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

INFRAFRONTIER-I3 CNR, THE JACKSON LAB, EMMA LABORATORY COURSE ON CRYOPRESERVATION OF MOUSE GERMPLASM Databases for Cryopreservation R. Matteoni. Mouse Mutant Strain Resource Database: different implementations (…). Paper records (paper spreadsheets, index cards, etc.) very cheap

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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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