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Merman User Guide - British Oceanographic Data Centre

1. Figure 204 Save Report Save the document to your local computer Close it by clicking the cross in the top right hand corner Document mermanuserguide_9 3_28may2014 Owner IBM Page 58 of 65 ul d alt Wi GA defra at for Environment Food and Rural Affairs ninand Select j Determinand cD n Number Seld Station Number ALL AFBI cadmium ug kg IrishSea_IrSGyreinterme 2007 G ze x Xx Ee l Data Screening Report OD PM GMT 01 wem Do you want to open or save Data_Screening_Report xls 41 5 KB from reports defra gov uk Open CL se JI ancel Figure 21 Save Options Screen There is a bug in Business Objects which occasionally causes the report to close the first time you go to save it to your computer Click the yellow bar at the top of the page to download the report which will take you back to the documents page To overcome this you will have to open the report a second time select the prompts and run the query again You won t have any problems saving the report the 2 time or any report thereafter within the same log in session 4 3 Overview of the MERMAN Database Structure The Business Objects database structure also known as the Universe is a logical grouping of reportable data items The data items are categorised into Classes higher level items and Objects lower level items In general Classes can be compared to database tables and Objects to attributes in a tabl
2. 7 2 List of Competent Monitoring Authorities CMA Description AFBI Agri Food and Biosciences Institute Centre for Environment Fisheries and Aquaculture CEFAS Science Defra Defra Northern Ireland Environment Agency NIEA Formerly DOEM Environment Heritage Services EANat Environment Agency National EANLS Environment Agency National Lab Service EA Llanelli Marine Science Scotland Formerly Fisheries Research MSS Services NRW Natural Resource Wales SEPA Scottish Environment Protection Agency Document mermanuserguide_9 3_28may2014 Owner IBM Page 64 of 65 ul d dy GA S 7 3 Merging Excel spreadsheets A future requirement of the system is to submit Fish Disease data At present the system does not support this In the future once the system has been upgraded users will need to create csv files where the number of records will exceed the Excel limit of 64 000 records This can be done as follows 1 If you need to create a submission file with more than that number of records then you can create the data in several spreadsheets and then combine the CSV files that are generated from the spreadsheets 2 Before you save the spreadsheets as CSV you need to delete the heading rows rows 1 and 2 from the second and subsequent spreadsheets but not the first so that they contain only the data rows Then save each spreadsheet as a CSV file and combine the
3. A meaningful unique station code is constructed by concatenating and abbreviating the region and stratum name and appending the matrix and a number 3 8 6 Adding new fixed stations to the MERMAN station Dictionary Only new fixed stations need to be added to the Station Dictionary A template for adding new stations is available as the last sheet in the station dictionary available at http www bodc ac uk projects uk merman project_specific This must be completed and sent to merman bodc ac uk who will then generate the station codes for you Guidance for completing the new station template e Fields shaded in grey should be completed by selection from drop down lists e The station code must not exceed 25 characters in length and should encompass a full or an abbreviated version of the stratum and region codes within which the station occurs The station name should not exceed 100 characters in length Ensure that there are no spaces after the station code or these will become part of the code e It is the responsibility of each CMA to ensure that proposed new station codes are unique Check the current station dictionary available from SEPA website or contact BODC and coordinate with other CMAs as appropriate e Bounding coordinates should be defined to alert the user if incorrect coordinates have been submitted or the vessel was significantly out of position It is therefore site specific and should be set with some field knowle
4. defr Field Name Submission_type Data_type Analytical_lab_code ICCOD V3 2 ICCOD V2 2 Assigned_value Determinand_code Determinand_units Mean_flag Mean Z_ Score Value Description The type of submission Water Sediment Biota Biology RID AQC AQC Biology PT ICES Data Type code Laboratory or institute responsible for the analysis and measurement of the parameter value or the laboratory responsible for sorting and identification of biological samples Intercalibration codes for 3 2 format Intercalibration codes for 2 2 format Value assigned by Quasimeme as Target concentration of determinand for PT assessment Parameter Code Measurement Units Flags applied to mean field Laboratory result Value assigned by QUASIMEME Ignore this field which is hidden Instructions PT Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled Code as defined by QUASIMEME Code is made up of the QUASIMEME round and exercise number and includes the matrix specific code Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled This field can only contain lt signs Actual value measured by analytical laboratory MERMAN can currently only accept numeric Z scores these are used to calculate a test PASS FAIL which is used in the filter 3 2 4 1 Furt
5. fefrat animathealth gt bcc Welcome hu Zo Home Document List Open Send To Dashboards Help Preferences About Log Ki New Add Organize Actions Search title P vii Jof2 gt 2 All Title Last Run F Type Owner SS ES My Favorites mm AQC_data_cross check Web Intelligence Report Administrator D E Inbox Shows which determinands PASS or F e AQC_final_scores Web Intelligence Report Administrator 0 ES MERMAN Report to identfiy final AQC scores per EI AOC PT report Web Intelligence Report Administrator D Report showing the PT analysis info fc AQC_Results_Tracker Web Intelligence Report Administrator D This report tracks the internal AQC e wi Biology Indices Desktop Intelligence Repc Administrator 0 e Biology_invert_matrix Web Intelligence Report Administrator 0 Matrix shows the abundance presenc d e Contaminants_Biota 11 Sep 2012 16 16 Web Intelligence Report Administrator 2 Allows queries for contaminants in bio Contaminants_Sediment 11 Sep 2012 16 31 Web Intelligence Report Administrator 1 Allows the extraction of contaminant it e Contaminants_Water 11 Sep 2012 16 40 Web Intelligence Report Administrator 2 Shows contaminant data in water an vi Data Screening Report Desktop Intelligence Repc Administrator D CHE wm e e D Total 26 obiects Figure 21 List of Available Reports for CMAs A prompt window will generally pop up asking for further information Enter the required pro
6. MERMAN Business Objects Business Objects can be used to view the data in the MERMAN database Click here to open the Business Objects InfoView Site Opens in new window The following data is available in the MERMAN database lax Macrobenhos Sediments Shel Fish Tew Chemical Contaminant SR EE Figure 13 Defra Portal Click the Choose File button to select your submission file Click OK defro Department for Environment Food and Rural Affairs MERMAN Home File Upload Business Objects Data Submission for Merman Step 1 Ensure you have a data file with your correct email address and having a CSV extension a file name ending with csv Step 2 Select the file by using the browse button Choose File No file chosen Step 3 To upload the selected file click on upload file button Upload File Step 4 Review the message which appears below Figure 14 File Upload Page Document mermanuserguide_9 3_28may2014 Owner IBM Page 41 of 65 defr ul d l Ga X Usoa Fie Once you have selected the input file click on Upload File button You will receive a confirmation message on the screen that the file has been submitted and within an hour of the submission you will receive a confirmation email informing the submitter if the file has been accepted and loaded to MERMAN If you do not receive a confirmation e mail from MERMAN you should assume that your file has NOT been successfully loaded a
7. CRMEV CRMMV Z SC SRCWT score and fields specific to bioassay data must SPECI RLIST ORGSP QCSTAT be entered Example types include Bioassays all mandatory ALABO_2 and CRMSD voluntary CODE Description Data Stage Rules Group FD Fish Disease 1 Document mermanuserguide_9 3_28may2014 Owner IBM Page 31 of 65 ul H Jk Ml GA EP defra IMP Imposex 1 INT Intersex 1 BIOW Bioassay Water 4 BIOS Bioassay Sediment 4 EROD EROD 3 DNA DNAAD 2 MT MT 2 PYR PYR1OH 2 OP Other Parameter 3 protein Other points to note are that at present MERMAN assumes that there will only be one BEAQC intercalibration exercise per year per determinant If this situation changes then some technical changes will have to be made to MERMAN 3 2 7 Sample and Sub sample Guidelines Care must be taken when completing the sample and sub sample fields as transfer to ICES may be compromised Please follow the guideline below for each data type It is mandatory to complete the sub sample field even if sub samples have not been taken as this field identifies the record as being unique in MERMAN In this event 1 should be entered in the sub sample field for the each unique sample 3 2 9 1 Sediment Contaminants Each individual sediment grab collected from a station is considered a sample and should be labelled A B C D E etc Subsequent samples taken from each grab are considered sub samples and should be numbered 1 2 etc For example one su
8. A new sub sample does not require a new sample time as this is the time of the trawl The matrix code can obviously vary within a sub sample as different parts of the fish batch of fish are used for various analyses For example No Sample Sub sample Matrix Species Determinand Individuals Sex Code A 1 LI Limanda limanda HCHA 5 M A 1 LI Limanda limanda CB101 5 M A 1 LI Limanda limanda HCB 5 M A 1 LI Limanda limanda LIPIDWT 5 M A 1 MU Limanda limanda CD 5 M A 1 MU Limanda limanda PB 5 M A 1 WO Limanda limanda MOCON 5 M A 1 WO Limanda limanda LNMEA 5 M A 1 WO Limanda limanda WTMEA 5 M A 2 LI Limanda limanda HCHA 10 A 2 LI Limanda limanda CB101 10 A 2 LI Limanda limanda HCB 10 A 2 LI Limanda limanda LIPIDWT 10 A 2 MU Limanda limanda CD 10 A 2 MU Limanda limanda PB 10 A 2 WO Limanda limanda MOCON 10 A 2 WO Limanda limanda LNMEA 10 A 2 WO Limanda limanda WTMEA 10 B 1 LI Pleuronectes platessa HCHA 10 X B 1 LI Pleuronectes platessa CB101 10 X B 1 LI Pleuronectes platessa HCB 10 X B 1 LI Pleuronectes platessa LIPIDWT 10 X Document mermanuserguide_9 3_28may2014 Owner IBM Page 37 of 65 D DD D w 4 LI LI LI WO 1 WO i ot Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa CD PB MOCON LNMEA WTMEA 10 10 10 10 10 X X X X X Shellfish taken within one area should also be considered as one sample if it is all of the same species H the shellf
9. A0 5 B0 5 B0 5 B0 5 B0 5 Enchytraeidae Paranais litoralis Paranais litoralis 1000 Limnodrilus hoffmeisteri 1000 Paranais litoralis 00 COP 00 3 2 9 3 Water Contaminants If a sample of water is taken by a Bucket or a Niskin each bucket or Niskin is a sample and should be labelled A B C D E Any samples taken from a bucket e g for separate analysis of nutrients chlorophyll metals etc are sub samples and should be labelled 1 2 3 4 etc In the event that there is not sufficient water within one bucket or Niskin for all analysis that are required then samples from a 2 bucket should be considered as being a separate sample On a visit to one station each sample should have a different start time or depth O Document mermanuserguide_9 3_28may2014 Owner IBM Page 34 of 65 ul d wu Wi GA defra Please see note 1 2 on page 18 on the submission of data at stations that have been visited more than once in a monitoring year Contaminants Chlorophyll Nutrients Temperature Water sampler bucket Niskin Salinity Determinand Sample Sub sample CD A 1 HG A 1 ZN A 1 CU A 1 FE A 1 PSAL A 2 TEMP A 2 CPHL A 3 NTRA A 4 NTRI A 4 Document mermanuserguide_9 3_28may2014 Owner IBM Page 35 of 65 q Affairs defr If water is taken by continuous flow then a sample is considered to be taken from a single location depth and within a time re
10. Database Jeira Home Contact Defra Log Ou Marine Environment Monitoring and Assessment National Database The National Manne Monitoring Programme NMMP was established to provide a coordinated approach to environmental monitoring in coastal and estuarine areas MERIMAN contains results of all chemical biological effects assessments for the NMMP performed in the UK from 1990 Data Supplied By England and Wales Scotland D e Environment amp lt gt Cefas C S E P AD 6 FISHERIES RESEARCH Steng a Lal Heritage Service SES Scottish Environment Protection Agency Crown copyright Terms amp condtions Privacy Hep Feedback Department for Environment Food and Rural Affairs Figure 7 MERMAN Home Page From the MERMAN home page the user can select either the File Upload for data submission or Business Objects option for downloading the data Document mermanuserguide_9 3_28may2014 Owner IBM Page 15 of 65 i ov TT yy e D gt EE A 3 Submitting Data 3 1 Obtaining Input Spreadsheets It is important that users always use the latest version of the data input sheet template when preparing their submission The MERMAN Data Manager is responsible for keeping the templates up to date with any changes in the reference data The spreadsheets are available for download from the Defra website Submitters will be informed of updates There are eight different i
11. coordinator of the submissions for any one organisation In smaller organisations it may be the same as the submitter Analytical Year AYEAR The year which the measurements are made in CMA The organization you work in Submission_type This is the template type BEQ for Biological effects Document mermanuserguide_9 3_28may2014 Owner IBM Page 27 of 65 9 defra Deviation of the Measured Mean Biological Effect Measurement BETYPE This is the type of biological effect measurement and once Type selected determines which other fields should be completed see Merman User Guide for details Data Type Measurement is made DTYPE This is the data type which may be biota sediment or water in For most biological effects it will be biota with the exception of bioassays in sediment and water Analytical Laboratory ALABO The analytical laboratory that made the measurements Method of Analysis METOA The analytical laboratory that made the measurements Limit of detection value DETLI Add the detection limit ICES reference for the formula FORML Add here any conversion factors used used in calculation Determinand_Code PARAM Choose the most appropriate method of analysis see MERMAN User Guide for suggestions Unit Of Measurement MUNIT Choose the correct unit of measurement for the parameter Protocol Used REFSK Choose the most appropriate p
12. files using the copy command Example Suppose you create the spreadsheets as CEFAS_Biota_2005_part1 xls CEFAS_Biota_2005_part2 xls CEFAS_Biota_2005_part3 xls The CSV files will be CEFAS_Biota_2005_parti csv CEFAS_Biota_2005_part2 csv CEFAS_Biota_2005_part3 csv Open a command prompt window Click Start gt Run then enter cmd Change to the drive and directory where you have saved the CSV files C cd My documents CSEMP copy B CEFAS_Biota_2005_parti csv CEFAS_Biota_2005_ part2 csv CEFAS_ Biota_2005_part3 csv CEFAS_Biota_2005 csv Document mermanuserguide_9 3_ 28may2014 Owner IBM Page 65 of 65
13. method Help User ID amp password Enter your User ID amp password Digital certificate User ID Forgotten your User ID Password Forgotten your password e When you have finished your online session you should either close the browser or log out e Please do not use the browser back button as it may not function as expected Crown copyright Terms amp conditions Privacy Help Feedback Figure 5 Security Validation Screen The Defra Portal home page opens This will show access to the applications which you have permission to see You should see either File Upload or Business Objects or both Document mermanuserguide_9 3_28may2014 Owner IBM Page 14 of 65 defr def gel Department for Environment Food and Rural Affairs MERMAN Home File Upload Business Objects Reporting and Viewing Data using Business Objects MERMAN Business Objects Business Objects can be used to view the data in the MERMAN database Click here to open the Business Objects InfoView Site Opens in new window The following data is available in the MERMAN database Matix Wacrobenthos Sediments Shell Chemical Contaminant SSES bo ll 1999 current Figure 6 Defra Portal Home Page Selecting MERMAN Home opens the MERMAN home page je Upload Business Objects q defra WA Llywodraeth Cynulliad Cymru Welsh Assembly Government Marine Environment Monitoring and Assessment National
14. o access the Marine Environment Monitoring and Assessment National Database een ee lt lt lt 909 5959454499499 Oooo n Internet Explorer browse to http caratest2 defra gov uk wps portal Be Defra Portal Homepage will appear a Click on the Log on to Defra link from the menu on the left hand side of the screen a Security Validation Page will appear EB nter your Government Gateway User ID and Password You must already have access to Defra Portal Applications 6 Click Login ou have now logged on to the Defra Portal 8 ick on the bere link within the Applications Home Page on the right hand side of the screen 9 Click on the MERMAN Marine Environment Monitoring and Assessment National Database link to enrol for access to the Marine Environment lonitoring and Assessment National Database Document mermanuserguide_9 3_28may2014 Owner IBM Page 13 of 65 ul d ul Ml GA defra Figure 4 Email Containing Instructions for Accessing MERMAN 2 3 Logon to MERMAN Normal Logon When the user has enrolled for both the Defra Portal and MERMAN application the user will be able to use the normal logon procedure from therein Follow this link to the Defra Portal https secure services defra qov uk wps myportal merman Enter User ID and password in the screen below Department for Environment Food and Rural Affairs Defra Login New user Register Please choose your log in
15. pass the filter i e deemed to be of a good enough standard are transferred to ICES and are viewable by the public on request Those data that fail the data filter remain in the database however are only seen by the submitters CMAs are able to view their QC data alongside the sample data to see where improvements need to be made The filter takes into account several aspects of internal QC for instance whether a lab is accredited the grade of reference material and the precision of the technique used The lab is scored for each aspect of the QC process for each determinand Internal QC contributes 70 to the final score and external PT contributes 30 It is therefore feasible for a lab to pass a determinand if there is only internal QC supplied The final score is out of 100 and a pass is given to determinands over 40 or 45 depending on their type e g organics or metals The sample data and the AQC are linked via the analytical laboratory code supplied in both the sample and the AQC input sheets If these codes are inconsistent with each other the sample data won t have any QC data attached to it and will therefore not pass the filter Labs must make sure that the analytical codes submitted are correct When analyses have been subcontracted out to another laboratory it is the responsibility of the analytical laboratory to submit the QC data to MERMAN if they are an official CMA However it is also important that the sample data inp
16. per the drop down menu when macros are enabled Document mermanuserguide_9 3_28may2014 Owner IBM Page 25 of 65 defr H Field Name Analytical_lab_code Determinand_code Determinand_units BIO_AQC_status METOA METCX METPT DETLI CRMMV CRMSD Description Laboratory or institute responsible for the analysis and measurement of the parameter value or the laboratory responsible for sorting and identification of biological samples Parameter Code Measurement Units Status of the AQC data Method of analysis Method of chemical extraction Method of pre treatment Detection limit value of analysis Reference material mean value found Reference material s standard deviation standard deviation Instructions Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled For abundance and biomass the status will be assigned by NMBAQC group If auto passing chemistry determinands this should be set to PASS Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled This value should be the measured limit of detection not the target limit of detection as defined by NUCAG All sample results should therefore be great
17. the regions they represent This document details an agreed protocol for naming monitoring stations in MERMAN Ideally the protocol should have a clear connection between sampling design data storage and data analysis However the protocol also needs to cope with drivers such as the Water Framework Directive WFD and Charting Progress and is thus something of a compromise It will be suitable for assessing our monitoring data but will require some post processing of data There are three main elements to the protocol 1 UK territorial waters will be divided into regions and strata Regions are aligned with the regional seas used for Charting Progress and strata are aligned with WFD water bodies Thus all CSEMP data can be allocated to a region and a stratum 2 All samples will be allocated to a sampling strategy that describes the method of data collection Four main sampling strategies are recognised in the CSEMP fixed station stratified random and stratified fixed and opportunistic monitoring However the difference between them is sometimes ambiguous so rules are proposed to clarify things 3 Each station name must be unique for ICES reporting purposes there is no concept of a region of stratum in the ICES database The station field is a character string with at most 20 characters The protocol is developed by way of examples using Scottish monitoring data 3 8 2 Regions and strata Document mermanuserguide_9 3_28may2014 O
18. unit Instructions enabled The type of station e g se wa fi sh has been appended to the number See Note 1 4 Format dd mm yyyy Format HH MM 24HR Format HH MM 24HR Format decimal degrees For example 52 0830 Format decimal degrees For example 6 536 Please refer to section 3 2 7 for detailed information on how to fill in this field Please refer to section 3 2 7 for detailed information on how to fill in this field At laboratory s discretion Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled This year links to the AQC information of the same year not necessarily the same as the sampling year if analysed later Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled Basis Status of weight measurement Codes as per the drop down menu when macros are enabled Document mermanuserguide_9 3_28may2014 Owner IBM Page 19 of 65 defr H Instructions See Note 1 5 Description Dependent on detection limits Actual value measured Field Name Determinand_qualifier Determinand_value Water_sample_depth Value in metres m where sample is taken Sediment depth m upper lower levels in sediment For sediment the upper level is generally Om i e ground level Sediment_depth_Upper Low
19. 6 Bioeffects AQC Input Template 27 3 2 7 Sample and Sub sample Guidelines 32 3 3 Saving SUBMISSION Fil js sdesded egae etZuncedeEeEer et EdEERS Ee devans coyadedscdesaans ce suddeaecesine airian waai 39 34 Uploading Dia TEE 40 3 4 1 Confirmation of SUBMISSION s at N a a a aaa a 43 239 Handing BCEE 43 36 Releasing Dla eericarenee E E S EA E E ESEE 44 3 7 Submission Checks by Responsible Officers cccccceeeceecneeeeeeeceeeeeeeaeeeeaeeseeeeeseaeeesaeeeeaaeeeeees 45 Document mermanuserguide_9 3_28may2014 Owner IBM Page 5 of 65 ul d dy GA defr 3 8 Station naming and new station submissions The protocol for naming monitoring stations in MERMAN oercciecetet saccades ehdcdysenegands a a cies sucduadeese cua a aa a aa 46 4 R nning Cen 54 4 1 Using Business Objects 0 0 c cece ceececeeece cece eeeeaeeeeeeeeeeeeeceaeeeeaaeseeaeeseaeeesaaesseaaesdneeseaeessaeeseaaeeseees 54 4 2 Running Standard Reports ccccccceecececeeeeeeeeeeeeceeeeecaeeeeaaesseneeseaeeesaaeeesaaesseeeeseaeeeseaeeseaaeeeneees 54 4 2 1 Downloading Java Runtime First Time Logon to Business Objects cccceseeeeeeeees 54 4 22 tee 58 4 3 Overview of the MERMAN Database Structure c cccccceeceeeeeneeceeeeeceaeeeeeaeeeeeeeseaeeesaeeseaaeeennees 59 Do CU eege eebe eegene 61 51 e EE 61 5 2 Defra Portal Seege deeg eege eege Eege died diane 61 5 3 Business Objects SOCUIILY i 0cisssescsavscecisdessescctase
20. A PARAM For use with biological effects measurements MUNIT REFSK ACREED when an intercalibration exercise possibly INTAQC CONCH INTSCH ICCOD QCSTAT all mandatory ALABO_2 informal and so not registered with ICES has voluntary CRMEV CRMMV been performed but the results to not conform to CRMSD Z_SC SRCWT SPECI be able to provide expected measured value sd RLIST ORGSP shuld be blank of measured value and z score Example types include fish disease imposex intersex 2 DTYPE ALBO_1 METOA PARAM For use with biological effects measurements MUNIT BE ACREED when an intercalibration exercise is not INTAQC QCSTAT all mandatory S ALABO_2 CONCH INTSCH established but is envisaged that results for ICCOD CRMEV CRMMV CRMSD expected measured value and z score may Z_SC voluntary SRCWT SPECI become possible to enter in the near future PLIST ORGSR Should beblank Example types include DNAAD MT PYR 3 NT Ce PARAM For use with biological effects measurements INTAQC CONCH INTSCH ICCOD when an intercalibration exercise is established CRMEV CRMMV GRMSD z sC and it is suitable for results for expected QCSTAT all mandatory ALABO_2 measured value and z score to be entered voluntary SRCWT SPECI RLIST Example types include EROD and Other ORGSP should be blank 4 Gate EC ee PARAM For use with bioassay measurements where INTAQC CONCH INTSCH ICCOD results for expected measured value and z
21. AQC Status of Passed AQC data not available to the Public Document mermanuserguide_9 3_ 28may2014 Owner IBM defr Affairs Page 62 of 65 6 How to Get Help Support for submission and access to MERMAN is provided by the MERMAN Data Manager MERMAN Data Manager MERMAN Management Team British Oceanographic Data Centre Joseph Proudman Building 6 Brownlow Street Liverpool L3 5DA Tel 01517954861 Fax 01517954912 e mail merman bodc ac uk Document mermanuserguide_9 3_ 28may2014 Owner IBM defr Page 63 of 65 ul d dy GA defr Affairs 7 Appendices 7 1 List of Abbreviations Abbreviation Description AQC Analytical Quality Control BEAQC Biological Effects Analytical Quality Control group BECME Biological Effects of Contaminants in the Marine Environment BODC British Oceanographic Data Centre CMA Competent Monitoring Authority CSEMP National Marine Monitoring Program DASSH UK Archive for Marine Species and Habitats Data EMODNET European Marine Observation and Data Network for chemistry chemistry ICES International Council for Exploration of Seas LoD Limit of Detection MERMAN Marine Environment Monitoring and Assessment National Database NMCAG National Marine Chemistry AQC Group PT Proficiency Testing QUASIMEME Quality Assurance of Information for Marine Environmental Monitoring in Europe RID Riverine and Indirect Discharges
22. ICES code must be used and is shown in yellow All latitude and longitudes to use WGS84 datum All latitude and longitudes decimal degrees e g 56 2675 3 1534 1 2 3 4 5 6 if 8 3 10 H 12 13 4 5 16 1 18 19 M 4 HA Water Nutrient Chlorophyll Reference Data Ready Figure 9 Sample Data Input Sheet The input file has two sheets the data entry sheet and the reference data sheet that contains the look up values for the drop down lists These will be updated by the Data Manager in accordance with the Green Book and ICES requirements and therefore it is important to always use the latest version Note the macros within the Input Spreadsheet only work with MS Excel version 2000 or greater If you are using a version of MS Excel which is lower than 2000 if the drop down is used to populate the cell the description relating to the code selected will need to be removed manually Populating the input sheet e Orange cells MUST be filled in They require mandatory information Without these the spreadsheet will be rejected by the system 3 2 1 Sample Data Input Sheets Field Name Description Instructions Submitter_email_address Email address of the person The consequent email detailing Document mermanuserguide_9 3_28may2014 Owner IBM Page 17 of 65 defra Description submitting data into the NMMP database Field Name Email address of the CMA business owner Re
23. SF Forth Middle Forth Estuary Forth_MiddleEst_se03 1 SF Forth Middle Forth Estuary Forth_MiddleEst_se04 1 Document mermanuserguide_9 3_28may2014 Owner IBM Page 49 of 65 DI III A D A A et in Aa DN Stratified random monitoring five sediment samples taken at random from the mud in the Minch North water body different locations each year The station and the stratum are effectively the same Note how all samples come from the same station In contrast to the previous example there is no link between sample 2 in one year and sample 2 in the next year except that they come from the same water body strategy region stratum name sample SR West Scottish Coast The Minch North WSctCst_MinchN_seO1 1 3 SR West Scottish Coast The Minch North WSctCst_MinchN_se01 2 SR West Scottish Coast The Minch North WSctCst_MinchN_se01 3 SR West Scottish Coast The Minch North WSctCst_MinchN_se01 4 SR West Scottish Coast The Minch North WSctCst_MinchN_se01 5 5 As before but suppose there is also a fixed station sediment monitoring site in the water body with three samples taken per year strategy region stratum name sample SR West Scottish Coast The Minch North WSctCst_MinchN_seO1 1 SR West Scottish Coast The Minch North WSctCst_MinchN_se01 2 SR West Scottish Coast The Minch North WSctCst_MinchN_se01 3 SR West Scottish Coast The Minch North WSctCst_MinchN_se01 4 SR West Scottish Coast The Minc
24. T Submitting Organisation FRS Submission Date 02 05 2006 Submission Time 14 12 Submitter Email liisa stuart uk ibm com Detailed Error Report Error 3014 Row 47 Invalid Latitude 57 8837 Error 3014 Row 48 Invalid Latitude 57 8837 Error 3014 Row 49 Invalid Latitude 57 8837 Error 3014 Row 50 Invalid Latitude 57 8837 Error 3014 Row 51 Invalid Latitude 57 8837 Error 3014 Row 52 Invalid Latitude 57 8837 Error 3014 Row 53 Invalid Latitude 57 8837 Error 3014 Row 54 Invalid Latitude 57 8837 Error 3014 Row 55 Invalid Latitude 57 8837 Error 3014 Row 56 Invalid Latitude 57 8837 Error 3014 Row 57 Invalid Latitude 57 8837 Error 3014 Row 58 Invalid Latitude 57 8837 Figure 18 Error Report The error report will help you to locate the error in the submission file and gives you the field where the error is in this example the Latitude is not correct At first the error list can be daunting but the situation is usually better than it looks You will find that once the common errors have been corrected e g units of measurement station numbers etc the volume of errors decreases substantially When the errors have been corrected in the input sheet you can re submit the data using the same procedure as before saving the data file as an updated version by appending the original filename As well as this resend the file to the Data Manager merman bodc ac uk 3 6 Releasing Data When
25. aken Sample_depth_max MXDEP Maximum depth of sample m Value in metres m Species SPECI Latin name of species or Codes as per the drop down aggregated genus family menu when macros are enabled Stage_development STAGE Stage of development Codes as per the drop down menu when macros are enabled Sex SEXCO Codes as per the drop down NN menu when macros are enabled Species_group_size Codes as per the drop down menu when macros are enabled Physical_state ASTSA Physical state at time of Codes as per the drop down sampling menu when macros are enabled Sampler_Area Insert the area of sediment Value in cm2 sampling gear Identification_type Shows Identification level e g Codes as per the drop down Genus menu when macros are enabled Abundance VALUE Number of organisms found In This must be filled However if sample the number cannot be physically counted the following column Abundance code must be filled instead Abundance_code PARAM SACFORP code e g P for Codes as per the drop down Presence menu when macros are enabled Used when the physical number of the species cannot be counted This must be filled if there is no value in abundance Biomass_dry_weight VALUE Biomass_wet_weight VALUE Biomass_ash_free_dry_weight Value measured VALUE 3 2 3 Chemistry Contaminants AQC Input Sheet Field Name Description Instructions CMA Competent Monitoring Auth
26. anuserguide_9 3_28may2014 Owner IBM Page 54 of 65 ul Ill mal Ml GA defra and Rural Affairs Instructions Log on to Business Objects gt SAP BusinessObjects InfoView Log On to DEFRA FARMING ONLINE MERMAN Business Help Objects Enter your user information and click Log On If you are unsure of your account information contact your system administrator User Name 1C bunt Password eeeeeeeee Figure 19 Log in Page Select Document List Lei animathealth f gt hen Welcome hun E Home Document List Open Send To Dashboards Help Preferences About Log Oy gt Welcome c_hunt Navigate Personalize View your Inbox Favorites or Document Lists Use the Help to learn Change your InfoView start page viewing options and preferences more about InfoView for daily tasks SC Document List BS Preferences JEC My Favorites G My Inbox Information OnDemand Services 2 Help Figure 20 Select Document List Document mermanuserguide_9 3_28may2014 Owner IBM Page 55 of 65 Department for r Environment Food and Rural Affairs defr Click on Public Folders gt MERMAN a list of available reports appears Nb the number of reports available to each user will depend on which category of user they are assigned see section Security Double click the desired report
27. ceccecceceeeeeeeee eens ee eeaeeeeeeeeeeeeeceaeeeeaaeedeaeeseeeeseaesseaaeseeeeeseaeeeeaeeneneeee 8 1 4 The UK National Marine Reporting Cycle cccccecceeeeeeeceeeeeeeeeeeeeeeeeeeeeeaeeeeaeeseeeeeseaeeesaeeneneeee 9 1 4 1 Submission Timetable er kas ieseect ieee dees a age ied eevee added ended 9 1 5 Quick Reference Guide for Data Submission Process A 10 Be EE 11 2 1 Requesting Access to MEDMAN AAA 11 2 1 1 User Details KNOWN Facts AA 11 2 1 2 REMOVING UTC 12 2 2 Logon to MERMAN First Time User 12 2 2 1 EIERE EE a E 12 2 2 2 Enrol tor KEE CEET 12 2 2 3 ENOHOnMERMAN coi seghc cod baie cab cd ec cy Sone cence ob bee cede op daa es eaepied ab deepest eda ce eae ceeee ses 13 2 3 Logon to MERMAN Normal Logon eeeseceeeeneeeeeeenneeeeeeaaeeeeeeaaeeeeeeaaeeeeeeaaeeeseeaeeeseenaeeeenenaes 14 3 Submitting RE 16 3 1 Obtaining Input Spreadsheets ssseeseeeseeeeenesi nesi resknssinestnesinsstnssinnttinstinstnnttnnannnntnnntnn nenn nenn nenn nnt 16 3 2 Populating Input Spreadsheets AA 16 3 2 1 Sample Data Input Gheete AA 17 3 2 2 Biology Input Sheet cee eeceeesceceeeeeceeeeeeaeseeneeecaeeecaaeegeaaeeeeeeeseaeeseaaeseeaeeseeeeesaeseeaeeseneeee 20 3 2 3 Chemistry Contaminants AQC Input Sheet ecccecceceeeeeeeeeeeceeeeeaeeeeeeeseeeeesaeeesaeeeeeeeee 21 3 2 4 Chemistry Contaminants PT Input Sheet cceccceceeeeeeeeeeeeeeseeeeeeeaeeeeeeeseeeeescaeeesaeeeeeeeees 24 3 2 5 Biology ele 25 3 2
28. dge e Station bounding box limits should be defined by the CMA An acceptable range of coordinates appropriate for each particular station should be identified and chosen to ensure all samples are included so if in doubt chose a larger range e Leave the WLTYPE field blank this will be completed for you e The minimum year is the year when sampling started at that station e Leave the maximum year of sampling blank if sampling is ongoing e All lat and longs to be in decimal degrees to a maximum of 5 decimal points e Ifthe ICES Rectangle is not known then leave blank e See MERMAN User Guidance section 3 8 for further details on sampling strategy Document mermanuserguide_9 3_28may2014 Owner IBM Page 52 of 65 ul d wu Wi GA defra 3 8 7 Generating opportunistic station codes BODC hold the master GIS file for strata and regions from which opportunistic station names can be generated from lat and long pairs CMAs should send a vs or csv file to BODC who will complete the analysis and will aim to send it back with the opportunistic station names within a few days The station dictionary is available for download from http www bodc ac uk projects uk merman project_specific Document mermanuserguide_9 3_ 28may2014 Owner IBM Page 53 of 65 ul d dn GA defr Affairs 4 Running Reports 4 1 Using Business Objects Business Objects is a web based reporting package that allows users to run standard r
29. e However the database table structure does not limit the grouping of data items into Classes There can also be several levels of Classes and Sub classes The proposed MERMAN Business Objects Universe is categorized as follows The seven categories are e Metadata o Information about the data in the database such as subject name and address of distributor geographic coordinates of the data e Which location o Examples of fields that can be selected for reporting are Latitude longitude region e Which measurements o Determinand Code Species Results e What matrix o Matrix RID Discharge type e Date Time of sample Document mermanuserguide_9 3_28may2014 Owner IBM Page 59 of 65 defra ul H Il i GA e Additional search criteria o Al other data elements that aren t stored in the other folders such as Submission details sample reason sampler type e AQC o Details of AQC and PT data submissions and results The Universe window has three panes e All Objects that can be selected for a query e Result pane that displays results of the query e Query Filter pane the query can be filtered WEBINTELLIGENCE A DE S P Eoit ouery E Edit Report Run Query D Query ees Bj Add Query sft Data Properties Result Objects To include data iNthe report select objects in the Data tab and drag them here Click Run Query R3 Metadata Fi return the data to th report Which
30. e Contaminant and biology data submitted to ICES by 1 September e RID data submitted to MERMAN by March e RID data submitted to OSPAR by 1 October outside of MERMAN scope 1 4 1 Submission Timetable Description of Deadline Responsible Deadline Date Organisation Final date for submission of new Station requests to CMAs 10 March BODC and for requests for new Parameter codes CMAs should inform BODC of any new parameters they are intending to submit by this date BODC need to be made aware of any parameters that CMAs intend to submit AQC for that previously had no AQC Any new parameters need AQC constraints assigning and these have to be decided by NUCAG Release of new templates for sediment water and biota BODC 15 March Deadline for submission of NEW Reference Material CMAs 15 April forms to BODC After this date ICES will not register new codes for reference materials and data against those parameters will not be able to be submitted Release of new templates for AQC PT Biology AQC and BODC 1 May BEAQC Advise on any new requirements for those templates and in particular the approach for BEAQC submissions Final date for delivery of MYEAR sample and AQC data CMAs 1 June to MERMAN These data should have been screened using the data screening and AQC checking reports in Business Objects and unheld by the Responsible Officer MYEAR Data delivered to BODC after this date will not be included in the s
31. e bar above the spreadsheet Bioeffects Parameter Method of Analysis Protocols REFSK type METOA EROD EROD FLM Fluorometric T23 Times No 23 determination Determinantion of CYP1A dependent mono oxygenase activity in dab by fluorimetric measurement of EROD activity DNA DNAAD To be confirmed by BEAQC T25 Times No 25 Measurement of DNA adducts in fish by 32P postlabelling MT MT To be confirmed by BEAQC T26 Times No 26 Quantification of metallothionein MT in fish liver tissue PYR PYR1OH To be confirmed by BEAQC T39 Times No 39 Review of Possibly FLM Fluorometric analytical methods for determination determining metabolites of polycyclic aromatic compounds PACs in fish bile Document mermanuserguide_9 3_28may2014 Owner IBM Page 29 of 65 defr IMP and INT VDSI RPSI IMPF GRS Gross examination T24 Times No 24 Use of LNFPE imposex in the dogwhelk Nucella lapillus as a bioindicator of tributyltin TBT pollution Bioassay MORT PNR To be confirmed by BEAQC T11 Times No 11 Oyster Water REDF Possibly CMP Crassostrea gigas embryo Comparative analysis bioassay Bioassay MORT PNR and To be confirmed by BEAQC T29 Times No 29 Sediment Sediment REDF Possibly CMP bioassay using the polychaete Comparative analysis Arenicola marina Bioassay MORT PNR and To be confirmed by BEAQC T28 Times No 28 Corophium Sediment REDF P
32. e benthic invertebrate data submission are ABUNDANCE and BIOMASS Example ABUNDNR BMDRYWT BMWETWT BMAFDWT MMP Database Submission optional fields in white text 1 2 3 4 5 6 T 8 9 5 10 11 4 Figure 10 Biology AQC Input Sheet This input sheet is also used for those determinands from other data types which do not currently have an AQC programme for instance temperature nitrate dissolved oxygen length and weight measurements This is because in order for data to be transferred to ICES a determinand has to have a status of PASS In order for CEMP determinands which do not have AQC to be transferred they should be added to this biology AQC input sheet to get an automatic PASS status Please note that a determinand may still pass the data filter if it just has AQC information but is not in the QUASIMEME scheme i e has PT data The pass threshold remains the same however the maximum score that can be achieved is 70 with AQC alone In these instances the AQC information for these parameters should still be submitted to MERMAN If the parameter is automatically set to pass via the Biology AQC template the sample data for that parameter may be downgraded in ICES assessments due to the lack of associated AQC data for that parameter Field Name Description Instructions Submission_type The type of submission Water Sediment Biota Biology RID AQC AQC Biology PT Data_type ICES Data Type code Codes as
33. ed EI a sample taken at random from a fixed station a pre defined usually small area within a strata stratified random SR a sample taken at random within a strata stratified fixed SF a sample from one of a network of fixed stations that give good coverage and are representative of a strata opportunistic OP a catch all for other sampling strategies Historically most CSEMP data would come from fixed stations based on the same time same place monitoring mantra Stratified random and stratified fixed will be reserved for data that come from core CSEMP monitoring activities and have been designed accordingly At present this will be restricted to contaminants biology and effects in sediment and maybe some fish and nutrient monitoring Sometimes there are several fixed stations in a stratum that have not explicitly been chosen to give good coverage and be representative of the stratum Examples include imposex stations around a harbour or shellfish sites chosen for various EU directives It is tempting to regard these stations as if they had come from a stratified fixed sampling programme However this leads to confusion and ambiguity The simplest and correct approach is to treat the stations as separate fixed stations It is intended at the analysis stage to see if there are common trends at these stations i e combine information across stations within strata and adjacent strata This would involve the same sort of a
34. eir organisation Note 1 3 Only data that has a Sample Reason 1 2 or 3 of CEMP will be transferred to ICES For biota sediment and biology data the codes CEMP and NATL should be used in Sample Reason fields 1 and 2 For CW data the codes CEMP EMP should be used in Sample Reason fields 1 and 2 NMP is now an obsolete term and should not be used If data submitted are to be used for national purposes only then the code NATL should be entered in Sample Reason 1 Note A Opportunistic stations are suitable for both spatial purposes and biological effects purposes and all water opportunistic stations also suitable for eutrophication purposes Thus the only difference will be that the opportunistic stations are spatial whereas the original stations are temporal Submitter should reflect these facts in their submissions to MERMAN in the Sample Purpose field Note1 5 Where measured results are below the detection limit reported in the AQC submission sheet the best option is to select QFLAG lt and set the RESULT DETLI 3 2 2 Biology Input Sheet Field Name Mesh_size MESHS Sample_depth_min MNDEP Description Mesh size of net or sieve Minimum depth of sample m i e the sediment bed from Instructions 500um or 1000um Value in metres m Document Owner IBM mermanuserguide_9 3_28may2014 Page 20 of 65 j Affairs where grab is t
35. ent 2008 current PT eme CC Se Biological Community Abundance 1988 current Biomass Ge This table will be updated as more data are added to the system Figure 1 MERMAN Components 1 3 Scope of this User Guide This user guide covers the following aspects of using the MERMAN database e Gaining access e Using the input spreadsheets e Loading data e Releasing data e Running standard reports e Managing reference data e How to get help This user guide does not give detailed instructions in using the Business Objects reporting package as it is assumed that the users will attend a specific training course where they are provided with Business Objects training material This document should be used in conjunction with the Green Book this user guide gives instruction on using the MERMAN system the Green Book instructs on the sampling policies and procedures Please refer to the Green Book http www cefas defra gov uk publications and data scientific series qreen book aspx A link can also be found from the BODC website www bodc ac uk projects uk merman project_specific Document mermanuserguide_9 3_28may2014 Owner IBM Page 8 of 65 9 Affairs S 1 4 The UK National Marine Reporting Cycle The Clean and Safe Seas working group sets the annual deadlines for data submissions to MERMAN The deadlines for reporting the annual data to ICES are as follows e Contaminant and biology data submitted to MERMAN by 1 June
36. ent view EJ Ga bas J 4 ft Jae gt m Edit lt Refresh Data Data Screening Report Date Last Updated 05 08 2013 CMA AFBI Data Type Contaminants and biological effects in biota data Matrix ALL Determinand cD Station Number ALL AFBI cadmium ug kg 2007 201 x Xx anos E Data Screening Report Figure 193 Report Results Screen Document mermanuserguide_9 3_28may2014 Owner IBM Page 57 of 65 RK defra Department for Environ Food and Rural Affairs Refresh this button takes you back to the Prompts window and you can re run the report Close if you don t want to save the report simply close the report window 4 2 2 Saving Reports When you want to save a report go to the Document menu at the top left corner of the screen Document gt Save to my computer as gt File format hefro animalhealth SA Welcome Home Document List Open Send To Dashboards Help Preferences About D Save Save as 05 08 2013 3 Matrix Select one ol Data d Contaminants and biological effects in biota data ALL Save to my computer as a Save report to my computer as 4 Matrix ALL 4 Determinand Select cD Determinand cD 5 Station Number Sel Station Number ALL ALL AFBI cadmium ug kg 2007 zoo x x I p eee
37. eports as well as easily build their own tailored reports which allow them to extract the quality assured data from the database This user guide does not give detailed instructions in using the Business Objects reporting package as it is assumed that the users will attend a specific training course where they are provided with Business Objects training material The MERMAN Data Manager will also be able to assist in using Business Objects For further help with starting up and using Business Objects BODC have written a manual which can be found on the BODC website http www bodc ac uk projects uk merman project_specific Business Objects User Guide pdf 4 2 Running Standard Reports There are an infinite number of ways in which the data held in MERMAN can be extracted However there will be many users who require the same kind of data report These standard reports have been created so that users do not need a detailed knowledge of Business Objects to extract and use the data Once the report is run the data can be downloaded to Excel or other formats of the user s choice 4 2 1 Downloading Java Runtime First Time Logon to Business Objects When you first logon to Business Objects it is likely that you will be asked to download the Java Runtime Environment Follow the on screen instructions to download this software to your machine Once this software is downloaded you will be able to access Business Objects Document merm
38. er Note 1 1 ICES define the Monitoring Year as the nominal year of sampling for a given monitoring programme For some internationally coordinated monitoring programmes sampling reporting of data and data assessment activities are based on an annual sampling programme However it is not always possible to complete the necessary sampling in the nominal sampling year winter sampling may continue into the early part of the following year Thus the Monitoring year entry will in most cases be identical with the year component of the Sampling date SDATE data field e the year in which the sample was collected However it may be that in some cases the year reported in the Sampling date will be the calendar year after Monitoring year entry for instance with nutrient data Note 1 2 The programming for the creation of the ICES report means that the cruise code must be different on each occasion that a station is visited in one monitoring year For sediment submissions this will not be an issue as in most instances a station is visited just once per year However for biota and water submissions some stations are visited on a number of different dates in one monitoring year If necessary the cruise code must be changed to be different on each sampling date In past cases some CMAs have added a suffix to the cruise code to overcome this problem while still linking to the original cruise code used within th
39. er than this detection limit Mean value calculated Taken from reference certificate 3 2 5 1 Further Biology _AQC Submission Information It must be remembered that both the biology determinands abundance biomass and those chemistry determinands temperature salinity for which there is AQC are submitted in the same Biology AQC sheet per CMA It is often the case that Biology AQC values come through later in the year than those from the Chemistry AQC It is possible to submit the determinands you have initially adding any later Document mermanuserguide_9 3_28may2014 Owner IBM Page 2 6 of 65 q H defr determinands to the bottom of the same sheet for resubmission This prevents any AQC data being overwritten in the database Communication between biology submitters and chemistry submitters is key BODC has recently upgraded the Biology_AQC template to allow for a greater amount of information to be submitted This has been driven by new ICES requirements for additional information at assessment All chemistry contaminants should be submitted with an associated uncertainty value and analytical methods are required for all determinands Previously the Biology AQC template did not store any of the above information BODC have therefore added 6 new fields to the template The input rules are as follows Uncertainty fields Uncertainty values are currently only required for chemistry parameters Please fil
40. eviation standard deviation SDNO Standard Deviation number of Number of measurements used measurements to establish std devn for control chart limits CRMWN Number of breaches of warning limits during period for which limits apply Document mermanuserguide_9 3_28may2014 Owner IBM Page 22 of 65 ul d wu Wi GA defra Note 1 4 This value should be the measured limit of detection not the target limit of detection as defined by NMCAG All sample results should therefore be greater than this detection limit However if your lab s LOD lt target LOD as specified by Green Book report target LOD Note 1 5 This column N has been filled with not applicable and hidden in the current version of the templates Note 1 6 Where you have more than one LRM for a determinand the LRM with results closest to the values of the samples should be used Note 1 7 The value must be changed if necessary to comply with the units that MERMAN uses for each parameter 3 2 3 1 Further AQC Submission Information One of the main strengths of MERMAN is that all data within it are quality controlled to the same standard MERMAN has an inbuilt data filter based on the method developed by several CSEMP members As both the sample data and the quality control data are submitted to MERMAN the filter calculates a score based on the QC information providing an automated quality control mechanism for the sample data Data that
41. g how to enrol onto the system Document mermanuserguide_9 3_28may2014 Owner IBM Page 11 of 65 i ov defra 2 1 2 Removing Users It is the responsibility of the Responsible Officers to inform BODC when a user account is no longer required in the event of that member of staff leaving or moving to a different project The number of Business Objects licences is limited and we therefore need to manage the number in use The Responsible Officer should email the management team at merman bodc ac uk to inform us 2 2 Logon to MERMAN First Time User 2 2 1 Overview In order to access the MERMAN database the steps below must be followed in sequence 1 Known Facts about the user registered by the IT Helpdesk See Figure 2 Known Facts User will receive two emails at the same time 2 Email 1 Defra Portal Enrolment Details are sent to the user 3 Email 2 MERMAN Enrolment Details are sent to the user 4 User to enrol on to Defra Portal 5 User to enrol on to MERMAN The MERMAN database is accessed via a portal from the internet The Defra Portal is shared with other Defra applications and thus the initial registration may seem cumbersome After the user has enrolled with both the Defra Portal and the MERMAN database they will be able to use the system with a single username and password 2 2 2 Enrol for Defra Portal When the helpdesk has registered the user s Known Facts the user will receive two emails
42. h North WSctCst_MinchN_se01 5 Fl West Scottish Coast The Minch North WSctCst_MinchN_se02 1 Fl West Scottish Coast The Minch North WSctCst_MinchN se 2 E West Scottish Coast The MinchNorth WSectCst_MinchN_se02 3 6 Some monitoring designs are not so neatly captured For example MSS monitors the sediment in part of the Fladen ground The sampling strategy is stratified random with five samples taken from each of four strata But the sampling area and strata are not compatible with the regions and strata proposed for MERMAN It is arguable that MSS should think again and monitor over the whole muddy part of the Fladen region However the current monitoring programme can be submitted to MERMAN by regarding each stratum as a fixed station with a larger area definition than is usually associated Document mermanuserguide_9 3_28may2014 Owner IBM 9 defra with a fixed station Thus the samples from the top two strata might be submitted as follows The four fixed stations can still be analysed together but this will require more intervention at the analysis stage strategy region stratum gt gt mame sample E Fladen Offshore Sladen Oitebore sei FI Fladen Offshore Fladen_Offshore_se01 2 FI Fladen Offshore Fladen_Offshore_se01 3 FI Fladen Offshore Fladen_Offshore_se01 4 FI Fladen Offshore Fladen_Offshore_se01 5 FI Fladen Offshore Fladen_Offshore_se02 1 FI Fladen Offshore Fladen_Offshore_se02 2 FI Fladen Offs
43. her PT Submission Information PT data usually set by QUASIMEME account for 30 of the final AQC score in the data filter Labs are encouraged to participate in proficiency testing The data are submitted to MERMAN in the PT_input_sheet MERMAN has been enhanced to cater for some specific results Document mermanuserguide_9 3_28may2014 Owner IBM Page 24 of 65 9 defra The mean_flag field has been added to the PT template to enable the submission of results with lt characters that are below the detection limit Populating this field does not have any follow on consequence to the data filter as the filter only uses the z score in its calculation e QUASIMEME typically assigns non numeric Z Score s to results reported with a lt symbol and can report a character result if there isn t sufficient information to calculate a z score For instance when there are not enough results to statistically generate a meaningful z score Letters such as C consistent and I inconsistent can be given instead These do have a direct consequence on the filter MERMAN is unable to accept a non numeric z score so in these cases the z score should be populated as 0 for a QUASIMEM result of C or 99 for a result of I as agreed by NMCAG 3 2 5 Biology AQC Input Sheet This input sheet is used for determinands from the benthic invertebrate data submission currently the only determinands used for th
44. his information is recorded in the station name Leave blank this information is recorded in the station name Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled See Note 1 4 Codes as per the drop down menu when macros are Document Owner mermanuserguide_9 3_28may2014 IBM Page 18 of 65 defr H Field Name Sample_date Sample_start_time Sample_end_time Latitude_degrees Longitude_degrees Sample_number Sub_sample_number Laboratory_sample_number Matrix Sampler_type Analytical_lab_code Analytical_year Determinand_code Determinand_units Description Date sample collected Start time of sample collection End time of sample collection Latitudinal position of sample collection Longitudinal position of sample collection Sample number for each species in haul each sediment core each sediment grab each water bottle Sub sample number identification Unique sample number assigned by Laboratory Matrix analysed Sampler type Laboratory or institute responsible for the analysis and measurement of the parameter value or the laboratory responsible for sorting and identification of biological samples The nominal year in which the Analytical Lab performs the sample analysis This typically is the same nominal year as the year of Monitoring but doesn t have to be Parameter code Measurement
45. hore Fladen_Offshore_se02 3 FI Fladen Offshore Fladen_Offshore_se02 4 Fl Eaden Offshore Eaden Oitsbore se 5 7 Four nutrient samples taken whilst steaming up the East Scottish Coast These are taken opportunistically so the station and the stratum are effectively the same as with stratified random sampling However the number has been removed to distinguish this catch all station from the other monitoring stations Care will be needed to ensure that the sample numbers are unique if many samples are collected opportunistically from the same water body maybe by different CMAs strategy region stratum gt mame sample Op East Scottish Coast Scurdie ness to Deil s Head ESctCst_Scurdie wa 1 OP East Scottish Coast Scurdie ness to Deils Head ESctCst_Scurdie_wa 2 OP East Scottish Coast Scurdie ness to Deils Head ESctCst_Scurdie_wa 3 OP East Scottish Coast Scurdie ness to Deis Head ESctCst_Scurdie wa 4 3 8 5 Opportunistic Stations Opportunistic stations are suitable for both spatial purposes and biological effects purposes and all water opportunistic stations also suitable for eutrophication purposes Thus the only difference will be that the opportunistic stations are spatial whereas the original stations are temporal Submitter should reflect these facts in their submissions to MERMAN in the Sample Purpose field Document mermanuserguide_9 3_28may2014 Owner IBM Page 51 of 65 ul d wu Wi GA defra
46. hould be made Once the checks have been completed then the submissions should be unheld 1 Ensure that all CRMCOs are registered with ICES well in advance 4 weeks of submission deadlines Registrations should be completed through BODC for CRMCOs used within the CSEMP Check that all new station codes to be used are sent to BODC using the format in section 3 8 at least 4 weeks prior to any submission round 2 Ensure that the Sample Reason Fields are correctly completed for each data type see note 2 1 of section 3 2 1 for details 3 Carry out the Data Screening Report for each parameter for each data type using the Business Objects report under Public Folders Carry out any remedial action 4 Check that all sample results are greater than the detection limit as specified in the AQC input spreadsheet 5 Check that all mandatory fields are submitted 6 Check that any parameters that do not have associated AQC information e g TEMP PSAL MOCON LNMIN LNMAX LNMEA WTMIN WTMAX WTMEA Grain Size parameters but should still be transferred to ICES are added to the Biology AQC template Other parameters such as LIPIDWT FATWT CORG may be passed in the Biology AQC template once agreed with the appropriate AQC chair 7 Review the final AQC score for each parameter for each data type Any parameters not passing the data filter will not be transferred to ICES Use the BO report Final AQC Scores in Public Folders for th
47. is check This report details the AQC scores for each parameter for each data type for a specified year 8 Also check the AQC_data_cross check report This enables ROs to easily see which determinands have AQC data supplied for them and which do not 9 Unhold submissions once happy with the data Document mermanuserguide_9 3_28may2014 Owner IBM Page 45 of 65 ul d wu Wi GA defra 3 8 Station naming and new station submissions The protocol for naming monitoring stations in MERMAN 3 8 1 Introduction Historically most data in the CSEMP or NMMP have come from a fixed station monitoring design in which several samples are taken from a small fixed area at the same time each year However the last NMMP report showed that the power of this programme for detecting temporal trends was often poor Further the programme could only support very localised environmental assessments The ensuing redesign proposed the monitoring of larger regions This would lead to greater power as local spatial variation would be controlled and would support more meaningful less localised environmental assessments Larger regions would be monitored by stratified sampling either random sampling within strata sub regions or sampling a network of fixed stations representative of the strata within a region The change in approach required a change in the protocol for naming monitoring stations in particular to link stations more closely to
48. ish have been taken at a number of sites at one CSEMP station then each collection should be considered as sub samples Please see Note 1 2 on page 18 on the submission of data at stations that have been visited more than once in a monitoring year Document Owner mermanuserguide_9 3_28may2014 IBM Page 38 of 65 ul d dy GA S 3 3 Saving Submission File When the submission file is complete it must be saved in the comma delimited format csv to be accepted into MERMAN e In Excel Select File gt Save As e Select Save as type CSV comma delimited File name Name your file using the following standard format CMA_ SubmissionType_Monitoring Year csv with subsequent versions of the file appended alphabetically i e a b c d etc e g CMA_ SubmissionType_Monitoring Yeara csv e For Biology AQC sheets the datatype i e biology should come before the AQC CMA_Biology_AQC_2005 Examples CEFAS_sediment_2006a csv MSS _biota_2006c csv SEPA_water_2006b csv AFBI_biology_2006d csv DOEM_aqc_2006b csv EANLS_biology_aqc_2006d csv MSS_beaqc_2009a csv e The naming of files which are used to unhold data should follow that of the submission type files but include unhold between the submission type and the year For example SEPA_water_unhold_2006b csv EANLS_biology_aqc_unhold_2006d csv This will make it easy for submitters reviewers and the Data Manager to identify which files have been subm
49. issions of the same data file made will overwrite what has been submitted previously for that data type for that year Therefore when submitting an updated version it is important to make sure that the whole file is resubmitted rather than a partial submission comprising the corrected data only This further substantiates the need to send a copy of the file to BODC as in the event that a submitted data set is lost due to being overwritten by an incomplete data submission BODC will be able to supply the original version Document mermanuserguide_9 3_28may2014 Owner IBM Page 42 of 65 defr 6 yod and Rural Affairs 3 4 1 Confirmation of Submission The user will receive a confirmation email within an hour of the submission The email will state whether the submission has been successful or not If you do receive a confirmation e mail from MERMAN you should assume that your file has NOT been successfully loaded and you should contact the MERMAN mangers on merman bodc ac uk immediately New Memo Reply Reply To All Forward Delete Follow Up Folder Copy into New Chat f Show Thread Tools Merman Submission MERMAN DEV To Liisa Stuar UK IBM IBMGB Jon Gould UK IBM IBMGB 10 05 2006 09 50 cc SS bec Default custom expiration date of 08 08 2006 i Subject Submission of CEFAS_AQC_2007_positive csv Thankyou for your submission It has been successfully loaded into the Mer
50. itted and what changes have been made to the data through the course of the submission process with any corrections made being easily tracked Please see a full list of competent monitoring authorities in appendix 2 Document mermanuserguide_9 3_28may2014 Owner IBM Page 39 of 65 A defra Department f Food and Rural Affairs Microsoft Excel Exi When you are ready to submit this file to MERMAN database please ensure you save the file in csv format Until such time please continue to save the file as x s Please use this convention for naming the file CMA_Biota_year_version csv e g CEFAS_Biota_2005_a csv Note Once you have the saved the file as csv the drop down functionality will not be available aa Figure 11 Prompt for Saving the Submission File A ax Save in EE D A X Ci E Tools SEPA_AQC_2005 csv SEPA_Biota_2005 csv SEPA_PT_2005 csv SEPA_Sediment_2005 csv SEPA_Biota_2005_a csv 7 Save as type csv Comma delimited csv D Wee Figure 12 Save File As CSV 3 4 Uploading Data Logon to the Defra Portal using your User ID and password given to you previously on enrolling Select File Upload from the toolbar Document mermanuserguide_9 3_28may2014 Owner IBM Page 40 of 65 ul i aul Wi GA defra def PO Department for Environment Food and Rural Affairs MERMAN Home File Upload Business Objects Reporting and Viewing Data using Business Objects
51. itting AQC and PT data to MERMAN Update links to Green Book and MERMAN portal Amendment to BEAQC template file name Corallie Hunt BODC Changes to how biology subsamples should Charlesworth BODC be numbered if only one mesh size is used Instructions on how to deal with parameters which have AQC data but no PT Updated information on station naming Needs a thorough check through for updates mermanuserguide_9 3_28may2014 Page 3 of 65 ul d dn GA defr Affairs 17jan2012 on uncertainty and METOA METCX and Mark Charlesworth BODC METPT and FINFL REFSK Updated information regarding the ZS RE Biology_AQC template upgrade including SERIES table of fields green book link removing users procedure general clean up 25Feb2013 General clean up Arwen Bargery BODC 05Aug2013 Bee logon screenshots and general Corallie Hunt BODC 19Aug2013 Updated logon screenshots and general Arwen Bargery BODC 06May2014 clean up 9 3 28May2014 Updated information relating to 2013 Arwen Bargery BODC enhancements undertaken Distribution This document has been distributed to Title Document mermanuserguide_9 3_ 28may2014 Owner IBM Page 4 of 65 ul H ill i in GA E defra Contents Me de le e DE 7 1 1 What is MERMAN Database Abu 7 1 2 Components of the MERMAN Database eeseeeeeneeeeeieesieernetttetttrttnunttnntnnntn nnn ntnnntnnnnnnnnnnnnn 7 1 3 Scope of this User Guide cee
52. l in all three of DETLI CRMMV and CRMSD for chemistry parameters An error is produced if they are partially completed It is not necessary to provide this information for physical parameters such as TEMP PSAL NTRA grain sizes weight and length measurements If you do however provide this information you will need to supply all three fields Methods and Analytical fields The methods information METPT METCX and METOA needs to be provided for ALL parameters Please use the drop down menus 3 2 6 Bioeffects AQC Input Template This template and functionality was added in February 2009 to the application The data is held to allow e the BEAQC group to assess national performance e pass or fail of parameters that are taken for biological effects and therefore pass or fail the data filter for transfer of the data to ICES e any ICES registered ICCOD codes to be transferred to the ICES report Any duplication with the submissions in the Biology AQC should be avoided This will require careful coordination with Responsible Officers The codes and description of the fields used in the BEAQC template are shown below and the parameters to be entered in the BEAQC template and the recommended entries to the METOA and REFSK fields are shown in the following table Title Code Description Submitter_email_address E mail address of the person submitting the file to the MERMAN application Reviewer_email_address E mail address of the
53. location A Which Measurements What Matrix xl Date Time of Sample All Objects A Additional Search Criteria aac Results SF Query Filters To filter the query dratyyredefined filters here or drag objects here then use the Filter Editor to d custom filters Query Filters Figure 22 Business Objects Universe Screen A typical query will contain elements from Location Measurements Matrix and Date Time folders all other MERMAN data items are can be found under the Additional Search Criteria folder To produce a query select an object and drop in Results Objects pane Continue to do this until all data items required appear on pane Move any data items what you wish to filter by into the Query Filter pane and make Query Filter selection When ready click Run Query Document mermanuserguide_9 3_28may2014 Owner IBM Page 60 of 65 ul d dy GA defr Affairs 5 Security 5 1 Overview This section explains who can access which parts of the database There are two levels of security implemented in MERMAN The first layer is governed by the Defra Portal which utilises the Government Gateway and Single Sign On to authenticate users A users portal user role allows them to access the data submission or reporting function or both The second layer of security is implemented within the Business Objects application and governs what functions and data the user can access within Business Objects When app
54. lying for a MERMAN logon the user will only need to know whether they need file upload or reporting access or both Public users will only be given reporting access The MERMAN Data Manager will decide on the Business Objects permissions given to each user 5 2 Defra Portal Security There may be 3 types of user who will have access to the MERMAN database functions as set out below User Group Access to Functions CSEMP Business Object User Business Objects reporting can view data only CSEMP Submission User File upload i e can add data only CSEMP Multiple Support User Business Objects reporting File upload Can both upload data and view it 5 3 Business Objects Security The data access i e what can be extracted from the BO reporting tool will be generated according to 4 user types as shown below The security levels and time frames may change in the future User Group Access to Data CMA User Can see all sample and AQC data for their own CMA Document mermanuserguide_9 3_28may2014 Owner IBM Page 61 of 65 CSEMP User Database Manager Can see sample data but not AQC for other CMAs when data are Unheld Can see all sample data but not AQC for their own CMA when data are Unheld Can see all sample data but not AQC for other CMAs when data are Unheld Can see all data for all CMAs Can see Sample data that are both Unheld Public User and have the
55. man Database Figure 16 Submission Confirmation Email If the submission file has an invalid email address or the submission file has an invalid file name the system will send an email to the data manager to inform of the failed submission 3 5 Handling Errors In the case of an erroneous submission the email will contain an attached error report Thankyou for your submission Unfortunately it failed to load into the database Please find attached the error report The original of this email was scanned for viruses by Government Secure Intranet GSi virus a Supplied exclusively by Cable amp Wireless in partnership with MessageLabs On leaving the GSI this email was certified virus free The MessageLabs Anti Virus Service is the first managed service to achieve the CSIA Claims Test Certificate Number 2006 04 0007 the UK Government quality mark initiative for information sec services For more information about this please visit www cctmark gov uk a_water2004 err Figure 17 Error Report Email Select gt Open with Word Pad program The report details the row number from your submission spreadsheet where the error occurred and the type of error in question Document mermanuserguide_9 3_28may2014 Owner IBM Page 43 of 65 ul H Jk Ml GA Il Ihi ail II oO OQ FRS_Biota_2005 err WordPad File Edit View Insert Format Help Cael 44 Aa Bo B ffitle DATA AUDIT REPOR
56. mpts as instructed Press the Run Query button Document mermanuserguide_9 3_28may2014 Owner IBM Page 56 of 65 Ate Department for Environment Food and Rural Affairs l ra a e A bas Vveiu11e C Home Document List Open Send To Dashboards Help Preferences About Le 2sktop Intelligence Data_Screening Report D Document View D ty 48 a bam lei ah la gt Edit 2 Refresh EA Reply to prompts before running the query 1 CMA ne or or Enter ALL 2 Data Type Select one or more or Enter ALL 3 Matrix Select one or more or Enter ALL 4 Determinand Select one or more or Enter ALL 5 Station Number Select one or more or Enter ALL eevee 1 CMA Select one or more or Enter ALL Berrrge fo Type values here gt Refresh Values Ze CMA Code AFBI a CEFAS Defra 3 EANat k EHS FRS NoCMA X Enter your search pattern here Fe More Information Select or type the values you want to return to reports for each prompt displayed here 1 at aa LUE E Run Query Cancel Refresh Date July 26 2011 3 37 32 PM GMT Figure 22 Report Prompt Window The report is generated and the report displayed on the screen defra Pounce er Sa Welcome c_nunt Zo Home Document List Open Send To Dashboards Help Preferences About Log Oui Desktop Intelligence Data Screening Report EX Docum
57. nalysis that is used for a stratified fixed design but would require more input at least initially from data providers about sensible groupings of stations Examples of opportunistic sampling might include nutrient measurements taken along a cruise track or one off surveys At the analysis stage the opportunistic tag provides due warning that the data do not come from a standard design and detailed scrutiny is required to make sense of them Although a fixed station is typically thought of as having a small area some fixed stations could be quite large An example of a sediment fixed station with a large area is shown later It is one of the compromises necessary to merge current CSEMP monitoring activities with WFD and Charting Progress The list of sampling strategies can be expanded later if sets of data are identified that are sampled ina standard way Typically sediment sites would be fixed stratified random or stratified fixed imposex sites would be fixed shellfish sites would be fixed Document mermanuserguide_9 3_28may2014 Owner IBM Page 48 of 65 9 H defr fish sites would be fixed but they could be stratified fixed multiple representative sites in a strata or stratified random random stations in a strata water sites would either fixed stratified fixed e g transects down a riverine strata that sample the same points each year stratified random e g transects down a riverine strata that
58. nd you should contact the MERMAN mangers on merman bodc ac uk immediately defra Department for Environment Food and Rural Affairs MERMAN Home File Upload Business Objects Data Submission for Merman Step 1 Ensure you have a data file with your correct email address and having a CSV extension a file name ending with csv Step 2 Select the file by using the browse button Choose File No file chosen Step 3 To upload the selected file click on upload file button Upload File Step 4 Review the message which appears below Your file has been submitted for processing by Merman You should receive an email within one hour stating whether the file has been processed successfully Please send the xls version of your spreadsheet to nmmp bodc ac uk Figure 15 Submission Confirmation Message on the Screen Once the file has been submitted to MERMAN the submitter must also send a copy of this file and any subsequent versions to the Data Manager The file should be attached to the e mail message received from MERMAN These files and their updated versions will be stored at BODC in an archive which will allow the user to trace any changes made to the data file if need be Having a copy of the data file will also help the Data Manager to identify problems which may be hindering its submission into MERMAN It is important to note that the database is setup to accept one data file per data type per CMA per year Any further subm
59. nput spreadsheets a Sample i Biota ii Water iii Sediment iv Biology v RID b Quality Data i AQC for contaminants ii Proficiency Testing PT data for contaminants iii AQC for Biology iv AQC for biological effects It is important to note that the database is setup to accept one data file per data type per CMA per year Any further submissions of the same data file made will overwrite what has been submitted previously for that data type for that year Therefore when submitting an updated version it is important to make sure that the whole file is resubmitted rather than a partial submission comprising the corrected data only 3 2 Populating Input Spreadsheets On opening the input sheet template Press Enable Macros button C Documents and Settings Administrator My Documents DEFRA UAT Files CEFAS Water 05 xls contains macros Macros may contain viruses It is usually safe to disable macros but if the macros are legitimate you might lose some functionality Document mermanuserguide_9 3_28may2014 Owner IBM Page 16 of 65 Ate Department for Environment Food and Rural Affairs ail Figure 8 Enable Macros Pop up The input sheet opens A Guidelines for Completing NMMP Database Submission Mandatory fields in orange text optional fields in white text Do not enter data into blue cells Do not add extra columns Only add extra rows after Row 4 Where a code is to be entered the
60. ority Document mermanuserguide_9 3_28may2014 Owner IBM Page 21 of 65 ul d wu Wi GA defra Field Name Description Instructions Submission_type AQC Data_type Codes as per the drop down menu when macros are enabled Analytical_lab_code Laboratory or institute Codes as per the drop down responsible for the analysis menu when macros are enabled and measurement of the parameter value Determinand_code Codes as per the drop down menu when macros are enabled Determinand_units Codes as per the drop down menu when macros are enabled ACCRED Codes as per the drop down for the specified determinand menu when macros are enabled METCX Codes as per the drop down menu when macros are enabled METOA Codes as per the drop down menu when macros are enabled METPT Codes as per the drop down menu when macros are enabled analysis of determinand ICCOD Not required See Note 1 5 format CONCH Codes as per the drop down as control chart basis menu when macros are enabled CRMCO Codes as per the drop down codes menu when macros are enabled Note 1 6 CRMMB Reference material basis of determination used in control chart analysis CRMEV See Note 1 7 CRMMV Mean value calculated found CRMNM Control chart number of Number of measurements of measurements of Reference reference material taken to Material acquire mean value CRMPE Period of time over which measurement weeks measurements are made CRMSD Taken from reference certificate d
61. orrected MERMAN e mail address and references to NMMP throughout document Document mermanuserguide_9 3_28may2014 Owner IBM Page 2 of 65 03 08 2007 01 04 2008 11 03 2009 20 09 2010 18march2011 Document Owner IBM defr H 3 2 1 Note 1 2 gives further instruction on the Mark Charlesworth BODC submission of cruise codes for stations that Corallie Hunt BODC have been visited more than once within one monitoring year 3 2 1 Note 1 3 gives further instruction on submission of codes for Sample Reason 3 6 Clarification on Submission held spreadsheet 3 8 Added in the paper on station sampling strategy and naming convention Also instructions on adding new stations to the MERMAN station dictionary 3 2 6 reference to note 1 2 on cruise codes for submissions of data taken at a station on more than one occasion within a monitoring year 3 2 6 Updated sample sub sample guidelines for biota sediment and water Note 1 3 Updated to highlight further rules regarding the MPROG fields 3 2 3 Further information added to the AQC Spreadsheet table Corallie Hunt BODC 4 1 Information provided on accessing Business Objects User Manual 3 2 6 A new section added on the addition and submission of BEAQC data Note added to reflect the choice for terms in the Sample Purpose list when submitting Opportunistic data Mark Charlesworth BODC 3 2 3 1 and 3 2 4 1 Additional information for subm
62. ossibly CMP sp sediment bioassay amp toxicity Comparative analysis test Fish Disease LYMP CYS LIVE GRS Gross examination T19 Times No 19 Common NOD SKEL DEF diseases amp parasites of fish in STEP STO SKIN the North Atlantic Training ULC XGIL LES guide for identification HPIGM FROT ANISAKIX ANISAKIX LATLIP LEPE OPH ACAN THO EPID PAP GLUG STE Fish Disease NECRCG APOPTS HIS PR Histopathology T38 Times No 38 Use of Liver STETMA STETMI HEMOSD GLYCCV MELAMC LYMCINF GRANLM FIBROS REGNR PHOSLD FIBINC HEPCNP HYVCBE SPNHEP CLCFC CLCFC VACFC EOSFC BASFC MXDFC HEPCA CHOLA HEMAGA PANACA HEPCC CHOLC PANACC HEPBCM HEMAS HEMAPS plastic resin Pathology of Flatfish for Monitoring Biological Effects of Contaminants When submitting data using the BEAQC template there are a number of rules in place to ensure that data are submitted to a set standard As biological effects measurements are very diverse one rule is not adequate for all measurement types Therefore biological effects measurements have been grouped Document Owner mermanuserguide_9 3_28may2014 IBM Page 30 of 65 defra according to what data may be available to be submitted The groups are shown in the table below and which measurements fall in which groups is shown in the following table Group Rules Description Code 1 DTYPE ALBO_1 METO
63. ou have not registered on the Government Gateway please press the Register button and proceed to Step 5 KR e E me Page will appear Enter your First and Last Names and your email address Then select Individual from the User Type drq down list 6 Choose a memorable Password between 8 and 12 characters including at least one digit 7 Enter the following Postcode and SASPIN Figure 3 Email Containing Instructions for Accessing the Defra Portal Applications 2 2 3 Enrol for MERMAN The second email details the steps to be followed to enrol for MERMAN The user will need the user ID allocated in the previous step New Memo Reply Reply To All Forward H Delete H Follow Up Folder Copy into New Chat Show Thread Tools lt MERMAN defra gsi gov uk gt To Liisa StuarVUK IBM IBMGB gege 14 41 cc Default custom expiration date of 29 08 2006 Subject Access to the Marine Environment Monitoring and Assessment National Database Dear Liisa You are invited to access the Marine Environment Monitoring and Assessment National Database which is secured via Defra s Single Sign On system and the Government Gateway To use the Marine Environment Monitoring and Assessment National Database please enrol for the service as described below You must already have a Government Gateway User ID and Password with access to Defra Portal Applications
64. quired to fill all bottles for analysis Bottles filled for different analysis are sub samples and should be labelled 1 2 3 4 etc A E Contaminants Continuous flow C Chlorophyll QO Temperature Salinity Nutrients Determinand Sample Sub sample CD A 1 HG A 1 ZN A 1 CU A 1 FE A 1 CPHL A 2 TEMP A 3 PSAL A 3 NTRA A 4 NTRI A 4 3 2 9 4 Contaminants in Biota and Fish Disease Document mermanuserguide_9 3_28may2014 Owner IBM Page 36 of 65 q Affairs defr With biota data each species collected at a station is considered a separate sample and should be labelled A B C etc If fish of the same species are aggregated from several trawls this is still all one sample Each individual fish or batch of fish i e aggregation of 5 fish for use in the same analysis subsequently analysed e g for fish disease biological effects or contaminants is considered a separate sub sample and should be numbered 1 2 3 4 5 etc The start time for all samples should reflect the time of the trawl and not the time that the species were batched off If more than one trawl was required to get enough fish for samples one start time should still be used At each station on a particular visit within a sample there will always be a consistent species start date time and cruise code Within a sub sample there will always be a consistent number of individuals and sex code if being used
65. reports is the UK s annual data submission of OSPAR data to the ICES database the system compiles the data according to the ICES reporting requirements v3 2 and the data can be submitted to ICES without any manual processing The data are submitted to the MERMAN database using standardised MS Excel spreadsheets where the users collate their annual submission They will then use the MERMAN portal to load the data into the database The data are automatically validated before they are loaded into the database giving users the benefit of Knowing that their data fulfils the set criteria The data submitter receives an email confirmation of the submission status and if there are any errors in the data these are detailed in an error report 1 2 Components of the MERMAN Database The MERMAN database will store the following data elements Macro Fish Fish Liver Filtered Unfilt RID benth Tissues Water ered enthos Wate r Chemical Contaminants Metas 1999 current 1999 current 1999 current 1999 current 1999 current PCBs 1999 current 1999 current 1998 current current Organochlorine 1999 current pesticides 1994 current Document mermanuserguide_9 3_28may2014 Owner IBM Page 7 of 65 defra ul H vat GA Biological effects Benthic 1999 current macrofauna imposex TBT TBT er kb 1999 current EPR embryo bioassay Fish disease disease Fish disease 2008 current 2008 curr
66. rface sample is taken from the first grab for metals PSA Sample A sub sample 1 and a second surface sample is taken from the same grab for organics Sample A sub sample 2 Records in the submission template could look like the following table TTL gt no Document mermanuserguide_9 3_28may2014 Owner IBM Page 32 of 65 ul d dn GA S Affairs Please see note 1 2 on page 18 on the submission of data at stations that have been visited more than once in a monitoring year 3 2 9 2 Biology Each individual grab or dredge is considered a sample and should be labelled A B C D E If only one mesh size is used then this should be specified in the mesh size field and the sub sample field should be marked with the sample ID and the mesh size Example below Sub sample meoo sao E 007 mmer Im eneen 7000 eeneg Te Enchytraeidae Corophium volutator 1000 e A A A A A A Nais elinguis o o M wo ER Effet Ss oo Limnodrilus hoffmeisteri 1000 bi EES rose Je ene Je rege le e Ee ES Paranais litoralis 1000 PCH Limnodrilus hoffmeisteri 1000 C PCH If the sample is sieved at 500 and 1000 um then the sub sample field should be marked AO P and A1 respectively Example below 1 1 1 1 1 1 B1 B1 B1 B1 B1 B1 B1 C1 C1 C1 Document mermanuserguide_9 3_28may2014 Owner IBM Page 33 of 65 ul d dn oa sil Affairs seo co 1 A1 A0 5 A0 5
67. rotocols see MERMAN User Guide for suggestions Laboratory UKAS Accreditation ACCRED If the laboratory making the measurements has UKAS Status accreditation for the method then indicate here Describe Internal AQC INTAQC Describe any internal laboratory AQC in less than 500 characters such as chemical standards training new staff tests of competence across analytical staff etc Type of Reference Material used CONCH Choose which type of reference material is most appropriate for Intercalibration for the inter laboratory intercalibration that has been performed Intercalibration Scheme INTSCH Choose the appropriate intercalibration scheme Other ICES registered is for intercalibrations with for example MEDPOL Unregistered is for an informal swapping of samples between a small number of labs Intercalibration Laboratory ALABO_2 Where an informal scheme has been used e g samples Provider swapped between labs state laboratory and country that has supplied the sample e g CEFAS UK Max characters 100 Cell is mandatory if INTSCH is Other ICES registered or Unregistered Intercalibation Exercise Code ICCOD Choose the appropriate intercalibration code Note if the scheme is not registered with ICES than the code will have been chosen by BODC Reference Material Expected CRMEV Give the expected value for the measurement made for the Value intercalibration Reference Material Measured CRMMV Give the meas
68. sample data are first submitted into the database each record is defaulted to Accepted status and will not be available to users outside your own organisation to view Once the data for a CMA have been loaded it must be reviewed in the MERMAN database by the responsible officer The responsible officer must then release the data by submitting an Unhold spreadsheet The unhold spreadsheet must be submitted for each data type sediment water biota biology AQC PT Biology AQC for each CMA and monitoring year Any subsequent data submissions will automatically set the data for the same year and CMA to be Accepted again All data must be unheld for the ICES report to be created Data should not be re held once the ICES report has been created as agreed at CSSEG Document mermanuserguide_9 3_28may2014 Owner IBM Page 44 of 65 ul d dn GA defr Affairs Submission Held Spreadsheet Column Name Instructions Submitter_email_address Monitoring_year CMA Submission_type Enter monitoring year Enter a submission type for that CMA Submission Held Flag N No 3 7 Submission Checks by Responsible Officers Once all submissions have been made for a monitoring year Responsible Officers or persons appointed by them should complete the following checks These checks should be completed by the deadline as specified in section 1 4 If any of these checks highlight any inaccuracies then resubmissions s
69. sample random points each year or opportunistic none of the above 3 8 4 Station names A meaningful unique station name is constructed by concatenating and abbreviating the region and stratum name and appending the matrix and a number Here are some examples 1 Fixed station monitoring three mussel stations at Lower Largo Braefoot Bay and Granton with one pool collected from each strategy region stratum name sample FI Forth Elie to Buckhaven Forth_Elie_sh01 1 FI Forth King Horn to Leith Docks Forth_KingHorn_sh01 1 FI Forth King Horn to Leith Docks Forth_KingHorn_sh02 1 2 Fixed station monitoring three imposex sites in the same water body one pool from each strategy region stratum name sample Fl Forth Port Seton to Eyebroughty Forth_PSeton_im01 1 Fl Forth Port Seton to Eyebroughty Forth_PSeton_im02 1 Fl Forth Port Seton to Eyebroughty Forth_PSeton_im03 1 Stratified fixed monitoring four sediment samples taken along a transect down the Forth Estuary same sites each year It is important that the data from each station are matched to the correct station name since this is required in the subsequent statistical analysis For example if the third station along the transect is not sampled one year the data are still be submitted to stations 1 2 and 4 strategy region stratum name sample SF Forth Middle Forth Estuary Forth_MiddleEst_se01 1 SF Forth Middle Forth Estuary Forth_MiddleEst_se02 1
70. sndcdnesesctadbessscddensacsdaseredsddensadsavesuedsdssavaceaaeesededs 61 6 FOW 0 21 E E 63 Tc EIERE 64 7 1 Listot ADDreviations E 64 7 2 List of Competent Monitoring Authorities ccccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaeeeeaeeseeeeeseaeeeeaeeeeeeeee 64 7 3 Merging Excel spreadsheets AAA 65 Document mermanuserguide_9 3_ 28may2014 Owner IBM Page 6 of 65 ul d wu Wi GA defra 1 Introduction 1 1 What is MERMAN Database The Marine Environment Monitoring and Assessment National Database MERMAN is a new database 2005 supporting the Clean and Safe Seas Evidence Group CSSEG in monitoring the UK waters It integrates chemistry biology and biological effects data from the participating agencies and is used for national and international reporting The MERMAN database was built to improve the collation and data management aspects of the previous NMMP and RID programmes The single database enables data integration and reporting across the different dataset types and geographic areas The database is accessible to all via a portal from the Defra intranet From the portal the users can both access the data submission pages and login to the Business Objects reporting application Business Objects is a web based reporting package that allows users to run standard reports as well as easily build their own tailored reports which allow them to extract the quality assured data from the database One of the key standard
71. the Unhold template this will allow other users outside of your CMA to view the data Document mermanuserguide_9 3_ 28may2014 Owner IBM Page 10 of 65 ul d dn GA defr Affairs 2 Access 2 1 Requesting Access to MERMAN The IBM project team will request access for all of the current NMMP users as a part of the project When new employees or additional users need access to MERMAN they will need to contact the MERMAN Data Manager see section 7 who will pass the relevant information to the Defra IT Helpdesk Users will be requested to provide details as follows 2 1 1 User Details Known Facts User Details Name Address incl County Home or work address Post Code Email Application Details Portal Access Yes No This will be Yes for all MERMAN users Application ID Marine Environment Monitoring and Assessment National Database MERMAN Role One of the three options to be selected NMMP Business Object User NMMP Submission User NMMP Multiple Support User Figure 2 User Details Known Facts The completed access request should be emailed to the MERMAN Data Manager MERMAN Management Team British Oceanographic Data Centre Joseph Proudman Building 6 Brownlow Street Liverpool L3 5DA Tel 01517954861 Fax 01517954912 E mail merman bodc ac uk The IT Helpdesk will register initial information about the user and send the user two emails detailin
72. the first one being the Defra Portal Enrolment details The email provides detailed instructions on the enrolment steps At the end of the enrolment a user ID is allocated which the user must keep safe An example of the email is as follows Document mermanuserguide_9 3_28may2014 Owner IBM Page 12 of 65 RI defra Department for Environment Food and Rural Affairs lt Portal defra gsi gov uk gt To Liisa StuarvUK IBM IBMGB 31 05 2006 14 41 cc bec Default custom expiratio d Subject Access to the Defra Portal Applications Dear Liisa You are invited to access the Defra Portal Applications which are secured via Defra s Single Sign On system and the Government Gateway To use Defra Portal Applications please register on the Government Gateway and enrol for the service as described below o access the Defra Portal Applications ees ES n Internet Explorer browse to http caratest2 defra gov uk wps portal 2 Defra Portal Homepage will appear EI Please click on the Register for access to Defra Portal applications option from the menu on the left hand side of the screen 4 e Security Validation and Registration Page will appear f you have already registered to access any other Government Gateway controlled service and have a Government Gateway User ID and Password then please press the Enrol button and proceed to step 11 to enrol for the access to Defra Portal Applications BS f y
73. ubmission to ICES Submission of QUASIMEME information CMAs 1 September Analytical labs are responsible for submitting their own QUASIMEME asc files directly to ICES via the sharepoint site or accessions ices dk by this date A copy ASCII should be sent to BODC as well Document mermanuserguide_9 3_28may2014 Owner IBM Page 9 of 65 q Affairs 1 5 Quick Reference Guide for Data Submission Process e Check your data are correct Compare against previous years data using the Data Screening Report available to Responsible Officers via Business Objects e Check you are using the latest version of the input templates found on the BODC website http www bodc ac uk projects uk merman project_specific e Open the relevant template using Excel at least 2000 and enable macros e Fill in the spreadsheet as per instructions breakout groups user guide example spreadsheets responsible officers BODC help facility e Check that you do not have transcription errors be careful when copying cells by dragging them down as this can introduce formatting errors particularly with numeric cells e Save template as a csv using the following naming convention CMA_submissiontype_year_version e g CEFAS_biota_2005 a e Log on to the DEFRA portal e After submission send your final csv file to BODC at merman bodc ac uk e Once all data monitoring and AQC have been submitted they must be released by submitting
74. ul d wu Wi GA defr Affairs Marine Environment Monitoring and Assessment National Database MERMAN User Guide Document mermanuserguide_9 3_28may2014 Owner IBM Page 1 of 65 ul d dy GA defra Document History Revision History Number Mark Charlesworth BODC Mark Charlesworth BODC 28 06 2006 1 4 Submission dates amended as agreed at Mark Charlesworth BODC AQC and WG meetings 3 2 1 to 3 2 5 A number of clarifications have been made to the description of the input spreadsheets Most edits are for the Contaminant AQC and PT spreadsheets in particular a number of subnotes 3 3 Examples given for naming submission files 3 3 Added sentence on what to do if a submission e mail is not sent from MERMAN to the submitter 3 3 New details on sending the submission file to MERMAN 3 6 Note that data should not be re held once the ICES submission has been made as per CSSEG agreements 3 7 Added a new section on tests that Responsible Officers should complete before finally signing off submissions for all AQC and data types for a monitoring year 4 2 6 2 Amended numbering of subsamples for the biology data so the prefix reflects the sample number 4 3 Removed section 4 3 which is specific to BODC to separate document 5 0 Removed section 5 that was specific to BODC requirements to separate document 7 0 Removed paragraph on contacting DEFRA IT to separate document that is specific to BODC requirements C
75. ured value for the intercalibration measurement Value completed by your laboratory Reference Material Standard CRMSD Give the standard deviation of the intercalibration measurement completed by your laboratory Note for some measurements it will be a single result so this field may not apply Document Owner IBM mermanuserguide_9 3_28may2014 Page 28 of 65 defr H Z Score If a z score for the intercalibration has been provide then give here Source of Reference Seawater SRCWT This field is specific to bioassays Latin Name of Test Organism SPECI This field is specific to bioassays Reference Code List used for RLIST This field is specific to bioassays Species ID Origin of Test Specimen ORGSP This field is specific to bioassays BEAQC Assessment of Quality QCSTAT Give here your assessment of if the measurement has Status sufficient AQC This will subsequently be approved by the BEAQC group Reference Material Basis of CRMMB This field is at present spare Determination Number of Measurements CRMNM This field is at present spare Reference Testing Period CRMPE This field is at present spare Intercalibration Reference CRMCO This field is at present spare Material Code To allow easier use of the template the 4 last fields which are currently not used are hidden and the bioassay specific fields are hidden or shown by use of the or button in th
76. ut sheet submitted by the sampling CMA has been assigned the correct analytical lab code There is a report in Business Objects AQC_data_cross check designed to easily check this link and it is the RO s responsibility to run this report before unholding their data The National Marine Chemistry Assurance Group discuss any new monitoring determinands and set the target limit of detection as well as other expected values such as standard deviation and bias These values are loaded into MERMAN s reference data to allow the data filter to calculate the correct scores These values should also be updated in the Green Book There are some determinands for which there is AQC information but no PT data no QUASIMEME scheme available such as Brominated Flame Retardants and alkyl PAHs It has been agreed by NMCAG that in these cases where it is still possible to pass the data filter with AQC data only then laboratories should always enter this data In the event of those determinands not passing using just the AQC data then after agreement with the NMCAG chair the CMAs can enter those determinands into the Biology AQC template which will then bypass the data filter 1 For further details the paper can be found at Implementation of a data filter for the UK National Marine Monitoring Programme Accred Qual Assur 2002 7 60 65 Document mermanuserguide_9 3_28may2014 Owner IBM Page 23 of 65 3 2 4 Chemistry Contaminants PT Input Sheet
77. viewer_email_address Monitoring_year sample Authority The type of submission Water Sediment Biota Biology RID AQC AQC Biology PT The laboratory responsible for submitting the CMA s submission in the CSEMP database CMA Submission_type Submitting_laboratory Ship_code Platform Ship code Cruise identifier series of sampling occasions Monitoring programme Cruise_ID Sample_reason1 Sample_reason2 Monitoring programme Monitoring programme Sampling laboratory code Region that sample was taken Geographic sampling area Sample_reason3 Sampling_lab_code Sample_region Stratum Sampling_strategy Strategy employed to obtain sample Purpose of monitoring Sample_purpose Station_number Station number Instructions whether the data submission has been successful or not will be sent to this address The consequent email detailing whether the data submission has been successful or not will be sent to this address for review purposes See Note 1 1 Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are enabled Specific to individual laboratory See Note 1 2 See Note 1 3 please note this should be consistent within a sample See Note 1 3 please note this should be consistent within a sample Codes as per the drop down menu when macros are enabled Leave blank t
78. wner IBM Page 46 of 65 The map shows Scottish territorial waters truncated to the west the Scottish border thin purple line the regional seas boundaries from Charting Progress slightly modified to align with WFD water bodies thick red lines WFD water bodies light blue areas sediment type in offshore areas green mud yellow sand pink rocky The regional seas have been sub divided into 12 CSEMP regions based on current monitoring activities sediment type hydrography results from the ICES Regional Assessment of the North Sea expert judgement and common sense The boundaries for the most southerly regions are ambiguous because they need to be agreed with England Wales and Northern Ireland It is arguable that e g the Forth region could be amalgamated with the East Scottish Coast region but given the high profile of major estuaries it is probably better treated separately Each region has many strata most of which are WFD water bodies The names of the strata are not shown but inherit their WFD water body names Most regions also have f Faroe Shetland Channel an Offshore strata At present there is no clear reason for further dividing the Offshore strata at least in Scottish waters Document mermanuserguide_9 3_28may2014 Owner IBM Page 47 of 65 ul d wu Wi GA defra 3 8 3 Sampling strategies There are four sampling strategies fix

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