1. www.infrafrontier.eu Monterotondo Cryopreservation Course, October 20-24, 2014 INFRAFRONTIER-I3 CNR, THE JACKSON LAB, EMMA LABORATORY COURSE ON CRYOPRESERVATION OF MOUSE GERMPLASM Databases for Cryopreservation R. Matteoni

2. 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 … 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 … Mouse Mutant Strain Resource Database: different implementations (…)

3. 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 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 Mouse Mutant Strain Resource Database: (…) different implementations

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

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

6. 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

7. Mutant Strain Database: “Stock” model STRAIN

8. Hardware/Operating Systems Software 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. 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

10. 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 with International Mouse DB Resources

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-Bcl2l11 tm1.1Ast /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

12. Mutant strain nomenclature assignment STRAIN NOMENCLATURE APPROVAL BY NOMEN. COMMITTEE ( MGD-MGI, IMSR) * Proposed full strain name (backgnd(s)-gene1 gene2 ….) (eg: NOD/LtSz-Prkdc scid B2m tm1Unc ) * 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: B2m tm1Unc : 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 “http://dels.nas.edu/global/ilar/Lab-Codes”

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

14. Practical: database access, retrieving stock data Using the CNR-EMMA frozen stock DB Using the CNR-EMMA live stock DB Using the CNR-EMMA IVF DB