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BioChem presented by M. Kennedy 10th Annual meeting AZMP Montreal March 18-20.

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Presentation on theme: "BioChem presented by M. Kennedy 10th Annual meeting AZMP Montreal March 18-20."— Presentation transcript:

1 BioChem presented by M. Kennedy 10th Annual meeting AZMP Montreal March 18-20

2 BioChem Steering Committee BioChem the Original Vision – Linkage between datasets BioChem – easy to use? User vs data manager requests AZMP role

3 BioChem National Steering Committee Membership NLGary Maillet MarMary Kennedy GulfRobert Nowlan QueLaure Devine C&A NCRClaude Guay PacTerry Sowden

4 BioChem National Steering Committee Terms of Reference – “Purpose” To provide a forum for input from stake holders/users external to the BioChem development team on the use and evolution of BioChem. To provide a forum for the discussion and prioritization of possible new development and on-going work and ensuring that these items fall within the National Data Management Strategy To provide direction and leadership in innovating and further nationalization of BioChem. To advise the NSDMC on recommendations, priorities, annual work plans, and other issues. To oversee the operation of BioChem, develop work plans, budgets and performance reports as required for submission to the NSDMC.

5 BioChem National Steering Committee Regional Reports 2007 - See appendix… NCR report Major effort directed towards conversion from Oracle Forms to Java BioChem has 2 basic modules The Query Module (used to extract data) The Edits Module (used to load data)

6 New Java Query Application Do you know your userid & password? If you have forgotten …. Contact: Claude Guay at ISDM GuayC@dfo-mpo.gc.ca

7 If you forget the link to BioChem… Do a Google search for AZMP Click on BioChem under SUBJECTS

8 New Java Query Application

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10 How to Guide…

11 BioChem Modifications Not perfect yet… 2006 Workshop Report listed data manager and user requests High priority Medium priority Low priority Major modifications to the existing applications were put on hold until the completion of the Java application. Funding for modifications currently comes thru NSDMC. This funding is not automatic nor is it guaranteed. The steering committee must prepare & submit a LOI/proposal.

12 BioChem National Steering Committee Proposal for 2008-09 Annual meeting of the Steering Committee. Development of a prioritized and costed set of tasks for BioChem support and development for 2009-10 Completion of the Edit module at ISDM. Selected enhancements to BioChem: 1.Facility to control access to CPR plankton data 2.Support for ITIS,,species registers, taxonomic nomenclature verification, etc 3.Changes to Query to return quality flags, etc., and provide the option to not return headers with no data, … 4.Development of functioning modules (tables and coding) for other kinds of data (e.g., continuous) 5.Reword and remap parameter and data type code tables to ensure consistent usage. Produce user manuals 6.Inclusion of a “in what medium” field for the vertical coordinate. Provide on-site training to regions, give presentations and demonstrations of BioChem. Pacific Region stuff…

13 BioChem the Original Vision “Linkage between datasets”

14 BioChem the Original Vision

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16 Documentation & Collaboration Standardized entries Common Mission, Event & Header level

17 Consultation/Collaboration Question #1: Do you need to tie datasets together with an ID or Will a simple temporal/spatial relationship be sufficient? Cruises…. Common MEDS assigned cruise number Events…cruise specific Headers…collector specific

18 Linkage The collector or program should define the “event” not the DM There are several definitions currently used in the Maritimes: MFD groundfish cruises use the term “set”. This is a grouping of everything done at a station at a particular time. Fixed station samples are similiarly grouped – all activities are grouped together under one event. BOS and Lab Sea cruises are different. Each operation is a separate event. Under this scheme a CTD and its rosette bottles would be one event but a net tow would be a separate. Does this matter? Perhaps data managers from AZMP regions should meet?

19 User vs Data Manager requests Data Manager - Load the data 1.Archive the data so that it does not get lost 2.Standardize the fields between operations (CTD/Nets/Acoustics) 3.Retain operation specific info to aid in data interpretation 4.Adopt standard formats & codes –regional/national/international Data User – Extract & Analyse the data 1.Yuk I hate this format! 2.Why do I have headers without data? 3.What do the QC codes mean? 4.Was the data all analysed the same? 5.Were the samples frozen? 6.Where is the CTD profile for this event?

20 User vs Data Manager requests Require Data Manager & User Manuals….

21 BioChem Data Types Definition & User Guide Class (Pigments) Parameter (Phaeophytin) Parameter (Chlorophyll) HolmHansenWelschmeyer Preservation Method Storage Method Sample Handling Method Analysis Method Units AZMP group support the request for production of a “Data Type Guide”? Is AZMP willing to assist by reviewing and providing feedback?

22 Quality Control This slide is not meant to open discussion on data QC... Different regions have different methods and this is OK….(for now) At this point wish to point out: 1.QC codes do exist for BioChem discrete data 2.Only “good” data returned in the existing query application 3.Regional data managers need to discuss code assignment. Is NLs “good” code the same as “IMLs” good code. What about the MEDS QC code? The IODE GE-BICH topic for discussion this fall is QC procedures.

23 Quality Control How do you QC plankton abundance data? Taxonomic Working Group Method to QC the taxonomic nomenclature –Correct/standardize the spelling Inclusion of the taxonomic authority Linkage to synonyms and currently accepted name Creation of taxonomic tree

24 Receive data collection Extract lists of names not in dbase code table Llist of new taxonomic names Is the name in ITIS? Name not in ITISName in ITIS Yes Append to dbase code table Assign TSN_local to ITIS value Is the name in local register? No Contact original source Name Corrected Name Confirmed Add to register Impossible to clarify name Assign TSN_local to -1000 series Yes Append to ITIS Temporarily assign TSN_local to - 7000 series Is the name in local register? No Contact original source Name Corrected Name Confirmed Add to register Impossible to clarify name Assign TSN_local to -1000 series Entire procedure requires long term funding and support for species registers and ITIS List of taxonomic slang List of groups of taxa Assign TSN_local to -5000 series Assign TSN_local to -6000 series

25 Regional Marine Species Registers: cmbcmb Currently four electronic marine species registers exist for the northwest Atlantic. The four areas covered by these registers are the Bay of Fundy, the Gulf of Maine, the Canadian Atlantic, and the northwest Atlantic. The maps below show the bounding box areas for each register. By including links to these registers on the CMB website we hope to to provide regional authoritative and comprehensive lists of names of marine organisms accessible in one location. Publishing the registers on the CMB web site should ensure that the information is accessible to a wider audience. The content of the registers is controlled by regional taxonomic experts, not by database managers or CMB. Each register/list has an editorial management system where each taxonomic group is represented by an expert who has the authority over the content, and is responsible to control the quality of the information. Each of these main taxonomic editors can invite several specialists of smaller groups within their area of responsibility. Links are also included for ERMS (European Register of Marine Species) and WoRMS (World Register of Marine Species) NARMS:http://www.marbef.org/data/erms.phphttp://www.marbef.org/data/erms.php WoRMS:http://www.marinespecies.org/http://www.marinespecies.org/

26 AZMP and BioChem role???

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