Beth GambleSenior Systems Analyst Jamie WhitacreScience Technology Systems Analyst and Liaison National Museum of Natural History Smithsonian Institution Washington, DC Oct 14, Genetic Sampling: from Field to Freezer and Sharing the Data

2 FIMS EMu FreezerPro GGBN Genetic Sampling: from Field to Freezer and Sharing the Data The Big Picture LIMS

Cataloging Samples in EMu, and integrating with FreezerPro 3 Genetic Sampling: from Field to Freezer and Sharing the Data

4 Completed in Spring 2011 in Pod 3 at the Museum Support Center (MSC) in Suitland, MD. Capacity to store over 4 million 2 ml cryotubes containing tissue or DNA. Storage temperatures range from -30°C to - 190°C 58 mechanical freezers 20 liquid nitrogen freezers A walk-in -20°C freezer is also available for short-term (>1 month) storage of unprocessed samples. Genetic Sampling: from Field to Freezer and Sharing the Data The Biorepository

EMu is the system of record. Specimen data is passed to FreezerPro either by creating a new record or linking to an existing record. FreezerPro syncs with EMu and passes back the Biorepository ID, location, and RFID to the Emu record. Genetic Sampling: from Field to Freezer and Sharing the Data

6 Genetic Sampling: from Field to Freezer and Sharing the Data How to Document the Samples in EMu? Early decision to embed different preparations in specimen record preparations grid. Due to extensive addition information needed to document samples and desire to share the sample data individually, the sample needed its own catalog record. What Fields were needed? Extensive compiling of researcher data and existing and emerging standards. Controlled Vocabulary needed for Sample Type hierarchy. Primary sample type had to be synchronized with FreezerPro system. (Blood; Cell; Clone; DNA, RNA, Proteins; Environmental Sample; Excretion & Secretion; Germplasm; Tissue & Parts; Whole Organism) Three level hierarchy created: Primary, Secondary, and Tertiary Sample Type.

In the Catalog module, “Genetic Sample” is selected from the Kind of object field, tab switching on the Genetic Sample tabs to the right of the Catalog tab. 7 Genetic Sampling: from Field to Freezer and Sharing the Data

Genetic Sample 1 tab Contains the Sample type information, voucher information, sample quality and location info, and the link to the Biorepository. 8 Genetic Sampling: from Field to Freezer and Sharing the Data

Genetic Sample 2 tab Contains fields for Embargo information, preservation details, tissue ID numbers, and other numbers, including Genbank numbers. 9 Genetic Sampling: from Field to Freezer and Sharing the Data

Genetic Sample 3 tab Related field groups editable when the Genetic Sample record has a Primary Sample Type of “RNA, DNA, Proteins”, “Cells” or “Clone”. For all other sample types it is read-only. 10 Genetic Sampling: from Field to Freezer and Sharing the Data

Parent or Voucher? Voucher specimen is always the topmost level of the hierarchy, unlike the Parent record, which is the level immediately above. A tissue sample taken directly from a USNM fish specimen is the Child of that object. The fish is both the Parent and the Voucher. A DNA sample taken from the tissue sample is the Child of the tissue. The tissue is the Parent of the DNA sample. The original USNM fish is the Voucher for both the tissue sample and the DNA sample. Children of that DNA sample will have the same Voucher as their DNA Parent, and the tissue as the Grandparent. 11 Genetic Sampling: from Field to Freezer and Sharing the Data

Parent and Voucher links 12 Genetic Sampling: from Field to Freezer and Sharing the Data

Parent /Child Tab Represents the hierarchal relationship of the current record to its Parent and Child(ren) records, and to the Voucher specimen where applicable. 13 Genetic Sampling: from Field to Freezer and Sharing the Data

Genbank Numbers Formerly applied at specimen level, Genbank numbers can and should now be assigned at the lowest level they apply, usually DNA level. GenBank record can be launched directly from the grid via web icon. The bottom grid is read-only and contains the accumulation of GenBank numbers and data from all child records (if any). This grid is automatically populated whenever GenBank data in a child record changes. GenBank numbers of a record’s children, its children’s children etc. will all display in the Child records section. 14 Genetic Sampling: from Field to Freezer and Sharing the Data

Genbank Numbers Genbank numbers can now be assigned at the lowest level sample or specimen they apply to. Numbers should be entered according to NCBI’s standard. 15 Genetic Sampling: from Field to Freezer and Sharing the Data

Genbank Numbers GenBank grid is located on Counts tab for Specimen records. The numbers assigned to Child records appear read only in their Parent. 16 Genetic Sampling: from Field to Freezer and Sharing the Data

Genbank Numbers Clicking the link icon opens the Genbank record in your browser. 17 Genetic Sampling: from Field to Freezer and Sharing the Data

Genetic Sample Menu Creates one or many GS records from existing Catalog records 18 Genetic Sampling: from Field to Freezer and Sharing the Data

Genetic Sample Menu New record(s) can be created from a Specimen or another Genetic Sample. Child(ren) automatically inherit data from Parent. 19 Genetic Sampling: from Field to Freezer and Sharing the Data

Linking Genetics Samples to FreezerPro records via the Biorepository ID 20 Genetic Sampling: from Field to Freezer and Sharing the Data

FreezerPro vial record with data from EMu 21 Genetic Sampling: from Field to Freezer and Sharing the Data

Sharing the Data: Global Genome Biodiversity Network 22 Genetic Sampling: from Field to Freezer and Sharing the Data

23 FIMS EMu FreezerPro GGBN Genetic Sampling: from Field to Freezer and Sharing the Data The Big Picture LIMS

24 Genetic Sampling: from Field to Freezer and Sharing the Data GGBN Data Portal Basic Architecture

Based on GBIF infrastructure –Two systems mainly in use for providers: Integrated Publishing Toolkit (IPT) BioCASE  Transform individual databases into a standard schema Currently only BioCASE in use for GGBN  June 2015 use of IPT enabled for GGBN too  June 2015 BioCASE providers migrated to new schema 25 Genetic Sampling: from Field to Freezer and Sharing the Data

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Pre- Register Generate Template Enter Data ValidateUpload NMNH Field Information Management System (FIMS) 27 Genetic Sampling: from Field to Freezer and Sharing the Data

Pre- Register Generate Template Enter Data ValidateUpload NMNH Field Information Management System (FIMS) 28 Genetic Sampling: from Field to Freezer and Sharing the Data

Pre- Register Generate Template Enter Data ValidateUpload NMNH Field Information Management System (FIMS) 29 Genetic Sampling: from Field to Freezer and Sharing the Data

30 Genetic Sampling: from Field to Freezer and Sharing the Data

31 Genetic Sampling: from Field to Freezer and Sharing the Data

Pre- Register Generate Template Enter Data ValidateUpload NMNH Field Information Management System (FIMS) 32 Genetic Sampling: from Field to Freezer and Sharing the Data

33 Genetic Sampling: from Field to Freezer and Sharing the Data

34 Genetic Sampling: from Field to Freezer and Sharing the Data

Pre- Register Generate Template Enter Data ValidateUpload NMNH Field Information Management System (FIMS) 35 Genetic Sampling: from Field to Freezer and Sharing the Data

36 Genetic Sampling: from Field to Freezer and Sharing the Data

37 Genetic Sampling: from Field to Freezer and Sharing the Data

38 Genetic Sampling: from Field to Freezer and Sharing the Data

39 Genetic Sampling: from Field to Freezer and Sharing the Data

Pre- Register Generate Template Enter Data ValidateUpload NMNH Field Information Management System (FIMS) 40 Genetic Sampling: from Field to Freezer and Sharing the Data

41 Genetic Sampling: from Field to Freezer and Sharing the Data

42 Genetic Sampling: from Field to Freezer and Sharing the Data

43 Genetic Sampling: from Field to Freezer and Sharing the Data

Comments? Questions? 44 Genetic Sampling: from Field to Freezer and Sharing the Data Beth GambleSenior Systems Analyst Jamie WhitacreScience Technology Systems Analyst and Liaison