relevant notes/info -- as text
* UNIQUE Strain database ID associated with each strain
Accessingthe INFRAFRONTIER-EMMA strain DB
Practical: database access, retrieving strain data
Accessing Integrated InternationalMouse Mutant DB Resources
Practical: database access, retrieving stock data
Using the CNR-EMMAfrozen stock DB
Using the CNR-EMMAlive stock DB
Using the CNR-EMMAIVF DB