Food Surveillance System ======================== The Food Surveillance System collects food and animal feed sample information taken by competent authorities across the UK. The sample and results data is submitted to the central database by the laboratories. Food sampling officers enter details of samples taken and of the analysis required into the FSSNet software application. The data is exported and sent as an encrypted file to the relevant Public Analyst laboratory. The file may be sent on a floppy disk, a USB memory stick, as an e-mail attachment or via the internet. Each laboratory will agree the most efficient method with each of the participating clients. In some instances, it is convenient to allow the officers to enter the sample data into a computer running the FSS software which is located on the laboratory premises. A separate procedure is also available for the data file to be transferred between the Competent Authorities client and the laboratory by way of the FSS website. The laboratory registers the samples into their own Laboratory Information Management System (LIMS) using the FSS data file for much of the information recorded. The laboratory will add such information as it needs during registration; however any changes to data originally entered by the officer should be audited and reported back to the relevant competent authorities client. Once registered, samples are treated in exactly the same way as any other sample within the laboratory. Only at sample approval is there any difference from other samples, see “Outcome Recording” below. Once samples have been approved and reported, the data is exported from LIMS in a predefined format and sent electronically to the FSS web administrator. The new data is incorporated into the FSS database, overwriting existing data if appropriate. Finally, the competent authorities clients download their own data from the FSS web site thus updating their own systems. It can be seen that:- 1. There is a training issue for the LIMS administrator 2. There is an ongoing maintenance issue for the LIMS administrator 3. There is a training issue for sample reception staff 4. There is a training issue for sample approvers 5. There is no impact on other staff who use LIMS 6. Any changes made to sample data as it passes through the laboratory LIMS are written back to the Client’s system thus updating their system. System diagram --------------- .. image:: media/image1.jpg :alt: Diagram Description automatically generated :width: 5.75833in :height: 4.62167in Data Structures ---------------- The data consists of a primary table of samples data along with associated results and labelling outcomes. The sample information is largely completed by the competent authority. The lab then applies a satisfactory/unsatisfactory judgement and comments along with a set of results and outcomes. The data structure and reference lists can be seen in appendices II – IX. Outcome recording ------------------ In order to provide the Competent Authority client with sufficient information to complete their FSA returns, it is necessary to indicate the category and judgement of each test result. The result outcome category is related to the determination applied. Further, labelling failures should be recorded against the sample. (See appendix VIII)It is understood that the only person able to make this judgement is the person approving the sample; only they have all of the analysis information available and the knowledge or experience to decide the categories of examination and failure. Consequently, at sample approval the approver will be presented with a dialogue to gather the appropriate information. It should not be possible to skip this dialogue. As the great majority of results will be “satisfactory”, it is useful to set this value as the default for all tests. The approver need only change the outcome for any or all results deemed to be unsatisfactory. A validation check should be enabled which prevents a sample being recorded as satisfactory overall while having one or more unsatisfactory outcomes recorded against it. Similarly an unsatisfactory sample must have at least one unsatisfactory outcome. Reference Lists Lab determinations ~~~~~~~~~~~~~~~~~~~ In order to avoid the need for each participating laboratory to use the same set of determination codes (Dets), a standardised list of determinations has been created (FD_Dets). Please see an extract of this reference list in Appendix VII. This list gives a code to each analyte/units combination taking no notice of methodology (except in a very few cases). It is a task for the Laboratory’s LIMS administrator to match their internal laboratory Det with the corresponding FD_Det. The precise method for doing this will depend on the LIMS application in use. This scheme should allow for the possibility of several Dets to have the same FD_Det. This process requires to be completed once only for each relevant Det. Not all Dets in any particular laboratory system will require an FD_Det entry as only reportable Dets related to FSS samples need be included. The FSS Support Team maintains the FD_Dets list and any requests for additional FD_Dets require to be raised with them. The FSS Support Team will provide the designated contact person within each of the participating laboratories with an updated FD-Dets table, when necessary, via e-mail. On receipt, the updated table should be used to overwrite the existing table. The accompanying e-mail text will, normally, specify the additions or changes and can be used to check if any are relevant to the recipient laboratory. Laboratories are responsible for the integrity of the matching process. Assistance may be sought from The FSS Support Team in providing tools to assist in completing this process. The FSS Support Team will periodically audit the matches at a particular laboratory and will require any corrections to be carried out timeously. Please note that only results which are included in the final report to the client should be exported to FSS. All other results, e.g. intermediate results, should be ignored. Food/feed categorisation ~~~~~~~~~~~~~~~~~~~~~~~~~ This is a reference list that provides all the food and feed categories currently in use. This list is fairly stable and rarely needs to be updated. Any updates will be circulated by The FSS Support Team. See appendix IV. A guidance document on food categorisation is also available on the FSS website: *https://www.envhealth.scot.nhs.uk/public/Documents/* Outcomes and Outcome Codes ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Each test result will have an outcome code applied (see appendix VIII), for the great majority of results, this will be the ‘satisfactory’ code. Furthermore, labelling outcomes are recorded against the sample in a separate outcomes table (see appendix VIII). The standard Outcome Code lists (in a suitable format) can be obtained from The FSS Support Team. Translation tables ~~~~~~~~~~~~~~~~~~~ In many LIMS, it will be necessary to set up a process whereby the data supplied in the FSS data file is matched to appropriate locations (fields) in the system. Similarly data exported must be translated from the LIMS structure into that expected by FSS. Clearly the manner in which this is achieved is system dependent. The input and output data files use an xml schema (see Appendix IX). Information tables -------------------- AUDITING ~~~~~~~~~ The LIMS should be capable of auditing changes made to the data supplied by FSS and periodically reporting these changes back to the relevant Competent Authority client. OUTCOME ~~~~~~~~ A process requires to be put in place to record the “Outcomes” (using the Outcome Codes as listed in appendix VIII) for each test applied to an FSS sample analysed at the laboratory. The Outcome data must be exported to FSS in an agreed structure. Changes to existing LIMS tables -------------------------------- Additional Fields ~~~~~~~~~~~~~~~~~~ It is highly likely that data relating to FSS samples will not be recorded currently in the LIMS in use. It will be necessary to be able to handle this additional data either by the creation of new, linked, tables or by the addition of fields to existing tables. The precise process to be used is system dependant but must maintain the integrity of the FSS data. Changes to Data type and/or length ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ It might also be necessary to amend the data type or field length of existing data fields so as to accept the FSS data. The disposition of the sample i.e. Satisfactory / Unsatisfactory needs to be recorded and transmitted to the FSS database. The structure for the FSS data includes this item. Changes to LIMS processes -------------------------- Apart from certain operations, e.g. sample registration and data export, there should be minimal impact on most LIMS processes. The main aim would be to remove any differentiation between FSS samples and others during the laboratory analysis and result recording process. Changes to screens or additional screens ----------------------------------------- In order to accommodate FSS samples, some screens may need to be redesigned. However this would be entirely system specific. Other changes -------------- Sample Reports ~~~~~~~~~~~~~~~ Sampling Officers name The standard information entered into FSS for the sampling officer is “Name” plus “Tel Number” and/or “E-Mail”. For some reports, it is necessary to hide, or remove, the unwanted text and leave only the contact name. This can be done by editing the LIMS sample record but is better achieved by modifying the report itself as this retains the integrity of the source data. The following guidance applies to ReportPro reports but is directly translatable into other report engines including R&R. In the report field which prints the sampling officer’s name, change the expression to: AllTrim( Left( Samples.Sampled_By, At("-", Samples.Sampled_By) -1)) Note: 1. This assumes that a dash (hyphen) has been used to separate the sampling officer’s name and the rest of the information in FSS. 2. Replace the field name “Samples.Sampled_By” with the appropriate one for your own system. 3. The “At()” function identifies the position of the “-“ in the sampled_by string. Hence the use of “-1” to exclude the hyphen itself from the name. 4. The leading “AllTrim” removes leading and trailing spaces from the generated string. Routine Tasks -------------- Audit reports to clients ~~~~~~~~~~~~~~~~~~~~~~~~~ As changes to sample details within LIMS are written back to the client’s FSS database, it is useful to highlight such changes to the clients. This serves two purposes; it is both a courtesy and serves as a training point. Where changes made during sample registration are recorded, it is recommended that reports of such changes are sent to the relevant clients on a weekly basis for all FSS samples registered during the previous 7 days. Where changes are made at later stages in the sample’s progress through the laboratory, it is recommended that extracts from this audit table be sent to the relevant clients on a monthly basis. This report should cover changes made to sample details during the previous calendar month. Updating Reference tables -------------------------- Maintain determinations ~~~~~~~~~~~~~~~~~~~~~~~~ It is necessary to ensure that the local Dets list is kept up to date with relevant FD_Det entries. It will be necessary to provide evidence to HPS on an annual basis, that the mapping is accurate and up to date. Please contact the FSS Support Team in order to agree how this might be carried out. Maintain the food & feed categorisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ It is essential that any internal reference lists which are used in sample categorisation are maintained up to date with the latest available reference lists. The reference lists are obtainable from the FSS Support Team. Export FSS data ---------------- Data, including sample details, results, comments and outcomes, require to be exported from LIMS to the FSS website. This should be carried out regularly, not less than weekly. Only FSS samples which have been approved/reported and which have not previously been exported should be included in each export process. Whenever data is exported, it must be encrypted and sent to the FSS web administrator. An agreed filename structure should be used. Details of this process are described elsewhere. It is helpful if a brief e-mail message giving the number of samples exported is sent to the FSS web administrator. Re-export FSS data ------------------- In some circumstances, sample data may need to be re-exported. The export process should be capable of achieving this. In the event of intentional re-export, the web administrator of FSS should be informed of the number of samples involved. Notes ------ Pre-registration of samples into LIMS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For a number of reasons, it is occasionally necessary to register samples into LIMS before the data file containing the FSS sample details has been received. The LIMS should be capable of achieving this without compromising the FSS data. With the exception of the field listed below, the incoming data should overwrite any existing data in the LIMS sample record. Any such changes should be recorded in the audit trail for the sample with a standard reason. Any empty sample record fields can be updated where appropriate but there need not be an audit record in this case. The field which it is recommended should NOT be changed during the input process is:- • Food category In this way, the sample categorisation applied at the lab, along with the associated suite and work information, is never changed. Outcomes - LIMS Outcome Recording ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A routine for recording reasons for failing a sample and for identifying the category of the work carried out. - Food samples are routinely analysed for one or more of the following categories of test .. o Bacteriology o Additive o Constituent o Nutritional Component o Undesirable Substances o Substitution o Labelling - In order to be able to complete FSA returns, both Public Analysts and .. Environmental Health Officers require to know:- 1. Count of Samples analysed for each category 2. Count of Samples failed in each category 3. A detailed breakdown of failures in each category - It is recognised that a scheme for collecting outcome data must: 1. Avoid undue additional input from users 2. Be capable of extension as areas of work other than foods are incorporated 3. Be tailored in such a way that export of the data to the Food Surveillance System (FSS) is feasible - The reference list for outcomes data should be obtained from the FSS Support Team. Multi-component Samples ------------------------ “Multi-component” samples are those where a single sample is submitted for analysis, but which is more conveniently split into 2 or more component parts. Examples of this are 5-part “Formal” dairy samples (milks, creams etc) for microbiological examination or packs of sweets where the colour content of each colour of sweet is identified and quantified separately. The following process ensures that related sample data is linked together on the FSS database. - Register the sample in the normal way from the data file supplied by the client - Using this sample record as a “seed”, replicate the record sufficient to provide a sample record for each separate component of the sample. Ensure that the national reference number for the sample is replicated in each component record. - The sample description text may be edited so as to describe the component to which the record relates. - The samples should be processed in the laboratory and have satisfactory/unsatisfactory and outcome data recorded as usual. - All data for the sample and its components must be exported to FSS in the same batch. Appendix I : Data Definitions ============================= Sample Data ----------- .. csv-table:: :file: data/sample-table.csv :widths: 30, 20, 20,70,30, 20, 20,70 :header-rows: 1 Result Table ------------ .. csv-table:: :file: data/result-table.csv :widths: 30, 20, 20,70,30, 20, 20,70 :header-rows: 1 Outcome Table ------------- .. csv-table:: :file: data/outcome-table.csv :widths: 30, 20, 20,70,30, 20, 20,70 :header-rows: 1 Appendix II : Competent Authorities =================================== .. csv-table:: :file: data/local-authority-list.csv :widths: 20,70 :header-rows: 1 Appendix III : Food/Feed Categorisations ======================================== Food Categorisations --------------------- `Food Category Tree Documentation `_ Feed Categorisations --------------------- .. csv-table:: :file: data/feed-category-tree-small.csv :widths: 20,20,60 :header-rows: 1 Appendix IV : Laboratories ========================== .. csv-table:: :file: data/laboratory-list.csv :widths: 20,70 :header-rows: 1 Appendix V : Animal Species =========================== .. csv-table:: :file: data/animal-species-list.csv :widths: 20,20,70 :header-rows: 1 Appendix VI : Lab Determinations (extract) ========================================== .. csv-table:: :file: data/determination-extract.csv :widths: 30, 20, 20,70,30, 20, 20,70 :header-rows: 1 Appendix VII : Outcome Failcodes ================================= Food Complaint -------------- .. csv-table:: :file: data/food-complaint-list.csv :widths: 20,40,20,70 :header-rows: 1 .. csv-table:: :file: data/food-complaint-outcome-list.csv :widths: 20,40 :header-rows: 1 Food Chemistry -------------- .. csv-table:: :file: data/food-chemistry-list.csv :widths: 20,40,20,70 :header-rows: 1 .. csv-table:: :file: data/food-chemistry-outcome-list.csv :widths: 20,40 :header-rows: 1 Food Microbiology ------------------ .. csv-table:: :file: data/food-microbiology-list.csv :widths: 20,40,20,70 :header-rows: 1 .. csv-table:: :file: data/food-microbiology-outcome-list.csv :widths: 20,40 :header-rows: 1 Animal Feeds ------------- .. csv-table:: :file: data/animal-feed-list.csv :widths: 20,40,20,70 :header-rows: 1 .. csv-table:: :file: data/animal-feed-outcome-list.csv :widths: 20,40 :header-rows: 1 Labelling ---------- .. csv-table:: :file: data/labelling-list.csv :widths: 20,40,20,70 :header-rows: 1 .. csv-table:: :file: data/labelling-outcome-list.csv :widths: 20,40,20,70 :header-rows: 1 Appendix VIII : XML Schema =========================== .. code-block:: sql :linenos: Appendix IX : EncExtract Setup =============================== Setup ----- .. image:: media/EncExtractSetUpPage1.png :alt: Diagram Description automatically generated File download ------------- .. image:: media/EncExtractSetUpPage2.png :alt: Diagram Description automatically generated