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