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Beth GambleSenior Systems Analyst Jamie WhitacreScience Technology Systems Analyst and Liaison National Museum of Natural.

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Presentation on theme: "Beth GambleSenior Systems Analyst Jamie WhitacreScience Technology Systems Analyst and Liaison National Museum of Natural."— Presentation transcript:

1 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 2 FIMS EMu FreezerPro GGBN Genetic Sampling: from Field to Freezer and Sharing the Data The Big Picture LIMS

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

4 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

5 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 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.

7 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

8 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

9 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

10 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

11 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

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

13 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

14 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

15 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

16 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

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

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

19 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

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

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

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

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

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

25 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

26 26

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

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

29 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 30 Genetic Sampling: from Field to Freezer and Sharing the Data

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

32 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 33 Genetic Sampling: from Field to Freezer and Sharing the Data

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

35 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 36 Genetic Sampling: from Field to Freezer and Sharing the Data

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

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

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

40 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 41 Genetic Sampling: from Field to Freezer and Sharing the Data

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

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

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


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