Home

(MERMAN) User Guide - British Oceanographic Data Centre

1. ul nil dn Ga defra 3 2 1 Sample Data Input Sheets Field Name Description Instructions Submitter_email_address Email address of the person The consequent email detailing submitting data into the NMMP whether the data submission database has been successful or not will be sent to this address Reviewer_email_address Email address of the CMA The consequent email detailing business owner whether the data submission has been successful or not will be sent to this address for review purposes Monitoring_year See Note 1 1 sample CMA Authorit Submission_type The type of submission Codes as per the drop down Water Sediment Biota Biology menu when macros are RID AQC AQC Biology PT enabled Submitting_laboratory The laboratory responsible for Codes as per the drop down submitting the CMA s menu when macros are submission in the CSEMP enabled database Ship_code Platform Ship code Codes as per the drop down menu when macros are enabled Cruise_ID Cruise identifier Ge of Specific to individual laboratory sampling occasions See Note 1 2 Sample_reasonl Monitoring programme See Note 1 3 please note this should be consistent within a sample Sample_reason2 Monitoring programme See Note 1 3 please note this should be consistent within a sample Sample_reason3 Sampling_lab_code Sampling laboratory code Codes as per the drop down menu when macros are enabled Sample_region dee have not been defined Stratum ee have not b
2. 114 Figure 10 Biology AQC Input Sheet 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 23 of 62 Gubmitter email address Reviewer_email_address Analytical Year AYEAR CMA Submission_type Biological Effect Measurement BETYPE Type Data Type Measurement is made DTYPE in Analytical Laboratory ALABO Method of Analysis METOA Determinand_Code PARAM Unit Of Measurement MUNIT Protocol Used REFSK Laboratory UKAS Accreditation ACCRED Status Describe Internal AQC INTAQC Type of Reference Material used CONCH for Intercalibration Intercalibration Scheme INTSCH Intercalibration Laboratory ALABO_2 Provider Intercalibation Exercis
3. Run Query Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 57 of 62 ul nil dn ov defra 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 applying fora 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 ge
4. Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 4 of 62 un dN il NI ov a ye A oO Say ken Q 4 Running Ge 51 4 1 Using BUSINESS ODJOCIS asinina aak aa A RAA AEAEE EE SAAE AN AER 51 4 2 Running Standard Heports sisisi iniaa aaa aa daa Taan 51 4 2 1 Downloading Java Runtime First Time Logon to Business Objects essees esenee 51 KC RE e CG 55 4 3 Overview of the MERMAN Database Structure eeseesseeeseeeeeeeeeeeeet tenn nenntnntnrnnsrnnsrnnnnnnnnnne 56 EE 58 GE e VT 58 52 Detra Portal Securty soree ennea eaaa nein igi anand aia eee 58 5 3 Business Objects S CUrity 22 ec cetceene cece eeeaeeeeeeeeceaeeeceaeseeaaesaeeeseaeeeeaaeseeaeesseeeessaaeseeaeeseeeeee 58 6 How to Get Help ege een 60 Dn Appendices EE 61 FA Listo ee E e EE 61 7 2 List of Competent Monitoring Authorities cccccesceeeeeeeeeeeeceeeeeeeeeeeaeeeeeaeeeeaeeseeeeesaeeeeaeeeeaeeee 61 7 3 Merging Excel epreacdsheets AAA 62 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 5 of 62 ul nil dn Ga defra 1 Introduction 1 1 What is MERMAN Database The Marine Environment Monitoring and Assessment National Database MERMAN is a new database 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
5. exercise is not established but is envisaged that results for expected measured value and z score may become possible to enter in the near future Example types include DNAAD MT PYR MermanUserGuide_6 0_20Sep2010 Owner IBM Page 27 of 62 ul d wu Wi Ga DTYPE ALBO_1 METOA PARAM MUNIT REFSK ACREED INTAQC CONCH INTSCH ICCOD CRMEV CRMMV CRMSD Z_SC QCSTAT all mandatory ALABO_2 voluntary SRCWT SPECI RLIST ORGSP should be blank DTYPE ALBO_1 METOA PARAM MUNIT REFSK ACREED INTAQC CONCH INTSCH ICCOD CRMEV CRMMV Z_SC SRCWT SPECI RLIST ORGSP QCSTAT all mandatory ALABO_2 and CRMSD defra For use with biological effects measurements when an intercalibration exercise is established and it is suitable for results for expected measured value and z score to be entered Example types include EROD and Other For use with bioassay measurements where results for expected measured value and z score and fields specific to bioassay data must be entered Example types include Bioassays voluntary CODE Description Data Stage Rules Group FD Fish Disease 1 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 t
6. g defra AQC to get around this they should be added to this biology AQC input sheet and submitted to get a Pass status Please note however that a determinand may still pass the data filter if it just has AQC information but not in the QUASIMME scheme ie has PT data The pass threshold remains the same however the maximum score that can be achieved is 70 whereas the maximum score for AQC and PT is 100 In these instances the AQC for these parameters should be submitted which will then be transferred to the ICES report If the parameter is automatically set to pass via the Biology AQC template then the sample data for that parameter may be downgraded in ICES assessments if there is no associated AQC data for that parameter It must therefore be noted 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 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 Example ABUNDNR BMDRYWT BMWETWT BMAFDWT 7 MMP Database Submission 8 optional fields in white text 95 10
7. 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 detailing how to enrol onto the system Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 9 of 62 Win al TL d gt OH Wull ID i OA 2 2 Logon to MERMAN First Time User 2 2
8. 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 n Internet Explorer browse to http caratest2 defra qov uk wps portal e Defra Portal Homepage will appear ai 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 i i 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 pe f you have not registered on the Government Gateway please press the Register button and proceed to Step 5 e oo Page will appear Enter your First and Last Names and your email address Then select Individual from the User Type dra down list EI hoose a memorable Password between 8 and 12 characters including at least one digit 7 Enter the following Postcode and SASPIN Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 10 of 62 RS defra Department for Leen Foe ard baal After 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
9. Sampler_Area 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 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 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 Biomass_wet_weight Biomass_ash_free dry weight Value measured 3 2 3 Chemistry Contaminants AQC Input Sheet Field Name Description Instructions CMA Competent Monitoring Authorit Submission_type The type of submission AQC Data_type ICES Data Type code 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 19 of 62 ul IW il li Ga EE defra Field Name Description Instructions 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 menu when macros are
10. e mail address and references to NMMP throughout document Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 2 of 62 03 08 2007 01 04 2008 11 03 2009 20 09 2010 Distribution defra 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 Corallie Hunt BODC regarding the MPROG fields 3 2 3 Further information added to the AQC Spreadsheet table 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 Mark Charlesworth BODC Note added to reflect the choice for terms in the Sample Purpose list when submitting Opportunistic data 3 2 3 1 and 3 2 4 1 Additional information for submitting AQC and PT data to MERMAN Update links t
11. elements Macro Fish Fish Liver Filtered Unfiltered Tissues Water Water benthos Chemical Contaminants me asa 1999 current Ge current a current 1999 current e Organochlorine 1999 current pesticides i ERR 1994 current Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 6 of 62 un dN pil NI GA l Il jn o M n o Biological effects Benthic 1999 current macrofauna Oyster embryo bioassay D EES ES eme meer TUELL Biological Community Abundance 1988 current Biomass 1988 current 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 7 of 62 ill MI Ga defra
12. 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 analysis 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 CRMMB Reference material basis of determination used in control chart analysis CRMEV See Note 1 6 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 Control chart period of Period of time over which measurement weeks measurements are made CRMSD Taken from reference certificate deviation standard deviation SDNO The number of measurements measurements made to calculate the standard deviation CRMWN Number of breaches of warning limits 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 The value must be changed if necessary to comply with the units that MERMAN uses for each parameter Document MermanUserGui
13. 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 OQ oO Oo CO Oo oO Di Di DI Di Di D 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 MermanUserGuide_6 0_20Sep2010 Owner IBM Page 31 of 62 Water sampler bucket Niskin Contaminants Chlorophyll Nutrients Temperature Salinity defra Determinand Sample Sub sample CD HG ZN CU FE PSAL TEMP CPHL NTRA NTRI gt gt S S Si gt Pi Pi Pi P 1 1 1 1 1 2 2 3 4 4 Document Owner MermanUserGuide_6 0_20Sep2010 IBM Page 32 of 62 g defra If water is taken by continuous flow then a sample is considered to be taken from a single location depth and within a time required to fill all bottles for analysis Bottles filled for different analysis are sub samples and should be labelled 1 2 3 4 etc E Contaminants Continuous flow C Chlorophyll C Temperature Salinity QO Nutrients Determinand Sample Sub sample CD A 1 HG A 1 ZN A 1 CU A 1 FE
14. 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 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
15. 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 Email 1 Defra Portal Enrolment Details are sent to the user Email 2 MERMAN Enrolment Details are sent to the user User to enrol on to Defra Portal 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 a FeO DN 2 2 2 Enrol for Defra Portal When the helpdesk has registered the user s Known Facts the user will receive two emails 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 lt Portal defra gsi gov uk gt To Liisa Stuar UK IBM IBMGB 31 05 2006 14 41 cc D bec Default custom expiration i 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
16. 6 0_20Sep2010 Owner IBM Page 44 of 62 Regions and strata 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 RK defra Department for Enwronment Food art baal After 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_6 0_20Sep2010 Owner IBM Page 45 of 62 g 557E defra Sam
17. 8 2006 r Subject Submission of CEFAS_AQC_2007_positive csv Thankyou for your submission It has been successfully loaded into the Merman 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_water_2004err 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_6 0_20Sep2010 Owner IBM Page 41 of 62 ul d wu Wi Ga BER FRS
18. 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 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 33 of 62 g defra 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 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 Sample Sub sample Documen Owner A D DD D DD DD fz SS SP SS P Si SG SS SS SS t YNN N N N NN
19. BusinessObjects InfoView Microsoft Internet Explorer provided by Defra File Edit View Favorites Tools Help Ort EE Ames E Address E http gb1 3qap020defa 1 8085 wijsp scripts login webiHome jsp BUSINESS OBJECTS Home My toen Options Help Corporate Documents Personal Documents sh Access documents available to you and other users SN Access the documents you saved for your personal use D a as well as the documents other users have sent to you Advanced Inbox New Document All Documents Uncategorized Documents Create a new document from a Universe You can also Add a document to InfoView from your computer Scheduled Documents View the scheduled list of documents and check their status ZS 2 Figure 19 Select Corporate Documents Screen 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 Select the desired report Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 52 of 62 un if 1j tt Ga BUSINESS OBJECTS Merman Corporate Categories gt Merman gt Merman A Document s in Merman iew Details Add to My Info View D Hame 2 weil Data Screening Report DI ICES weil Riverine and Indirect Discharges si Figure 20 List of Available Reports A Prompt window wi
20. GIL LES HPIGM FROT ANISAKIX ANISAKIX LATLIP LEPE OPH ACAN THO EPID PAP GLUG STE To be confirmed by BEAQC To be confirmed by BEAQC Possibly FLM Fluorometric determination GRS Gross examination To be confirmed by BEAQC Possibly CMP Comparative analysis To be confirmed by BEAQC Possibly CMP Comparative analysis To be confirmed by BEAQC Possibly CMP Comparative analysis GRS Gross examination MermanUserGuide_6 0_20Sep2010 IBM g defra T26 Times No 26 Quantification of metallothionein MT in fish liver tissue T39 Times No 39 Review of analytical methods for determining metabolites of polycyclic aromatic compounds PACs in fish bile T24 Times No 24 Use of imposex in the dogwhelk Nucella lapillus as a bioindicator of tributyltin TBT pollution T11 Times No 11 Oyster Crassostrea gigas embryo bioassy T29 Times No 29 Sediment bioassy using the polychaete Arenicola marina T28 Times No 28 Corophium sp sediment bioassy amp toxicity test T19 Times No 19 Common diseases amp parastites of fish in the North Atlantic Training guide for identification Page 26 of 62 g defra Fish Disease NECRCG APOPTS 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 HEMAP
21. N YM A ch Fe fe Ff ck ch ch eck sch sch sch sch sch sch sch Matrix LI LI LI LI MU MU WO WO WO LI LI LI LI MU MU WO WO WO LI LI LI LI LI LI LI WO Species Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Limanda limanda Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa Pleuronectes platessa MermanUserGuide_6 0_20Sep2010 IBM Determinand HCHA CB101 HCB LIPIDWT CD PB MOCON LNMEA WTMEA HCHA CB101 HCB LIPIDWT CD PB MOCON LNMEA WTMEA HCHA CB101 HCB LIPIDWT CD PB MOCON LNMEA No Individuals oa Om OO Om a aun uo zech ch sik ea sch zeck wb zech sik zech zb sek web O O O O O O O Oli OO O O O O O O O O Om Sex Code Zz Z Z ZS SZ ZS ZS E28 X XxX KKK KK X Page 34 of 62 g defra B 1 WO Pleuronectes platessa WTMEA 10 X Shellfish taken within one area should also be considered as one sample if it is all of the same species If the shellfish 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 sub
22. S T38 Times No 38 Use of Liver Pathology of Flatfish for Monitoring Biological Effects of Contaminants HIS PR Histopathology plastic resin When submitting data using the BEAQC template there are a number of rules in place to ensure that data is 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 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 Code 1 DTYPE ALBO_1 METOA Description For use with biological effects PARAM MUNIT REFSK ACREED INTAQC CONCH INTSCH ICCOD QCSTAT all mandatory ALABO_2 voluntary CRMEV CRMMV CRMSD Z_SC SRCWT SPECI RLIST ORGSP should be blank 2 DTYPE ALBO_1 METOA PARAM MUNIT REFSK ACREED INTAQC QCSTAT all mandatory ALABO_2 CONCH INTSCH ICCOD CRMEV CRMMV CRMSD Z_SC voluntary SRCWT SPECI RLIST ORGSP should be blank Document measurements when an intercalibration exercise possibly informal and so not registered with ICES has been performed but the results to not conform to be able to provide expected measured value sd of measured value and z score Example types include fish disease imposex intersex For use with biological effects measurements when an intercalibration
23. _Biota_2005 err WordPad File Edit View Insert Format Help Cee SLk Aa a a ffitle DATA AUDIT REPORT 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 I 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 or
24. a and adjacent strata This would involve the same sort of analysis 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 Itis 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 in a 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_6 0_20Sep2010 Owner IBM Page 46 of 62 g defra 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 ra
25. be a single result so this field may not apply If a z score for the intercalibration has been provide then give here This field is specific to bioassays This field is specific to bioassays This field is specific to bioassays This field is specific to bioassays Give here your assessment of if the measurement has sufficient AQC This will subsequently be approved by the BEAQC group This field is at present spare This field is at present spare This field is at present spare This field is at present spare 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 the 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Measurement of DNA adducts in fish by 32P postlabelling Page 25 of 62 4 IMP and INT Bioassay Water Bioassay Sediment Bioassay Sediment Fish Disease Document Owner MT PYR10OH VDSI RPSI IMPF LNFPE MORT PNR REDF MORT PNR and REDF MORT PNR and REDF LYMP CYS LIVE NOD SKEL DEF STEP STO SKIN ULC X
26. boratory intercalibration that has been performed 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 Where an informal scheme has been used eg samples 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 Choose the appropriate intercalibration code Note if the scheme is not registered with ICES than the code will have been chosen by BODC Give the expected value for the measurement made for the intercalibration Page 24 of 62 Reference Material Measured CRMMV Value Reference Material Standard CRMSD Deviation of the Measured Mean Z Score Source of Reference Seawater SRCWT Latin Name of Test Organism SPECI Reference Code List used for RLIST Species Dr Origin of Test Specimen ORGSP BEAQC Assessment of Quality QCSTAT Status Reference Material Basis of CRMMB Determination Number of Measurements CRMNM Reference Testing Period CRMPE Intercalibration Reference CRMCO Material Code g defra Give the measured value for the intercalibration measurement completed by your laboratory Give the standard deviation of the intercalibration measurement completed by your laboratory Note for some measurements it will
27. ceccceeececeeeeeeeeeeceeeeecaeeeeaaeeeeeeeseaeeesaaeeesaaeseeeeeesaeeesaeeseneeseeees 14 3 2 Populating Input Spreadsheets cccccccceeceeeeeeeeeeeeeeeceeeeeeeaeeeeaaeeceaeeesaaeeesaaeseeeeeseeeeesaeeeeaeeenees 14 3 2 1 Sample Data Input Gheete cae eeeaaeeeeeeeseaeeesaaaeseeeeeseeeesaeseeeeseeeeess 16 3 2 2 eet Vgl LEE 18 3 2 3 Chemistry Contaminants AQC Input Geet 19 3 2 4 Further AQC Submission Information 21 3 2 5 Chemistry Contaminants PT Input Sheet cecccceeeeceeeeeeeeeeeeeeeeaeeeeaeeseeeeeseaeeneeeeeeeeees 21 3 2 6 Further PT Submission Informations ccccceeeecceceeeceeceeeeeaeeceeeeeeceaeeeeaaeseeeeeseeeeseaeeeenaeeseaees 22 CR E Eeer 22 3 2 8 Bioeffects AQC Input Template 23 3 2 9 Sample and Sub sample Guidelines 28 33 Saving Submission FilO ss x secasscseeken ceeceesace vaihdacecaedaneecvacechaesesdce dete colds eesdeceveeasdedavaaualedunessestiastarene 36 34 Uploading Data rechscsecnctssvceswestatan le encenm ets Regen d eege ee aaa aiea a aaa aa aaaea h iere egeg d 37 3 4 1 Confirmation Of Gubmjeeslon seas eeeaaeeeeeeeseaeeecaaeseeaeeseeeeeseaeeeseaeeseeneeds 40 3 5 Handling Errors egenart aaa a EE a a A Ea EAR EE 41 3 6 Releasing RRE TEE 42 3 7 Submission Checks by Responsible Officers c ccceccceeceeeeeeeeceeeeecaeeeeaaeseeeeeceaeeeseaeeseneeseaees 43 3 8 Station naming and new Station SUDMISSIONS c ccceeeeeeeeeeeeeeeeeeeeeceaeeeeaaeseeeeeseaeeesaeeeeeaeeeeaees 44
28. d by the deadline as specified in section 1 4 If any of these checks highlight any inaccuracies then resubmissions should 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 Corporate Reports 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 LIPWT 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 t
29. d 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 Defra website http www defra gov uk environment water marine uk science merman htm 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 ad 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 MermanUserGuide_6 0_20Sep2010 Owner IBM Page 51 of 62 Win al UI GO OK 2 m ID i Instructions Logon to Business Objects Select Corporate Documents gt MERMAN Ka
30. de_6 0_20Sep2010 Owner IBM Page 14 of 62 Wull ID i A al def tewronment Feed d baal Attain Figure 8 Enable Macros Pop up The input sheet opens A E e D E E G H 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 Where a code is to be entered the 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 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 15 of 62
31. de_6 0_20Sep2010 Owner IBM Page 20 of 62 g defra 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 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 have been and 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 li
32. e Code ICCOD Reference Material Expected CRMEV Value Document MermanUserGuide_6 0_20Sep2010 Owner IBM g defra E_mail address of the person submitting the file to the MERMAN application E mail address of the coordinator of the submissions for any one organisation In smaller organisations it may be the same as the submitter The year which the measurements are made in The organization you work in This is the template type BEQ for Biological effects This is the type of biological effect measurement and once selected determines which other fields should be completed see Merman User Guide for details This is the data type which may be biota sediment or water For most biological effects it will be biota with the exception of bioassays in sediment and water The analytical laboratory that made the measurements The analytical laboratory that made the measurements Choose the most appropriate method of analysis see MERMAN User Guide for suggestions Choose the correct unit of measurement for the parameter Choose the most appropriate protocols see MERMAN User Guide for suggestions If the laboratory making the measurements has UKAS accreditation for the method then indicate here Describe any internal laboratory AQC in less than 500 characters such as chemical standards training new staff tests of competence across analytical staff etc Choose which type of reference material is most appropriate for the inter la
33. e accessed from the navigation bar above Log out Before accessing Defra applications you must register for access Some applications will require pre registration activities For further information about what applications are available through the Defra portal click here YOSIN Done A Stan 3 TestManagertttachments Online home Microsoft 1 29 Rational ClearQuest IN Oracle SQL Developer Ie Defra UK Portal 11 25 Figure 13 Defra Portal Click the Browse button to select your submission file Click OK Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 38 of 62 g defra Duncan Cameron g Marine Environment Monitoring and Assessment National Database defra Home MERMAN Home File Upload Business Objects File Upload Defrahome ContactDefra Log out 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 Ca Step 2 Select the file by using the browse button 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 Spied Fie 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 bee
34. e 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 number one Example below Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 29 of 62 Paranais litoralis 1000 Limnodrilus hoffmeisteri 1000 Heterochaeta costata 1000 Enchytraeidae 1000 Corophium volutator 1000 Limnodrilus hoffmeisteri 1000 Paranais litoralis 1000 Limnodrilus hoffmeisteri 1000 CO OO o w Di Di w WD wD wD gt gt gt gt Pi gt defra Sub sample 1 1 1 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 spaces o i e Enchytraeidae 1000 Enchytraeidae 500 Limnodrilus hoffmeisteri 1000 Heterochaeta costata 1000 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Sample w Di Di gt gt S Pi YS Pi Pl Si Pi gt Sub sample Al Al Al A1 A1 A1 Page 30 of 62 un nil dn Ga defra Sample Sub sample B1 B0 5 B0 5 B0 5 B0 5 B0 5 C1 C1 C1 Ee 00 Paranais litoralis Enchytraeidae Corophium volutator Paranais litoralis 1000 Paranais litoralis 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
35. e01 5 Fl West Scottish Coast The Minch North WSctCst_MinchN_sed2 1 Fl West Scottish Coast The Minch North WSctCst_MinchN_se02 2 Fl West Scottish Coast The Minch North WSctCst_MinchN se02 3 6 Some monitoring designs are not so neatly captured For example FRS 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 FRS 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_6 0_20Sep2010 Owner IBM g 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 name Sample E Eden Offshore Fladen Offshore sei 01 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 Offshore Fladen_Offshore_se02 3 FI Fladen Off
36. een defined yet Sampling_strategy Strategy employed to obtain Codes as per the drop down sample menu when macros are enabled Sample_purpose Purpose of monitoring Codes as per the drop down menu when macros are enabled See Note 1 4 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 16 of 62 Station number Field Name Station_number Date sample collected Start time of sample collection End time of sample collection collection collection Sample number for each species in haul each sediment core each sediment grab each water bottle Sample_date Sample_start_time Sample_end_time Latitude_degrees Longitude_degrees Sample_number Sub_sample_number Sub sample number identification Laboratory_sample_number Unique sample number assigned by Laborator Matrix 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 Sampler_type Analytical_lab_code Analytical year sample analysis This typically is the same nominal year as the year of Monitoring Determinand_code Parameter code Determinand_units Measurement unit Basis Status of weight measurement Document MermanUserGuide_6 0_20Sep2010 Owner IBM g defra Instructions Codes as per the drop down m
37. enu when macros are 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 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 Page 17 of 62 Ga ESEE defra Field Name Description Instructions Po ena led Determinand_qualifier Determinand_value Water_sample_depth Water amp biota Pressure depth Value in metres m where sample is taken Sediment_depth_Upper Lower Sediment depth m upper For sediment the upper level is lower levels in sediment generally Om 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 acti
38. er 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 56 of 62 ul ih hi oa ll yy del OD Ge SCH Do Q WEBINTELLIGENCE SS D E S E Edit Query Edit Report Run query 4 Query 19 R 9 Aaaa auen i Data Properties Merman To include data iNthe report select objects in the Data tab and drag them here Click Run Query Ba Metzadata D return the data to ths Which location A Which Measurements What Matrix Date Time of Sample All Objects A Additional Search Criteria aac Results Sf Query Filters To filter the query dratjyredefined filters here or drag objects here then use the Filter Editor to d custom filters Query Filters Figure 25 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
39. for MERMAN The user will need the user ID allocated in the previous step Forward Follow Up Chat lt MERMAN defra gsi gov uk gt To Liisa Stuar UK IBM IBMGB 31 05 296 14 41 cc bec 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 o the Marine Environment Monitoring and Assessment National Database n Internet Explorer browse to http caratest2 defra gov uk wps portal e Defra Portal Homepage will appear 3 lick on the Log on to Defra link from the menu on the left hand side of the screen EX e Security Validation Page will appear si 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 E E lick 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 Assessmen
40. g Programme ICES International Council for Exploration of Seas BODC British Oceanographic Data Centre CMA Competent Monitoring Authority AQC Analytical Quality Control PT Proficiency Testing CSV Comma Separated Value 7 2 List of Competent Monitoring Authorities CMA Description CEFAS Science Centre for Environment Fisheries and Aquaculture FRS Fisheries Research Services SEPA Scottish Environment Protection Agency EHS Environment Heritage Services AFBI Agri Food and Biosciences Institute EANLS Environment Agency National Lab Service EA Llanelli EAWal Environment Agency Wales EATha Environment Agency Thames EASou Environment Agency Southern EA SW _ Environment Agency South West EA NW Environment Agency North West EANE Environment Agency North East EAAng Environment Agency Anglian EANat Environment Agency National EAMid Environment Agency Midlands Defra Defra Document MermanUserGuide_6 0_20Sep2010 Owner IBM defra Page 61 of 62 g defra 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
41. gation bar above Log out Before accessing Defra applications you must register for access Some applications will require pre registration activities For further information about what applications are available through the Defra portal click here Figure 6 Defra Portal Home Page Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 12 of 62 ul H mat d EA al II ia OD e gt en Qa The MERMAN home page opens Marine Environment Monitoring and Assessment National Databa Duncan Cameron Defrahome ContactDefra Log Programme Sponsored By Marine Environment Monitoring and Assessment National Database ETN The National Marine Monitoring Programme NMMP was established to provide a coordinated approach to 8 SCOTTISH EXECUTIVE environmental monitoring in coastal and estuarine areas MERMAN contains results of all chemical biological effects assessments for the NMMP performed in the UK from 1990 Data Supplied By WE Llywodraeth Cynulliad Cymru Welsh Assembly Government g Ce fas Department of Agriculture and Rural Development Environment www dardni gov uk Agency SCOTTISH ENVIRONMENT PROTECTION AGENCY ENI A E E CEDAS 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_6 0_20Sep2010 Owner IBM Page 13 of 62 ul
42. he data filter will not be transferred to ICES Use the BO report Final AQC Scores in Corporate Documents for this check This report details the AQC scores for each parameter for each data type for a specified year 8 Unhold submissions Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 43 of 62 ul d wu Wi Ga defra 3 8 Station naming and new station submissions The protocol for naming monitoring stations in MERMAN 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 requires a change in the protocol for naming monitoring stations in particular to link stations more closely to the regions they represent This document proposes a protoc
43. hen 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 28 of 62 ul nil dn Ga defra 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 surface 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 ANTH C Z C A 1 1 P P 1 P 2 2 2 2 P P 1 P P 2 u n d l 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 E ES E E Bo C 2 u B 3 2 9 2 Biology Each individual grab or dredge is considered a sample and should b
44. http www cefas co uk publications scientific series green book aspx 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 2006 data to ICES are as follows Contaminant and biology data submitted to MERMAN by 1 June 2007 Contaminant and biology data submitted to ICES by 30 October 2007 RID data submitted to MERMAN by March 2007 RID data submitted to OSPAR by 1 October 2006 outside of MERMAN scope 1 5 Quick Reference Guide for Data Submission Process Check your data are correct Compare against previous years data Check you are using the latest version of the input templates Open the relevant template using Excel at least 2000 and enable macros Fill in the spreadsheet as per instructions breakout groups user guide example spreadsheets responsible officers BODC help facility Check that you do not have transcription errors Save template as a csv using the following naming convention CMA_submissiontype_year_version e g CEFAS_biota_2005_a Log on to the DEFRA portal After submission send your xls file to nmmp bodc ac uk Once all data monitoring and AQC have been submitted they must be released by submitting the Unhold template this will allow other users outside of your CMA to view the data Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 8 of 62 ul nil dn ov defra 2
45. iddle Forth Estuary Forth_MiddleEst_se02 1 SF Forth Middle Forth Estuary Forth_MiddleEst_se03 1 SF Forth Middle Forth Estuary Forth_MiddleEst_se04 1 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 47 of 62 9 defra Attam A 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_se01 1 SR West Scottish Coast The Minch North WSciCst_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_se01 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 Minch North WSctCst_MinchN_s
46. iginal filename As well as this resend the file to the Data Manager CSEMP bodc ac uk 3 6 Releasing Data When sample data are first submitted into the database each record is defaulted to Held 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 a Submission Held spreadsheet The release spreadsheet must be submitted for each data type sediment water biota biology AQC PT Biology AQC for each that CMA and monitoring year Any subsequent data submissions will automatically set the data for the same year and CMA to be Held again All data must be unheld for the ICES report to be created Data should not be reheld once the ICES report has been created as agreed at CSSEG Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 42 of 62 ul nil di Ga defra 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 complete
47. 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 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 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 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 40 of 62 un RN pi d A Il Ih al TL ja LO im HO New Memo Reply Repl To All Forward v J Delete Fonow Up Folder Copy into New ES show Trvead Tools Merman Submission MERMAN DEV To Liisa StuarvUK IBM IBMGB Jon Gould UK IBM IBMGB 10 05 2006 09 50 cc CR bec Default custom expiration date of 08 0
48. ll open Enter the required prompts as instructed Press the Run Query button Reply to all promptis before running the query Monitoring Year 2005 Show Yalues Cancel Figure 21 Report Prompt Window Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 53 of 62 Wull ID i A defra Department for Enwronmer Feed act baal Attain The report is generated and the report displayed on the screen DEI Riverine and indirect Discharges Mal Figure 22 Report Results Screen 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 54 of 62 Wull ID i Za defra food and hani Atta 4 2 2 Saving Reports When you want to save a report select Save from the top left corner of the screen BUSINESS OBJECTS Add to My InfoView Work Status Date Last Updated 30 05 2006 Monitoring Year 2005 n Ses Figure 23 Save Report The Save options window opens and you can select how you want to save the report BUSINESS OBJECTS Work Status To save this document select one ofthe actions below Save as a corporate document Save this documentto corporate documents Save as a personal document Save this document to InfoView for your per
49. mission PT Water Sediment Biota Biology RI D AQC AQC Biology PT Data_type ICES Data Type code Codes as per the drop macros are enabled Analytical_lab_code Laboratory or institute responsible for the Codes as per the drop analysis and measurement of the parameter down menu when value or the laboratory responsible for macros are enabled sorting and identification of biological samples ICCOD V3 2 Intercalibration codes for 3 2 format Code as defined by QUASIMEME Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 21 of 62 ul IW ill i lin Ga Il Ihi l T A D HO Field Name Description ___ Instructions ICCOD V2 2 Intercalibration codes for 2 2 format Code is made up of the QUASI MEME round and exercise number and includes the matrix specific code Assigned_value Value assigned by Quasimeme as Target concentration of determinand for PT assessment Determinand_code Parameter Code Codes as per the drop macros are enabled Determinand_units Measurement Units Codes as per the drop macros are enabled Mean Actual value measured by analytical laborator Z_score Actual Z score achieved by Analytical Lab This CANNOT be null If you do not have a Z score remove the entr Value Ignore this field which is hidden 3 2 4 1 Further 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 partici
50. mission of data at stations that have been visited more than once in a monitoring year Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 35 of 62 un nil dn Ga defra 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 FRS_biota_2006c csv SEPA_water_2006b csv AFBI_biology_2006d csv EHS_aqc_2006b csv EANLS_biology_aqc_2006d 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 submitted 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 a
51. must be taken to ensure that stations are numbered sequentially If more than 1 CMA samples in the same strata them coordination between responsible officers is required The latest version of the station dictionary can be viewed on the SEPA website A spreadsheet for adding new stations has been circulated to Responsible Officers It must be completed for any new stations Specific instructions are held in the spreadsheet and are shown below Fields shaded in grey should be completed by selection from drop down lists All lat and longs to be in decimal degrees If the ICES Rectangle is not known then leave blank See MERMAN User Guidance section 3 8 for further details on sampling strategy 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 with some field knowledge The station code must not exceed 20 characters in length The station name should not exceed 100 characters in length Fill in as many MSTAT fields as appropriate Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 50 of 62 defra ul nil dn ov 4 Running Reports 4 1 Using Business Objects 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 This user guide does not give detaile
52. n accepted and loaded to MERMAN Once you have selected the input file click on Upload File button 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 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 39 of 62 ul IW li ul Ml Ga defra File Uplbad 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 Step 3 To upload the selected file click on upload file button 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 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
53. ndom e g transects down a riverine strata that sample random points each year or opportunistic none of the above 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 FI 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 M
54. nerated according to A user types as shown below The security levels and time frames may change in the future User Group Access to Data Can see all sample and AQC data for their CMA User own CMA Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 58 of 62 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 AQC Status of Passed AQC data not available to the Public Document MermanUserGuide_6 0_20Sep2010 Owner IBM defra Page 59 of 62 ul nil dn Ga defra 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_6 0_20Sep2010 Owner IBM Page 60 of 62 7 Appendices 7 1 List of Abbreviations Abbreviation Description Marine Environment Monitoring and MERMAN Assessment National Database RID Riverine and Indirect Discharges CSEMP National Marine Monitorin
55. nil dn Ga defra 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 input spreadsheets a Sample i Biota ii Water iii Sediment iv Biology v RID b Quality Data i AQC for contaminants ii Proficiency Testing data for contaminants iii AQC for Biology 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 SES Document MermanUserGui
56. nked 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 will not 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 input 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 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 3 2 4 Chemistry Contaminants PT Input Sheet Field Name Description Instructions Submission_type The type of sub
57. o Green Book and MERMAN portal Corallie Hunt BODC This document has been distributed to Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 3 of 62 ul IW il Ml ov Il Ih d A p HO Contents Mz eu dee le e EE 6 1 1 What is MERMAN Databaee cece cccceceeeceeeeeceeeeeeeeeeeeeeee eae eeeaaeedeeeeseeeeeaaeeseaaeseneeeseaeeesaeeseneeee 6 1 2 Components of the MERMAN Database eseeseeseeeeeeseeestenrtrnntetntetnnsttnttnnntnntnnstnnsnnnsntnsnnnnnt 6 1 3 Scope of this User Guide 0 cc eecceccceccceeeeeeeeeeee cece eeeeaeeeeeeeeeaeeeeeaeedeaeeseaeeesaaeeseaeeseeeeeseeeesaeeneneeee 7 1 4 The UK National Marine Reporting Cvcle ccecccccccceeeseeceeeeeeeceeteeeeceeeesaeeeeaeeseeeeeseaeeeeeeseeneeds 8 1 5 Quick Reference Guide for Data Submission Process 8 EE Eegen Tee aa eee eee en rere eee eee 9 2 1 Requesting Access to MERMAN 0 ccccceceecceeeeeeeeeeeeeeeeeeeeeseeceseesaeeeseesaeseeeeeneeeeseeneneeeeesenaeeeenenaes 9 2 1 1 User Details Known Facts AAA 9 2 2 Logon to MERMAN First Time User 10 2 2 1 OEI E ege A Eed E A AE 10 22 2 Enrolfor Detra Portal eteigegeteusgerigees dees ces ceecvavenexdebeadeveluyencelantnesaxehens E NEAN aaae A 10 22 3 Enrol for MERMAN s issn anainn aaa AAA E LAAT Eaa NA aes 11 2 3 Logon to MERMAN Normal Logon sssssssesssssssssssssissrisssissrissrissirsstissrisstisstnnstnsntnnstnnstnnnstnnstnn te 11 Be enn rale RE 14 3 1 Obtaining Input Spreadsheet
58. ol 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 Where possible regions will be aligned with the regional seas used for Charting Progress and strata will be 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 Three main sampling strategies are recognised in the CSEMP fixed station stratified random and stratified fixed monitoring However the difference between them is sometimes ambiguous so rules are proposed to clarify things An additional sampling strategy opportunistic is needed as a catch all for other monitoring activities 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 Document MermanUserGuide_
59. pate in proficiency testing The data are submitted to MERMAN in the PT_input_sheet Currently MERMAN cannot cater for some specific results as a result these results have to be omitted from the submission These results are e Unable to submit a non numeric z score QUASIMEME 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 however MERMAN cannot currently accept these e Unable to submit a lt character in the result field e g LOD Currently this symbol cannot be submitted in the result field A change to allow this should not have any follow on consequence to the filter as the filter only uses the z score in its calculation We hope to be able to enhance MERMAN in the future to cope with these results and prevent any further loss of data 3 2 5 Biology AQC Input Sheet This input sheet will be used for determinands from the biology data This input sheet is also to be used for those determinands from other data types which do not currently have AQC for instance temperature nitrate and dissolved oxygen This is because to be submitted to ICES a determinand has to have a Pass status In order for CSEMP determinands which do not have Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 22 of 62
60. pling strategies There are four sampling strategies fixed 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 Itis 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 Itis intended at the analysis stage to see if there are common trends at these stations i e combine information across stations within strat
61. shore Fladen_Offshore_se02 4 FI Fladen Offshore Fladen Offshore se02 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 name Sample _ Op East Scottish Coast Scurdie ness to Deil s Head ESctCst_Scurde_ 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 Deil s Head ESctCst_Scurdie_wa 4 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_6 0_20Sep2010 Owner IBM Page 49 of 62 g defra Adding new stations to the MERMAN station Dictionary Care
62. sonal use Save to my computer Save this documentto your computer as Microsoft Excel format xls PDF format HusinessObjects document rep Figure 24 Save Options Screen 9 Press the Save button Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 55 of 62 ul nil dn Ga defra 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 table 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 e Additional search criteria o All other data elements that aren t stored in the other folders such as Submission details sample reason sampl
63. t National Database link to enrol for access to the Marine Environment lonitoring and Assessment National Database 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 gov uk wps myportal merman Enter User ID and password in the screen below Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 11 of 62 un if 1j lli Ga defra 2 Security Validation Before you proceed to Defra Portal Applications In order to login your browser must be configured to accept cookies If you do not accept cookies sea any error messages Please supply your Goverment Gateway User ID and Password Unauthorised access may constitute a criminal offence User ID Password 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 g Defra Portal Duncan Cameron Defrahome ContactDefra Log out Home MERMAN Home File Upload Business Objects Home laD Navigator Applications Home Page Change password The applications you have previously registered for can be accessed from the navi
64. 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 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_part1 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_part1 csv CEFAS_Biota_2005_part2 csv CEFAS_Biota_2005_part3 csv CEFAS _Biota_2005 csv Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 62 of 62
65. uld be used in Sample Reason fields 1 2 and 3 If data is submitted that is to be used for national purposes only then the code NATL should be entered in Sample Reason 1 Note1 4 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 3 2 2 Biology Input Sheet Field Name Description Instructions Mesh_size Mesh size of net or sieve 500um or 1000um Sample_depth_min Minimum depth of sample m Value in metres m i e the sediment bed from where grab is taken Sample_depth_max Maximum depth of sample m Value in metres m Species Latin name of species or Codes as per the drop down Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 18 of 62 defr g a aggregated genus family menu when macros are enabled Stage_development Stage of development Codes as per the drop down menu when macros are enabled Sex Codes as per the drop down menu when macros are enabled Codes as per the drop down menu when macros are Species group size enabled Physical_state Physical state at time of Codes as per the drop down sampling menu when macros are enabled
66. un nil dn ov defra Marine Environment Monitoring and Assessment National Database MERMAN User Guide Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 1 of 62 un nil dn ov defra Document History Revision History Number Mark Charlesworth BODC Ke 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 rehld 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 Corrected MERMAN
67. uthorities in appendix 2 Document MermanUserGuide_6 0_20Sep2010 Owner IBM Page 36 of 62 E defra Imn el Ii ul Pax foad ard baal After Microsoft Excel x 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 xls 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 es Figure 11 Prompt for Saving the Submission File ST As 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 X Save as type esv Comma delimited csv OE aly 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_6 0_20Sep2010 Owner IBM Page 37 of 62 Defra UK Portal Mozilla Firefox File Edit View Go Bookmarks Tools Help ei CG IER co C Defra Portal User7 Merman Defrahome ContactDefra Log out defra Home MERMAN Home File Upload Business Objects Navigator Applications Home Page Change password The applications you have previously registered for can b
68. vities 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 i 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 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 their 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 and NMP sho

(MERMAN) User Guide - British Oceanographic Data Centre

Contents

Download Pdf Manuals

Related Search

Related Contents