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INFRAFRONTIER-I3 CNR, THE JACKSON LAB, EMMA LABORATORY COURSE ON

Explore different implementations of the Mouse Mutant Strain Resource Database and its essential features for managing genetic and phenotypic strain data with interconnected packages. Benefit from user-friendly interfaces, data exchange protocols, and integration with other databases.

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INFRAFRONTIER-I3 CNR, THE JACKSON LAB, EMMA LABORATORY COURSE ON

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  1. INFRAFRONTIER-I3 CNR, THE JACKSON LAB, EMMA LABORATORY COURSE ON CRYOPRESERVATION OF MOUSE GERMPLASM Databases for Cryopreservation R. Matteoni www.infrafrontier.euMonterotondoCryopreservationCourse, October20-24, 2014

  2. Mouse Mutant Strain Resource Database: different implementations (…) • Paper records(paper spreadsheets, index cards, etc.) • very cheap • fast data input • slow data query/retrieve/sorting/backup • very 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 input • slow data query/retrieve/sorting • fast data backup • difficult complex queries/autom. connection among ‘DB components’ • difficult multi-user access • difficult automatic error checking • require user training • …

  3. 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 input • fast data query/retrieve/sorting/backup • allow complex queries/automatic connect. among ‘DB components’ • automatic error checking • require user training (building/using input/query interfaces, etc.) • Relational DB Management Systems (DBMS) • very cheap(open source: mySQL …)- or expensive (commerc.: Oracle …) • slower data input • very fast data query/retrieve/sorting/backup • very fast complex queries/automatic connect. among ‘DB components’ • built-in multi-user access • automatic error checking • require dedicated programmer (building input/query interfaces, etc.) • require user training (using input/query interf. and/or query language (SQL …) • optimized for UNIX/Linux OS

  4. Mouse Mutant Strain Resource Database: packages Mutant Strain Stock (live+cryo) … (space for extension) Sanitary Control Shipping (import/export)

  5. Mutant Strain Database: data flow Strain data input Strain data output Manually (web interfaces) MUTANT STRAINS DB automatically (from XML or formatted Excel files)

  6. Mouse Mutant Strain Resource Database: essential features • 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.

  7. Mutant Strain Database: “Stock” model STRAIN

  8. Hardware/Operating SystemsSoftware tools • Testing and Production machines (CNR, EBI): Dell/Linux Sun/SunSolaris Apple 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

  9. INFRAFRONTIER-EMMA Data Curation 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 MRC-MGU, Harwell (UK) M. Fray, S. Ball, J. Kenyon, A. Blake, A.-M. Mellon S. Brown CERBM-GIE ICS, Strasbourg, (F) L. Vasseur Y. Hérault Helmholtz Zentrum-IEG, München (D) M. Hagn, S. Fessele M. Hrabé de Angelis INFRAFRONTIER-I3 is supported by the EU FP7 Capacities Specific Programme

  10. EMMA-RDB: integration with International Mouse DB Resources • 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) • …

  11. 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/KcttB6;D2-Tg(CD4-cre)1Cwi/Cnrm current breeding facility “Cnrm”(CNR, M.rotondo) Allele “(knock-out) targeted mutation 1.1, Andreas Strasser” Transgene “CD4-cre transgene, insertion 1, Christopher B. Wilson” Gene “BCL2-like prot.11(apoptosis facilitator)” Synonym: Bim (Bcl2-interact. mediator) 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) UNIQUE DB strain ID UNIQUE DB strain ID

  12. 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) * MGDgene 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

  13. Practical: database access, retrieving strain data Accessing the INFRAFRONTIER-EMMA strain DB Accessing Integrated International Mouse Mutant DB Resources

  14. Practical: database access, retrieving stock data Using the CNR-EMMAfrozen stock DB Using the CNR-EMMAlive stock DB Using the CNR-EMMAIVF DB

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