Classification and Coding of Data About IgE-mediated Food Allergic Reactions

Classification and Coding of Data About IgE-mediated Food Allergic Reactions | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Classification and Coding of Data About IgE-mediated Food Allergic Reactions Chloe French, Benjamin Green, Saskia Lawson-Tovey, Bushra Javed, and 11 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-118179/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background: Collation of clinical data on IgE-mediated food allergies is essential to provide evidenced-based approaches to managing and treating food allergies and prevent accidental reactions. However, this can be a time consuming and difficult process due to the heterogeneous way in which studies collect such data. In order to facilitate data harmonisation a set of standardised terminologies have been identified and a consensus technique established to code food allergy data. Methods: Different terminologies to encode the most common signs, symptoms and problematic foods associated with IgE-mediated food allergies were identified. Their suitability for classifying and coding information about the signs and symptoms of food allergic reactions, causative foods and reaction severity of was assessed. The assessment included existing conceptual coverage and data descriptions, classification schemes and additional relevant information. Results: All of the terminologies reviewed included classification schemes, allowing broader concepts to be related to those that are more specialised. Additional information was often present such as equivalence. Of the clinical coding systems assessed, the Systemized Nomenclature of Medical Clinical Terms (SNOMED-CT) provided the most complete coverage with options to code symptom severity. Only food coding systems, such as FoodEx2, provided comprehensive conceptual coverage of the food terms. Conclusions: Utilising SNOMED-CT and FoodEx2 standards together will support the harmonisation of data regarding food allergy from diverse sources, providing a transparent and effective way to collate relevant data required for effective food allergen management in the future. Translational Medicine Allergy & Immune Disorders Ontology Terminology Vocabulary standards Data harmonisation Food Allergy Hypersensitivity ThRAll Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Introduction IgE-mediated food allergies are estimated to affect around 1% of infants 1,2 and up to 4% of adults 3 in Europe. The prevalence varies between countries with rates being higher in Australia 4,5 and lower in countries such as India and parts of China 6 . Approved therapies are currently only available in the USA and are solely used to treat peanut allergy in children and adolescents. The therapy can protect allergic individuals from accidental reactions 7 but are not accessible to all and not available for all the different foods that can precipitate an allergic reaction. Consequently, avoidance of the causative food is generally the only recourse and in order to help individuals avoid their problem food, labelling of a group of priority allergenic foods has been made mandatory in most parts of the world. However, traces of allergenic ingredients can find their way, unintentionally, into food products and can cause adverse reactions 8 . In order to warn allergic consumers of the potential hazard posed by the presence of unintended allergens, food manufacturers place precautionary allergen labels (PAL) on such foods. PAL should only be used in conjunction with a risk assessment 9 but such approaches require reference doses of allergens that are accepted as being generally safe for the majority of food allergic consumers and are usually derived from oral food challenge data 10 . Such risk based approaches to food allergen management also provide a transparent and consistent system to prevent the overuse of ‘may contain’ labelling on foods where allergens are less likely to pose a risk and avoid mistrust from allergic consumers which can lead to risky choices being made of foods that could result in a reaction. The ThRAll project aims to support the application of risk-based approaches to food-allergen management 11 . This involves the collation, harmonization and integration of data from individuals with IgE-mediated allergies undergoing a diagnostic procedure called an oral food challenge 12 . These can be used to identify doses of allergens below which food allergic subjects are unlikely to react, or react with only mild symptoms 13 . Through the ThRAll project a publicly available database of oral food challenges is being developed, which can be used for dose distribution modelling that underpins identification of doses that have an acceptable level of risk of eliciting a reaction in the allergic population 10 . Data from oral food challenges are often collected and reported in a heterogeneous manner, with studies conducted in different ways (double blind placebo controlled, single blind [when only the patient is blinded], interspersed, open challenge), using different dosing protocols and food matrices to deliver the allergenic food. In addition, different investigators can use multiple terminologies to describe the same clinical symptom (i.e. a change in function, sensation or appearance which indicates disease which is reported by the patient) or sign (i.e. an objective observation or evidence of disease) even within the same study centre. This ambiguity can lead to different interpretations when harmonizing existing datasets. To facilitate the integration of existing data and support repeatability of future studies it is important to have a consensus approach to encoding and reporting food allergy information. This paper aims to identify and encode common variables relating to food allergy to promote the repeatability of data analysis and facilitate the interoperability of data being collated in the ThRAll project relating to food allergies. Materials And Methods Relevant concepts that are used to understand, describe and diagnose food allergies were first identified and defined (Supplementary material Table 1). Clinical record forms used for recording oral food challenges from the EuroPrevall (The prevalence, cost and basis of food allergy across Europe) and iFAAM (Integrated approaches to food allergen and allergy management) studies were then used to identify common signs and symptoms experienced during an IgE-mediated reaction, which were also defined (Supplementary material Table 2) 9,14−17 . In addition, key food terms were compiled based on the foods that initiate an allergic reaction (including species of origin, common derivative ingredients and manufactured foods) based on the 14 major allergens which must be stated on food labelling as described by Annex II of the EU Food Information for Consumers Regulation 1169/2011 18,19 (Supplementary material Table 3). In the next step the utility of different terminologies for classifying and encoding this information was assessed. Clinically relevant and validated terminologies were identified using The National Library of Medicine. These were the Systemized Nomenclature of Medical Clinical Terms (SNOMED-CT), Medical Subject Headings (MeSH) and the Medication Dictionary for Regulatory Activities (MedDRA) systems (Table 1 ). LOINC (Logical Observation Identifiers Names and Codes) was also considered for classifying and encoding the symptom concepts. However, this system is used to represent the type or “question” for a clinical test or measurement. This is not in scope for this study, where we focus on coding observation results or “responses”, and LOINC was removed from further consideration. In addition, the European Food Safety Authorities FoodEx2, LanguaL alimentaria (LanguaL) and a vocabulary developed by the Food and Agriculture Organisation (AGROVOC) were compared for their classification of food products (Table 1 ). Table 1 Terminologies assessed for their utility in encoding food allergy data. Terminology Description SNOMED-CT (Systemized nomenclature of medicine- clinical terms) 20 SNOMED-CT is the most comprehensive and international clinical terminology system. MeSH (Medical subject headings) 21 MeSH is used for indexing, cataloguing and searching biomedical and health-related information. MedDRA (Medical Dictionary for Regulatory Activities) 22 MedDRA provides a clinically validated and internationally recognised medical terminology. LOINC (Logical Observation Identifiers Names and Codes) 23 LOINC is an international standard, which facilitates the storage, exchange and harmonization of data. FoodEx2 24 FoodEx2 is a standardised food classification and description system. Data is compiled from EU organizations, industries and academic research. LanguaL (Langua aLimentaria" or "language of food") 25 LanguaL provides a standardised technique for describing foods based on the combination of characteristics of that food 26 . AGROVOC (Agriculture and Vocabulary) FAO (Food and Agriculture Organization of the United Nations) 27 AGROVOC is a controlled vocabulary including both food and nutrition that can translate concepts into 37 languages. The ThRAll project aimed to evaluate the classification of symptoms, signs and food relating to an IgE-mediated food allergy from a risk management and public health perspective. Given this objective each terminology was assessed in four areas: Conceptual coverage : Every symptom and food term identified was searched in each of the terminologies to quantitatively compare which system provided the greatest existing conceptual coverage. Concept descriptions : A clear and validated definition was identified for each symptom or sign and food term. This was used as a ‘benchmark’ definition to be assessed and compared with the descriptions provided in each of the terminologies. Classification : The information provided by each terminology to support classification of specific symptoms and signs together with food were compared. The inclusion and clinical appropriateness of information that expresses the relationships between general and specialised concepts (classification schemes) was considered to be a key differentiator. Additional information : Each terminology was assessed for support for synonyms specified in the ThRAll protocol. This was completed for symptoms and signs, but not for food where equivalence is more complex to determine. Any additional information was also assessed for use in the ThRAll study. Results Conceptual coverage For the symptom and sign concepts (Supplementary material Table 1) both SNOMED-CT and MedDRA provided complete coverage, whilst MeSH covered 88%. FoodEx2, LanguaL and AGROVOC did not cover any of the symptom concepts but did provide superior coverage for food concepts (Table 2 ). AGROVOC covered 85% of the food concepts, LanguaL had complete coverage and FoodEx2 covered all of the food concepts except for sulphur dioxide. In addition, LanguaL uses the EFSA FoodEx2 coding and classification system for products in the European Union, which validates the legitimacy and effectiveness of FoodEx2. Table 2 Comparison of five terminologies for the classification and coding of food allergy information. Terminology Conceptual coverage Classification Concept description Additional information Symptom (n = 25) Food (n = 47) SNOMED-CT 25 42 Concepts are arranged into a hierarchical structure. Detailed and unambiguous definition. Preferred term and synonyms. MeSH 22 32 Concepts are arranged into a logical and detailed hierarchical structure. Detailed and unambiguous definition. Provides related concepts (where available) for each term. MedDRA 25 6 Terms are arranged into a 5 tier branching system expanding from very specific to more general concepts. No definition provided. Includes a preferred name and related synonyms. FoodEX2 0 46 Concepts are categorised into one of 21 groups and facets can encode additional detail including ingredients or processing techniques. Clear description along with common and scientific name N/A LanguaL 0 47 Concepts are classified systematically based on 14 key terms including product type, food source and cooking method. Clear description along with common and scientific name N/A AGROVOC 0 40 Terms are arranged in a hierarchical and non-hierarchical system to classify a range of concepts and to indicate related terms. No description is provided, but the broader concept is included to provide context. A list of related concepts are included for some terms. Description of concepts The term definitions provided by each of the coding systems were reviewed and compared with the definitions found in the literature (Supplementary material Tables 2 and 3). MedDRA does not provide formal definitions for the symptom and sign concepts and so fails to provide any additional clarity or description for each term. In contrast, SNOMED-CT and MeSH provide clear and unambiguous descriptions for each concept. This is illustrated in Table 3 using “urticarial rash” and “hazelnut” as an example sign and food respectively. Thus, both MeSH and SNOMED-CT include a detailed definition to describe the sign “Urticarial rash” which is consistent with the key definitions (Supplementary material Table 2). Similarly, FoodEx2, LanguaL and AGROVOC all provide a detailed description for each food term as well as detailing both the common and the Latin name for each food to reduce ambiguity (Supplementary material Table 3). Table 3. Comparison of the definition of exemplar symptom (urticarial rash) and food (hazelnuts) terms according to the different terminologies. Terminology Definition Urticarial rash SNOMED-CT “A raised, erythematous papule or cutaneous plaque usually representing short-lived dermal oedema.“ MeSH “A vascular reaction of the skin characterised by erythema and wheal formation due to localized increase of vascular permeability. The causative mechanism may be allergy, infection or stress.” MedDRA N/A ThRAll approach “A condition characterized by the development of wheals (hives), angioedema or both” Hazelnut SNOMED-CT “Tree nut (substance)” MeSH “A plant genus of the family BETULACEAE known for the edible nuts” FoodEX2 “Tree nuts from the plant classified under the species Corylus avellana L ., commonly known as Hazelnuts or Cobnuts or Common hazelnut. The part consumed/analysed is not specified. When relevant, information on the part consumed/analysed has to be reported with additional facet descriptors. In case of data collections related to legislations, the default part consumed/analysed is the one defined in the applicable legislation.” LanguaL “The group includes kernels of the seeds of all species similar to Hazelnuts or similar nuts sharing the same pesticide to the maximum residue level (MRL) as Hazelnuts.” AGROVOC “The fruit of small trees of shrubs of the Corylaceae family. The round-oval nuts are surrounded by a leafy involucre, which comes out easily when the fruit is mature. Remains the nut, with a pericarp, the shell, more or less woody, and depending on varieties. Inside is the seed, covered by a very thin tegument.” Where appropriate, MedDRA aggregates and highlights similar terms related to the specific concept and so allows comparable terms to be easily accessed. For example, ‘urticaria rash’ is the preferred name that classifies 33 related concepts including ‘urticaria localized’ and ‘generalised urticarial rash’, which provide varying levels of detail and alternative terms that include a level of clinical interpretation. This is useful but the large number of similar terms may reduce the specificity and level of detail initially identified by a term. In contrast, concepts in SNOMED-CT are associated with a unique Fully Specified Name (FSN); this is the ideal term that a clinician would use in a particular language, dialect or context. SNOMED-CT also identifies relationships to other similar and related concepts and considers the preferred name for ‘urticarial rash’ to be ‘weal’ with ‘wheal’, ‘welt’, ‘hives’ and ‘nettle rash’ being noted as alternative terms. Since concepts are coded in MeSH for the purpose of indexing publication records, each MeSH term can comprise several synonyms; for example, ‘urticaria’ also includes ‘urticarias’ and ‘hives’. All concepts that come under one record are considered equivalent and this is useful when trying to maximise the number of relevant articles identified in a search but not necessarily when identifying synonyms in the context of compiling data on food allergy in the ThRAll database. LanguaL and FoodEx2 do not provide related concepts since this is not appropriate in the context of a food classification system as there would be no suitable synonyms. In certain cases AGROVOC provides equivalent terms and where appropriate states the broader and/or narrower relevant concepts as well as identifying what the product is produced (i.e. the plant/ animal species of origin). Mechanistic basis to classify an adverse reaction It was also important to compare the pathway that each of the terminologies used to classify an adverse reaction. Food can induce a range of adverse reactions but, although the symptoms and signs may be similar, the mechanistic basis of allergies, intolerances and sensitivities are completely different. An adverse reaction to food 28 encompasses both immune- and non-immune mediated adverse reactions (Fig. 1 ). Sub-types of immune-mediated adverse reactions include those involving the development of food-specific IgE antibody responses. This type of food allergy results in symptoms and signs that appear immediately (in less than 2 hours, usually within 30 minutes) sometimes even after ingesting a small dose of the allergen, and can involve multiple organs including the skin, respiratory, digestive and cardiovascular systems. A second type of well-defined non-IgE-mediated adverse reaction to food is the T-cell mediated syndrome triggered by ingestion of gluten, known as coeliac disease (CD) 29 . This life-long disease involves sensitivity to gluten and individuals with CD often present with gastrointestinal signs and symptoms, including diarrhoea, together with weight loss due to the malabsorption of nutrients. In contrast, food intolerance conditions are not immune mediated but nevertheless can be reproducibly induced following ingestion of specific foods. One example is lactose intolerance where individuals lack the lactase enzyme, which is involved with the digestion of lactose. Symptoms appear shortly after drinking milk or consuming dairy and are commonly reported as stomach pain, bloating and diarrhoea. Lactose intolerance is different to an IgE mediated milk allergy, which is an IgE mediated reaction where symptoms appear within 2 h of consuming milk-containing foods. The classification of an adverse reaction used in the ThRAll project (Fig. 1 ) was used to benchmark how the different terminologies classify an IgE mediated food allergy (Fig. 2 ). SNOMED-CT considers the trigger of an allergic reaction as the causative food and then links this back to the allergic hypersensitivity. It provides an overview of the process of the reaction but also filters into specific details about the adverse response, including branching to the causative agent and a qualifier for the severity of the reaction. This is consistent with terminology from the World Allergy Organisation (WAO) and the European Academy of Allergy and Clinical Immunology (EAACI) 30 . MedDRA and MeSH classify food allergy from a disease perspective and then acknowledge the response as a consequence from ingestion of the problematic food. MeSH also includes a logical and clear flow using the descriptor “food hypersensitivity” as a type of “immediate hypersensitivity” which is used as a synonym of IgE-mediated food allergy. This is linked to the causal food and the eliciting symptoms. In contrast, MedDRA utilizes a tree flow diagram to show how a food allergy is classified but this was a simpler and less detailed pathway compared to MeSH and SNOMED-CT. Since the ThRAll project is considering the reaction from a food and public health perspective, the SNOMED-CT approach to classify a food allergy was considered the most appropriate. Figure 3 illustrates how MeSH, MedDRA and SNOMED-CT classify a non-IgE immune mediated adverse reaction to food and coeliac disease. MedDRA and MeSH both provide multiple ways to classify the pathway of coeliac disease. These terminologies consider this disease as a nutritional or gastrointestinal disorder that leads to malabsorption, which clearly demonstrates the reaction is triggered by food. MedDRA has a third pathway to classify coeliac disease from a disease perspective as an autoimmune disorder; this is consistent with the ThRAll approach, which classifies coeliac disease as an immune-mediated reaction. Again, SNOMED-CT has a different way of approaching the classification of coeliac disease in comparison to MedDRA and MeSH but still considers it a malabsorption syndrome caused by the ingestion of gluten. Figure 3 demonstrates that coeliac disease is an adverse response with a clear food trigger, yet the pathway to classify this reaction is very different to the classification of a food allergy and so these reactions should be considered separately. Lastly the pathways to describe a non-immune mediated adverse reaction by specifically looking at the classification of lactose intolerance are shown in Fig. 4 . MedDRA, MeSH and SNOMED-CT all describe lactose intolerance as a metabolic or gastrointestinal disorder which disrupts the absorption of carbohydrates. The ThRAll approach classifies lactose intolerance as a non-immune mediated reaction due to a disorder of an enzymatic process. The lack of lactase enzyme in lactose intolerance patients causes the malabsorption of the carbohydrate lactose and so demonstrates the similarities between these classifications. Classification schemes for symptoms and signs MedDRA has a logical five-tier structure expanding from very specific to more general concepts. Lowest Level Terms (LLTs) represent the most specialised concepts including symptoms, medical procedures and personal characteristics. LLTs can be considered the preferred term (PT) or a synonym of the preferred term (PT) 31 . Similar PTs are aggregated into High Level Terms (HLT) based upon anatomy, pathology, physiology or aetiology. These HLTs are further categorised into High Level Group Terms (HLGT) that are then split into one of 26 System Organ Classes (SOC’s) providing the most general classification. This is a logical and methodical organisation system but concepts are confined to these five levels and further clarification or granularity cannot be expressed beyond the LLT to indicate the severity or manifestation of a symptom. Concepts in SNOMED-CT can vary in their specificity; more general concepts are aggregated together which filter down to more specific terms. Relationships are used to portray a confirmed association between multiple concepts. The branching structure in SNOMEC-CT is useful to be able to code and represent clinical data at a level of detail that is appropriate to a range of different uses. In contrast MeSH is a cataloguing system with a slightly different framework to the other terminologies as terms do not identify clinical phenomena but instead represent a category. MeSH is used to categorise and retrieve records and is organised in a hierarchical structure with 16 primary categories that splits into subcategories providing more detailed terms. A letter corresponding to a category and a number representing the hierarchical level provides an identifier for each term. Classification schemes for food There are many levels of granularity that need to be considered when describing and encoding a food product including the origin of the food, the food matrix and processing techniques. For example, when considering a food allergy, we need to identify differences in the frequency or severity of a reaction,1 which may be affected by cooking technique (e.g. dry roasted compared to raw peanuts) or the food matrix/ vehicle used (e.g. peanut butter, whole peanut, baked goods containing peanuts). It is useful to have a system with the ability to encode multiple levels of detail depending on the amount of data and information that is available. This is important given that the literature shows that some food allergens are sensitive to food-processing techniques and a high fat content may increase the allergenicity of the protein 32,33 . The structure of these different classification systems represents their primary use whether that is to understand nutritional value, physical characteristics or the type of food product. FoodEx2 is arranged into 21 clearly defined food groups, such that every food aligns to exactly one group. The system is made up of base terms and facets; the base term is defined by a unique five-character alphanumeric code and represents the specific foods within the hierarchy. Facets provide additional detail to the base term, such as the origin of the product; its ingredients and the process involved in its preparation. This additional information can be combined with the base term to provide a more detailed and complete description of the food product. This demonstrates the range of granularity and amount of information that has been considered in this classification system making it useful for encoding allergenic foods and common matrices or derivatives used in oral food challenges. LanguaL systematically classifies food in a systematic way according to 14 key concepts including product type, cooking method and packing medium. These concepts are used to encode the product and enable almost any food product to be classified to the level of detail that is required. A unique code is provided for each food concept, which can then be translated into multiple languages. AGROVOC relates concepts in a hierarchical and non-hierarchical structure. A branching logic is used whereby the term becomes more specific and precise. For example, nuts provides a broader way of describing hazelnuts. There is also a non-hierarchical relationship and this expresses related concepts where appropriate. Figure 6 demonstrates how each of the standards classifies hazelnuts as an example of a food concept. The figure shows that LanguaL utilises the logic from FoodEx2 and that each of the terminologies distinguish between plant and animal products before identifying the relevant concept from a list of key categories and then filtering into the specific species. Encoding symptom severity When considering the dose at which an allergen induces an objective reaction it is useful to encode the severity of that reaction. Thus, when identifying the dose that elicits a reaction in p% of the allergenic population (eliciting dose, ED p ), it is useful to understand the proportion of individuals that presented with either a mild, moderate or severe reaction at this dose. Some studies, such as iFAAM, have collected detailed information on severity which can also be used to identify criteria for stopping a challenge [ 16 ]. This information can be used to identify eliciting doses that present a tolerable level of risk of reaction in allergic individuals, as observed in the Peanut Allergen Threshold study 13 . The classification of reaction severity is inherently subjective, arising from clinical interpretation of signs and symptoms and many different approaches have been developed and compared 34,35 . SNOMED-CT codes do not always provide sufficient detail to describe the severity as well as symptom presence but this can be addressed by using an additional qualifier code (mild, moderate or severe) to fully express the specific, observed sign or symptom. This is illustrated for the iFAAM oral food challenge record where symptoms have been classified and coded with both the symptom code and the terms, mild, moderate or severe using the approach of Sampson 36 (Table 4 ). This shows, for example, if a patient experienced one episode of diarrhoea this would be coded as the SNOMED-CT code for diarrhoea and the code of mild severity and paired in a structure to indicate one episode of diarrhoea: 62315008–255604002. Table 4 Encoding severity alongside symptoms and signs using SNOMED-CT. Symptom SNOMED- CT code Description for relevant severity grade (SNOMED-CT code) Mild (255604002) Moderate (6736007) Severe (24484000) Pruritus 418363000 • Occasional scratching • Continuous scratching for > 2 min at a time • Hard continuous scratching leading to excoriations • Scratching of palms, soles, genitals, scalp Erythema 247441003 • Few areas of faint erythema • Areas of erythema ( 50%) Urticarial rash (wheal) 247472004 Up to 10 new hives Generalised involvement (> 10 new hives) Angioedema 41291007 Mild lip oedema • Significant lip oedema • Whole face oedema Rhinitis 70076002 • Rare bursts, occasional sniffing • < 10 bursts, frequent sniffing or intermediate rubbing of nose; • Long bursts, persistent rhinorrhoea or continuous rubbing Ocular Intermittent rubbing of eyes Continuous rubbing, periocular swelling, reddening Wheezing 56018004; 272040008 • Expiratory wheezing to auscultation • Inspiratory and expiratory wheezing to auscultation • Use of accessory muscles or audible wheezing Gastrointestinal pain Nausea 21522001 422587007 • Complaints of nausea or abdominal pain • Frequent complaints of nausea or pain with abnormal activity • Notably distressed due to GI symptoms with decreased activity Emesis 422400008 • 1 episode of emesis • > 1 episode of emesis Diarrhoea 62315008 • 1 episode of diarrhoea • > 1 episode of diarrhoea Signs and Symptoms recorded in the iFAAM challenge record [ 16 ] were classified and coded as to their severity using a combination of the approach of Sampson 36 as being either mild (Sampson grade 1), moderate (Sampson grades 2 and 3) or severe (Sampson grades 4 and 5) and then encoded using SNOMED-CT. Discussion The results demonstrate the complexity required to encode food allergy information and each terminology has a different way of classifying an allergic reaction. Furthermore, each terminology varies in the system used to classify and organise concepts, which depend on the primary purpose of the classification system. The analysis showed that SNOMED-CT encoded all of the key terms and provided the conceptual coverage required to maximise the representation and classification of food allergy data for public health purposes aimed at food allergen management. In addition, SNOMED-CT provides a classification scheme that relates specific and more general concepts and that considers food as the trigger of an allergic reaction which is clinically relevant. Therefore, it was chosen as the most appropriate terminology to code data relating to food allergies collated within the ThRAll project. Additionally, SNOMED-CT also provides severity code, allowing for more precise, qualified records of reactions. Although FoodEx2, SNOMED-CT, MeSH, LanguaL and AGROVOC all provide terms for foods, FoodEx2 provided the greatest conceptual coverage including species of origin and food processing methods. Consequently, FoodEx2 was selected to code the foods that initiate an allergic reactions, enabling analysis to be undertaken to identify how factors, such as food processing, may influence eliciting dose threshold and reaction severity. Conclusion The ThRAll study has determined that SNOMED-CT and FoodEx2 are presently the most competent terminologies for the representation of clinical knowledge relating to food allergy, the former delivering encodings for observed symptoms or signs and the latter representing eliciting foods (Fig. 6 ). This combined set of terminologies provides not only complete conceptual coverage, but a depth of granularity providing a structured flexibility to encoding a given required level of detail, via symptom severity in SNOMED-CT, and facets for food matrices and processing techniques in FoodEx2. It is expected that by defining a coding system for the ThRAll oral food challenge database will increase accessibility through standardisation. This will in turn extend the usefulness of these data into the future. Furthermore, the approach taken could also be expanded in future to encompass data from other clinical studies and registries of food anaphylaxis such as the network of severe allergic reactions (Network for Online-Registration of Anaphylaxis, NORA) 37 . The proposed pairing of codes to qualify severity of reaction is supported in HL7’s FHIR (Fast Healthcare Interoperability Resource), a standard for exchanging healthcare information electronically. This system represents data as a set of related hierarchical elements and values into resources. For the purpose of capturing data relating to allergic reactions, it is possible to record a symptom element, a severity element and a food element within the same resource meaning that there is a standard definition of the relationships between the codes. Using the proposed approach to coding within this standard could further increase the future utility of these data making for a promising approach for recording and storing reusable datasets. The coding approach is also applicable to representing an individual’s food allergy information in a standardised way in their electronic health records by including other metadata, such as diagnostic certainty (e.g. whether the data was a self-reported, negative, possible, probable or confirmed allergy) which could ensure correct interpretation across medical systems. Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Availability of data and materials Not applicable. Competing interests The authors declare no competing interests in relation to the published work. Funding This project has received financial support from the European Food Safety Authority (EFSA), Grant GP/EFSA/AFSCO/2017/03. The present article, however, is under the sole responsibility of the authors. The positions and opinions presented in this article are those of the authors alone and do not necessarily represent the views/any official position or scientific works of EFSA. EFSA guidance documents and other scientific outputs of EFSA, can be found in the EFSA website: http://www.efsa.europa.eu . The ThRAll project is also co-funded by the UK Food Standards Agency FS101209. This work was partly funded by the European Union through the iFAAM project: Integrated Approaches to Food Allergen and Allergy Risk Management (Grant Agreement N° 312147) and the Medical Research Council Health eResearch Centre, Farr Institute (MR/K006665/1). Authors' contributions PC and ENCM were responsible for the original concept and design of the work and have overall supervision of its execution. CF, BJ, BG and S L-T were responsible for its execution.MM, AK, T-ML, AS, SD, NdJ, BB-W, MF-R and KB were involved in providing clinical oversight and revision of the work. The manuscript was drafted by CF, BJ, ENCM and PC and all authors were involved in its review and revision and final approval. References Schoemaker AA, Sprikkelman AB, Grimshaw KE, et al. Incidence and natural history of challenge-proven cow's milk allergy in European children--EuroPrevall birth cohort. Allergy. 2015;70(8):963-972. Xepapadaki P, Fiocchi A, Grabenhenrich L, et al. 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Eller E, Muraro A, Dahl R, Mortz CG, Bindslev-Jensen C. Assessing severity of anaphylaxis: a data-driven comparison of 23 instruments. Clinical and translational allergy. 2018;8:29. Muraro A, Fernandez-Rivas M, Beyer K, et al. The urgent need for a harmonized severity scoring system for acute allergic reactions. Allergy. 2018;73(9):1792-1800. Sampson HA. Anaphylaxis and emergency treatment. Pediatrics. 2003;111(6 Pt 3):1601-1608. Worm M, Moneret-Vautrin A, Scherer K, et al. First European data from the network of severe allergic reactions (NORA). Allergy. 2014;69(10):1397-1404. Supplementary Files FrenchetalFoodAllergyCodingSupplInformationver8.docx Additional information Relationships between concepts are important to understand the broader meaning and context of each term and is done in different ways by MedRA, MeSH and SNOMED-CT as illustrated by how the different terminologies classify the symptom ‘urticarial rash’ (Figure 5). 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","description":"","filename":"FrenchetalFigure1.eps.jpg","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/0aad9aeae75a1746bda0c7b4.jpg"},{"id":4079371,"identity":"273a0937-3be3-4d26-b992-01503822ea7d","added_by":"auto","created_at":"2020-12-07 21:42:37","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":673974,"visible":true,"origin":"","legend":"Comparison of the pathways to describe the onset of IgE-mediated food allergy according to MedDRA, MeSH, SNOMED-CT and the ThRAll approach.","description":"","filename":"FrenchetalFigure2.eps.jpg","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/246be46ceb5345189ec0dd7c.jpg"},{"id":4079372,"identity":"b601a9bf-090b-403d-bc10-579bf63da21c","added_by":"auto","created_at":"2020-12-07 21:42:37","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":865713,"visible":true,"origin":"","legend":"Comparison of the pathways to describe Coeliac disease, a non-IgE immune mediated adverse reaction to food, according to MedDRA, MeSH, SNOMED-CT and the ThRAll approach.","description":"","filename":"FrenchetalFigure3.eps.jpg","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/0b21357ca42d91f721d116d6.jpg"},{"id":4079373,"identity":"285d8ec7-67c1-400a-b7ce-b836b08a9fff","added_by":"auto","created_at":"2020-12-07 21:42:37","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":834234,"visible":true,"origin":"","legend":"Comparison of the pathways to describe lactose intolerance, a non-immune mediated adverse reaction to food, according to MedDRA, MeSH, SNOMED-CT and the ThRAll approach.","description":"","filename":"FrenchetalFigure4.eps.jpg","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/fa70c569f6e4f37c0e763e40.jpg"},{"id":4079374,"identity":"fe4133a3-de6a-4f18-a0f9-b08fb5464ec2","added_by":"auto","created_at":"2020-12-07 21:42:37","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":721028,"visible":true,"origin":"","legend":"Branching logic to classify the sign “urticarial rash” according to MedDRA, MeSH and SNOMED-CT. *SNOMED-CT preferred tem is Wheal (disorder) with urticarial rash as a synonym. ","description":"","filename":"FrenchetalFigure5231120.eps.jpg","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/41c8a252284e3f20238da097.jpg"},{"id":4079375,"identity":"b77cf5af-216b-42b2-b93d-780f0f798e4c","added_by":"auto","created_at":"2020-12-07 21:42:37","extension":"jpg","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":418784,"visible":true,"origin":"","legend":"Branching logic to classify hazelnuts according to FoodEx2, LanguaL and AGROVOC.","description":"","filename":"FrenchetalFigure6281120.eps.jpg","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/afe7342e382aa51aab870826.jpg"},{"id":4079376,"identity":"2ed21271-ebcf-4897-a631-80ca90bef222","added_by":"auto","created_at":"2020-12-07 21:42:37","extension":"jpg","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":513721,"visible":true,"origin":"","legend":"The ThRAll pathway for coding food allergy information using SNOMED-CT and FoodEX2","description":"","filename":"FrenchetalFigure7.eps.jpg","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/76193e20023bac2554e45cd6.jpg"},{"id":13624124,"identity":"76defcaa-918d-4858-b73f-cdf4cd5dfc12","added_by":"auto","created_at":"2021-09-17 07:21:18","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1077620,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/5d82952c-f9a7-4f6e-bde1-26decf4e8dc8.pdf"},{"id":4079370,"identity":"a4c9d252-5eb8-4874-bd45-c37504d4263b","added_by":"auto","created_at":"2020-12-07 21:42:36","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":91907,"visible":true,"origin":"","legend":"Additional information\nRelationships between concepts are important to understand the broader meaning and context of each term and is done in different ways by MedRA, MeSH and SNOMED-CT as illustrated by how the different terminologies classify the symptom ‘urticarial rash’ (Figure 5).\n","description":"","filename":"FrenchetalFoodAllergyCodingSupplInformationver8.docx","url":"https://assets-eu.researchsquare.com/files/rs-118179/v1/3724d6239d34c1c8132d7aee.docx"}],"financialInterests":"","formattedTitle":"\u003cp\u003eClassification and Coding of Data About IgE-mediated Food Allergic Reactions\u003c/p\u003e","fulltext":[{"header":"Introduction","content":" \u003cp\u003eIgE-mediated food allergies are estimated to affect around 1% of infants \u003csup\u003e1,2\u003c/sup\u003e and up to 4% of adults \u003csup\u003e3\u003c/sup\u003e in Europe. The prevalence varies between countries with rates being higher in Australia \u003csup\u003e4,5\u003c/sup\u003e and lower in countries such as India and parts of China \u003csup\u003e6\u003c/sup\u003e. Approved therapies are currently only available in the USA and are solely used to treat peanut allergy in children and adolescents. The therapy can protect allergic individuals from accidental reactions \u003csup\u003e7\u003c/sup\u003e but are not accessible to all and not available for all the different foods that can precipitate an allergic reaction. Consequently, avoidance of the causative food is generally the only recourse and in order to help individuals avoid their problem food, labelling of a group of priority allergenic foods has been made mandatory in most parts of the world. However, traces of allergenic ingredients can find their way, unintentionally, into food products and can cause adverse reactions \u003csup\u003e8\u003c/sup\u003e. In order to warn allergic consumers of the potential hazard posed by the presence of unintended allergens, food manufacturers place precautionary allergen labels (PAL) on such foods. PAL should only be used in conjunction with a risk assessment \u003csup\u003e9\u003c/sup\u003e but such approaches require reference doses of allergens that are accepted as being generally safe for the majority of food allergic consumers and are usually derived from oral food challenge data \u003csup\u003e10\u003c/sup\u003e. Such risk based approaches to food allergen management also provide a transparent and consistent system to prevent the overuse of \u0026lsquo;may contain\u0026rsquo; labelling on foods where allergens are less likely to pose a risk and avoid mistrust from allergic consumers which can lead to risky choices being made of foods that could result in a reaction.\u003c/p\u003e \u003cp\u003eThe ThRAll project aims to support the application of risk-based approaches to food-allergen management \u003csup\u003e11\u003c/sup\u003e. This involves the collation, harmonization and integration of data from individuals with IgE-mediated allergies undergoing a diagnostic procedure called an oral food challenge \u003csup\u003e12\u003c/sup\u003e. These can be used to identify doses of allergens below which food allergic subjects are unlikely to react, or react with only mild symptoms \u003csup\u003e13\u003c/sup\u003e. Through the ThRAll project a publicly available database of oral food challenges is being developed, which can be used for dose distribution modelling that underpins identification of doses that have an acceptable level of risk of eliciting a reaction in the allergic population \u003csup\u003e10\u003c/sup\u003e. Data from oral food challenges are often collected and reported in a heterogeneous manner, with studies conducted in different ways (double blind placebo controlled, single blind [when only the patient is blinded], interspersed, open challenge), using different dosing protocols and food matrices to deliver the allergenic food. In addition, different investigators can use multiple terminologies to describe the same clinical symptom (i.e. a change in function, sensation or appearance which indicates disease which is reported by the patient) or sign (i.e. an objective observation or evidence of disease) even within the same study centre. This ambiguity can lead to different interpretations when harmonizing existing datasets. To facilitate the integration of existing data and support repeatability of future studies it is important to have a consensus approach to encoding and reporting food allergy information. This paper aims to identify and encode common variables relating to food allergy to promote the repeatability of data analysis and facilitate the interoperability of data being collated in the ThRAll project relating to food allergies.\u003c/p\u003e "},{"header":"Materials And Methods","content":" \u003cp\u003eRelevant concepts that are used to understand, describe and diagnose food allergies were first identified and defined (Supplementary material Table\u0026nbsp;1). Clinical record forms used for recording oral food challenges from the EuroPrevall (The prevalence, cost and basis of food allergy across Europe) and iFAAM (Integrated approaches to food allergen and allergy management) studies were then used to identify common signs and symptoms experienced during an IgE-mediated reaction, which were also defined (Supplementary material Table\u0026nbsp;2) \u003csup\u003e9,14\u0026minus;17\u003c/sup\u003e. In addition, key food terms were compiled based on the foods that initiate an allergic reaction (including species of origin, common derivative ingredients and manufactured foods) based on the 14 major allergens which must be stated on food labelling as described by Annex II of the EU Food Information for Consumers Regulation 1169/2011 \u003csup\u003e18,19\u003c/sup\u003e (Supplementary material Table\u0026nbsp;3).\u003c/p\u003e \u003cp\u003eIn the next step the utility of different terminologies for classifying and encoding this information was assessed. Clinically relevant and validated terminologies were identified using The National Library of Medicine. These were the Systemized Nomenclature of Medical Clinical Terms (SNOMED-CT), Medical Subject Headings (MeSH) and the Medication Dictionary for Regulatory Activities (MedDRA) systems (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). LOINC (Logical Observation Identifiers Names and Codes) was also considered for classifying and encoding the symptom concepts. However, this system is used to represent the type or \u0026ldquo;question\u0026rdquo; for a clinical test or measurement. This is not in scope for this study, where we focus on coding observation results or \u0026ldquo;responses\u0026rdquo;, and LOINC was removed from further consideration. In addition, the European Food Safety Authorities FoodEx2, LanguaL alimentaria (LanguaL) and a vocabulary developed by the Food and Agriculture Organisation (AGROVOC) were compared for their classification of food products (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eTerminologies assessed for their utility in encoding food allergy data.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"2\"\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTerminology\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eDescription\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSNOMED-CT (Systemized nomenclature of medicine- clinical terms) \u003csup\u003e20\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSNOMED-CT is the most comprehensive and international clinical terminology system.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMeSH (Medical subject headings) \u003csup\u003e21\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMeSH is used for indexing, cataloguing and searching biomedical and health-related information.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMedDRA (Medical Dictionary for Regulatory Activities) \u003csup\u003e22\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMedDRA provides a clinically validated and internationally recognised medical terminology.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLOINC (Logical Observation Identifiers Names and Codes) \u003csup\u003e23\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLOINC is an international standard, which facilitates the storage, exchange and harmonization of data.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eFoodEx2 \u003csup\u003e24\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFoodEx2 is a standardised food classification and description system. Data is compiled from EU organizations, industries and academic research.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLanguaL (Langua aLimentaria\" or \"language of food\") \u003csup\u003e25\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLanguaL provides a standardised technique for describing foods based on the combination of characteristics of that food \u003csup\u003e26\u003c/sup\u003e.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAGROVOC (Agriculture and Vocabulary) FAO (Food and Agriculture Organization of the United Nations) \u003csup\u003e27\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAGROVOC is a controlled vocabulary including both food and nutrition that can translate concepts into 37 languages.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe ThRAll project aimed to evaluate the classification of symptoms, signs and food relating to an IgE-mediated food allergy from a risk management and public health perspective. Given this objective each terminology was assessed in four areas:\u003c/p\u003e \u003cp\u003e \u003col\u003e \u003cspan\u003e \u003cli\u003e \u003cp\u003e \u003cem\u003eConceptual coverage\u003c/em\u003e: Every symptom and food term identified was searched in each of the terminologies to quantitatively compare which system provided the greatest existing conceptual coverage.\u003c/p\u003e \u003c/li\u003e \u003c/span\u003e \u003cspan\u003e \u003cli\u003e \u003cp\u003e \u003cem\u003eConcept descriptions\u003c/em\u003e: A clear and validated definition was identified for each symptom or sign and food term. This was used as a \u0026lsquo;benchmark\u0026rsquo; definition to be assessed and compared with the descriptions provided in each of the terminologies.\u003c/p\u003e \u003c/li\u003e \u003c/span\u003e \u003cspan\u003e \u003cli\u003e \u003cp\u003e \u003cem\u003eClassification\u003c/em\u003e: The information provided by each terminology to support classification of specific symptoms and signs together with food were compared. The inclusion and clinical appropriateness of information that expresses the relationships between general and specialised concepts (classification schemes) was considered to be a key differentiator.\u003c/p\u003e \u003c/li\u003e \u003c/span\u003e \u003cspan\u003e \u003cli\u003e \u003cp\u003e \u003cem\u003eAdditional information\u003c/em\u003e: Each terminology was assessed for support for synonyms specified in the ThRAll protocol. This was completed for symptoms and signs, but not for food where equivalence is more complex to determine. Any additional information was also assessed for use in the ThRAll study.\u003c/p\u003e \u003c/li\u003e \u003c/span\u003e \u003c/ol\u003e \u003c/p\u003e "},{"header":"Results","content":" \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003eConceptual coverage\u003c/h2\u003e \u003cp\u003eFor the symptom and sign concepts (Supplementary material Table\u0026nbsp;1) both SNOMED-CT and MedDRA provided complete coverage, whilst MeSH covered 88%. FoodEx2, LanguaL and AGROVOC did not cover any of the symptom concepts but did provide superior coverage for food concepts (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). AGROVOC covered 85% of the food concepts, LanguaL had complete coverage and FoodEx2 covered all of the food concepts except for sulphur dioxide. In addition, LanguaL uses the EFSA FoodEx2 coding and classification system for products in the European Union, which validates the legitimacy and effectiveness of FoodEx2.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eComparison of five terminologies for the classification and coding of food allergy information.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eTerminology\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003eConceptual coverage\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eClassification\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eConcept description\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eAdditional information\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eSymptom (n\u0026thinsp;=\u0026thinsp;25)\u003c/b\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eFood (n\u0026thinsp;=\u0026thinsp;47)\u003c/b\u003e\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSNOMED-CT\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e42\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eConcepts are arranged into a hierarchical structure.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eDetailed and unambiguous definition.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003ePreferred term and synonyms.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMeSH\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eConcepts are arranged into a logical and detailed hierarchical structure.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eDetailed and unambiguous definition.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eProvides related concepts (where available) for each term.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMedDRA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTerms are arranged into a 5 tier branching system expanding from very specific to more general concepts.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNo definition provided.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIncludes a preferred name and related synonyms.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eFoodEX2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e46\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eConcepts are categorised into one of 21 groups and facets can encode additional detail including ingredients or processing techniques.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eClear description along with common and scientific name\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eN/A\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLanguaL\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e47\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eConcepts are classified systematically based on 14 key terms including product type, food source and cooking method.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eClear description along with common and scientific name\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eN/A\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAGROVOC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTerms are arranged in a hierarchical and non-hierarchical system to classify a range of concepts and to indicate related terms.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNo description is provided, but the broader concept is included to provide context.\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eA list of related concepts are included for some terms.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003eDescription of concepts\u003c/h2\u003e \u003cp\u003eThe term definitions provided by each of the coding systems were reviewed and compared with the definitions found in the literature (Supplementary material Tables\u0026nbsp;2 and 3). MedDRA does not provide formal definitions for the symptom and sign concepts and so fails to provide any additional clarity or description for each term. In contrast, SNOMED-CT and MeSH provide clear and unambiguous descriptions for each concept. This is illustrated in Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e using \u0026ldquo;urticarial rash\u0026rdquo; and \u0026ldquo;hazelnut\u0026rdquo; as an example sign and food respectively. Thus, both MeSH and SNOMED-CT include a detailed definition to describe the sign \u0026ldquo;Urticarial rash\u0026rdquo; which is consistent with the key definitions (Supplementary material Table\u0026nbsp;2). Similarly, FoodEx2, LanguaL and AGROVOC all provide a detailed description for each food term as well as detailing both the common and the Latin name for each food to reduce ambiguity (Supplementary material Table\u0026nbsp;3).\u003c/p\u003e\n\u003cp\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 3.\u003c/strong\u003e Comparison of the definition of exemplar symptom (urticarial rash) and food (hazelnuts) terms according to the different terminologies.\u003c/p\u003e\n\u003ctable border=\"1\"\u003e\n\u003ctbody\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003e\u003cstrong\u003eTerminology\u003c/strong\u003e\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u003cstrong\u003eDefinition \u003c/strong\u003e\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd colspan=\"2\" width=\"601\"\u003e\n\u003cp\u003e\u003cstrong\u003eUrticarial rash\u003c/strong\u003e\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eSNOMED-CT\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u0026ldquo;A raised, erythematous papule or cutaneous plaque usually representing short-lived dermal oedema.\u0026ldquo;\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eMeSH\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u0026ldquo;A vascular reaction of the skin characterised by erythema and wheal formation due to localized increase of vascular permeability. The causative mechanism may be allergy, infection or stress.\u0026rdquo;\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eMedDRA\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003eN/A\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eThRAll approach\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u0026ldquo;A condition characterized by the development of wheals (hives), angioedema or both\u0026rdquo;\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd colspan=\"2\" width=\"601\"\u003e\n\u003cp\u003e\u003cstrong\u003eHazelnut \u003c/strong\u003e\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eSNOMED-CT\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u0026ldquo;Tree nut (substance)\u0026rdquo;\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eMeSH\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u0026ldquo;A plant genus of the family BETULACEAE known for the edible nuts\u0026rdquo;\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eFoodEX2\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u0026ldquo;Tree nuts from the plant classified under the species \u003cem\u003eCorylus avellana L\u003c/em\u003e., commonly known as Hazelnuts or Cobnuts or Common hazelnut. The part consumed/analysed is not specified. When relevant, information on the part consumed/analysed has to be reported with additional facet descriptors. In case of data collections related to legislations, the default part consumed/analysed is the one defined in the applicable legislation.\u0026rdquo;\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eLanguaL\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u0026ldquo;The group includes kernels of the seeds of all species similar to Hazelnuts or similar nuts sharing the same pesticide to the maximum residue level (MRL) as Hazelnuts.\u0026rdquo;\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd width=\"145\"\u003e\n\u003cp\u003eAGROVOC\u003c/p\u003e\n\u003c/td\u003e\n\u003ctd width=\"456\"\u003e\n\u003cp\u003e\u0026ldquo;The fruit of small trees of shrubs of the Corylaceae family. The round-oval nuts are surrounded by a leafy involucre, which comes out easily when the fruit is mature. Remains the nut, with a pericarp, the shell, more or less woody, and depending on varieties. Inside is the seed, covered by a very thin tegument.\u0026rdquo;\u003c/p\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003c/p\u003e\n \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003cp\u003eWhere appropriate, MedDRA aggregates and highlights similar terms related to the specific concept and so allows comparable terms to be easily accessed. For example, \u0026lsquo;urticaria rash\u0026rsquo; is the preferred name that classifies 33 related concepts including \u0026lsquo;urticaria localized\u0026rsquo; and \u0026lsquo;generalised urticarial rash\u0026rsquo;, which provide varying levels of detail and alternative terms that include a level of clinical interpretation. This is useful but the large number of similar terms may reduce the specificity and level of detail initially identified by a term. In contrast, concepts in SNOMED-CT are associated with a unique Fully Specified Name (FSN); this is the ideal term that a clinician would use in a particular language, dialect or context. SNOMED-CT also identifies relationships to other similar and related concepts and considers the preferred name for \u0026lsquo;urticarial rash\u0026rsquo; to be \u0026lsquo;weal\u0026rsquo; with \u0026lsquo;wheal\u0026rsquo;, \u0026lsquo;welt\u0026rsquo;, \u0026lsquo;hives\u0026rsquo; and \u0026lsquo;nettle rash\u0026rsquo; being noted as alternative terms. Since concepts are coded in MeSH for the purpose of indexing publication records, each MeSH term can comprise several synonyms; for example, \u0026lsquo;urticaria\u0026rsquo; also includes \u0026lsquo;urticarias\u0026rsquo; and \u0026lsquo;hives\u0026rsquo;. All concepts that come under one record are considered equivalent and this is useful when trying to maximise the number of relevant articles identified in a search but not necessarily when identifying synonyms in the context of compiling data on food allergy in the ThRAll database.\u003c/p\u003e \u003cp\u003eLanguaL and FoodEx2 do not provide related concepts since this is not appropriate in the context of a food classification system as there would be no suitable synonyms. In certain cases AGROVOC provides equivalent terms and where appropriate states the broader and/or narrower relevant concepts as well as identifying what the product is produced (i.e. the plant/ animal species of origin).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eMechanistic basis to classify an adverse reaction\u003c/h2\u003e \u003cp\u003eIt was also important to compare the pathway that each of the terminologies used to classify an adverse reaction. Food can induce a range of adverse reactions but, although the symptoms and signs may be similar, the mechanistic basis of allergies, intolerances and sensitivities are completely different. An adverse reaction to food \u003csup\u003e28\u003c/sup\u003e encompasses both immune- and non-immune mediated adverse reactions (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Sub-types of immune-mediated adverse reactions include those involving the development of food-specific IgE antibody responses. This type of food allergy results in symptoms and signs that appear immediately (in less than 2 hours, usually within 30 minutes) sometimes even after ingesting a small dose of the allergen, and can involve multiple organs including the skin, respiratory, digestive and cardiovascular systems. A second type of well-defined non-IgE-mediated adverse reaction to food is the T-cell mediated syndrome triggered by ingestion of gluten, known as coeliac disease (CD)\u003csup\u003e29\u003c/sup\u003e. This life-long disease involves sensitivity to gluten and individuals with CD often present with gastrointestinal signs and symptoms, including diarrhoea, together with weight loss due to the malabsorption of nutrients. In contrast, food intolerance conditions are not immune mediated but nevertheless can be reproducibly induced following ingestion of specific foods. One example is lactose intolerance where individuals lack the lactase enzyme, which is involved with the digestion of lactose. Symptoms appear shortly after drinking milk or consuming dairy and are commonly reported as stomach pain, bloating and diarrhoea. Lactose intolerance is different to an IgE mediated milk allergy, which is an IgE mediated reaction where symptoms appear within 2\u0026nbsp;h of consuming milk-containing foods.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec9\" class=\"Section2\"\u003e \u003cp\u003eThe classification of an adverse reaction used in the ThRAll project (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e1\u003c/span\u003e) was used to benchmark how the different terminologies classify an IgE mediated food allergy (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e2\u003c/span\u003e). SNOMED-CT considers the trigger of an allergic reaction as the causative food and then links this back to the allergic hypersensitivity. It provides an overview of the process of the reaction but also filters into specific details about the adverse response, including branching to the causative agent and a qualifier for the severity of the reaction. This is consistent with terminology from the World Allergy Organisation (WAO) and the European Academy of Allergy and Clinical Immunology (EAACI)\u003csup\u003e30\u003c/sup\u003e. MedDRA and MeSH classify food allergy from a disease perspective and then acknowledge the response as a consequence from ingestion of the problematic food. MeSH also includes a logical and clear flow using the descriptor \u0026ldquo;food hypersensitivity\u0026rdquo; as a type of \u0026ldquo;immediate hypersensitivity\u0026rdquo; which is used as a synonym of IgE-mediated food allergy. This is linked to the causal food and the eliciting symptoms. In contrast, MedDRA utilizes a tree flow diagram to show how a food allergy is classified but this was a simpler and less detailed pathway compared to MeSH and SNOMED-CT. Since the ThRAll project is considering the reaction from a food and public health perspective, the SNOMED-CT approach to classify a food allergy was considered the most appropriate.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003cp\u003eFigure \u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e3\u003c/span\u003e illustrates how MeSH, MedDRA and SNOMED-CT classify a non-IgE immune mediated adverse reaction to food and coeliac disease. MedDRA and MeSH both provide multiple ways to classify the pathway of coeliac disease. These terminologies consider this disease as a nutritional or gastrointestinal disorder that leads to malabsorption, which clearly demonstrates the reaction is triggered by food. MedDRA has a third pathway to classify coeliac disease from a disease perspective as an autoimmune disorder; this is consistent with the ThRAll approach, which classifies coeliac disease as an immune-mediated reaction. Again, SNOMED-CT has a different way of approaching the classification of coeliac disease in comparison to MedDRA and MeSH but still considers it a malabsorption syndrome caused by the ingestion of gluten. Figure\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e3\u003c/span\u003e demonstrates that coeliac disease is an adverse response with a clear food trigger, yet the pathway to classify this reaction is very different to the classification of a food allergy and so these reactions should be considered separately.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003cp\u003eLastly the pathways to describe a non-immune mediated adverse reaction by specifically looking at the classification of lactose intolerance are shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e4\u003c/span\u003e. MedDRA, MeSH and SNOMED-CT all describe lactose intolerance as a metabolic or gastrointestinal disorder which disrupts the absorption of carbohydrates. The ThRAll approach classifies lactose intolerance as a non-immune mediated reaction due to a disorder of an enzymatic process. The lack of lactase enzyme in lactose intolerance patients causes the malabsorption of the carbohydrate lactose and so demonstrates the similarities between these classifications.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003cdiv id=\"Sec13\" class=\"Section3\"\u003e \u003ch2\u003eClassification schemes for symptoms and signs\u003c/h2\u003e \u003cp\u003eMedDRA has a logical five-tier structure expanding from very specific to more general concepts. Lowest Level Terms (LLTs) represent the most specialised concepts including symptoms, medical procedures and personal characteristics. LLTs can be considered the preferred term (PT) or a synonym of the preferred term (PT) \u003csup\u003e31\u003c/sup\u003e. Similar PTs are aggregated into High Level Terms (HLT) based upon anatomy, pathology, physiology or aetiology. These HLTs are further categorised into High Level Group Terms (HLGT) that are then split into one of 26 System Organ Classes (SOC\u0026rsquo;s) providing the most general classification. This is a logical and methodical organisation system but concepts are confined to these five levels and further clarification or granularity cannot be expressed beyond the LLT to indicate the severity or manifestation of a symptom. Concepts in SNOMED-CT can vary in their specificity; more general concepts are aggregated together which filter down to more specific terms. Relationships are used to portray a confirmed association between multiple concepts. The branching structure in SNOMEC-CT is useful to be able to code and represent clinical data at a level of detail that is appropriate to a range of different uses. In contrast MeSH is a cataloguing system with a slightly different framework to the other terminologies as terms do not identify clinical phenomena but instead represent a category. MeSH is used to categorise and retrieve records and is organised in a hierarchical structure with 16 primary categories that splits into subcategories providing more detailed terms. A letter corresponding to a category and a number representing the hierarchical level provides an identifier for each term.\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eClassification schemes for food\u003c/h2\u003e \u003cp\u003eThere are many levels of granularity that need to be considered when describing and encoding a food product including the origin of the food, the food matrix and processing techniques. For example, when considering a food allergy, we need to identify differences in the frequency or severity of a reaction,1 which may be affected by cooking technique (e.g. dry roasted compared to raw peanuts) or the food matrix/ vehicle used (e.g. peanut butter, whole peanut, baked goods containing peanuts). It is useful to have a system with the ability to encode multiple levels of detail depending on the amount of data and information that is available. This is important given that the literature shows that some food allergens are sensitive to food-processing techniques and a high fat content may increase the allergenicity of the protein \u003csup\u003e32,33\u003c/sup\u003e. The structure of these different classification systems represents their primary use whether that is to understand nutritional value, physical characteristics or the type of food product.\u003c/p\u003e \u003cp\u003eFoodEx2 is arranged into 21 clearly defined food groups, such that every food aligns to exactly one group. The system is made up of base terms and facets; the base term is defined by a unique five-character alphanumeric code and represents the specific foods within the hierarchy. Facets provide additional detail to the base term, such as the origin of the product; its ingredients and the process involved in its preparation. This additional information can be combined with the base term to provide a more detailed and complete description of the food product. This demonstrates the range of granularity and amount of information that has been considered in this classification system making it useful for encoding allergenic foods and common matrices or derivatives used in oral food challenges.\u003c/p\u003e \u003cp\u003eLanguaL systematically classifies food in a systematic way according to 14 key concepts including product type, cooking method and packing medium. These concepts are used to encode the product and enable almost any food product to be classified to the level of detail that is required. A unique code is provided for each food concept, which can then be translated into multiple languages.\u003c/p\u003e \u003cp\u003eAGROVOC relates concepts in a hierarchical and non-hierarchical structure. A branching logic is used whereby the term becomes more specific and precise. For example, nuts provides a broader way of describing hazelnuts. There is also a non-hierarchical relationship and this expresses related concepts where appropriate.\u003c/p\u003e \u003cp\u003eFigure \u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e demonstrates how each of the standards classifies hazelnuts as an example of a food concept. The figure shows that LanguaL utilises the logic from FoodEx2 and that each of the terminologies distinguish between plant and animal products before identifying the relevant concept from a list of key categories and then filtering into the specific species.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec15\" class=\"Section2\"\u003e \u003cdiv id=\"Sec16\" class=\"Section3\"\u003e \u003ch2\u003eEncoding symptom severity\u003c/h2\u003e \u003cp\u003eWhen considering the dose at which an allergen induces an objective reaction it is useful to encode the severity of that reaction. Thus, when identifying the dose that elicits a reaction in p% of the allergenic population (eliciting dose, ED\u003csub\u003ep\u003c/sub\u003e), it is useful to understand the proportion of individuals that presented with either a mild, moderate or severe reaction at this dose. Some studies, such as iFAAM, have collected detailed information on severity which can also be used to identify criteria for stopping a challenge [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. This information can be used to identify eliciting doses that present a tolerable level of risk of reaction in allergic individuals, as observed in the Peanut Allergen Threshold study \u003csup\u003e13\u003c/sup\u003e. The classification of reaction severity is inherently subjective, arising from clinical interpretation of signs and symptoms and many different approaches have been developed and compared \u003csup\u003e34,35\u003c/sup\u003e. SNOMED-CT codes do not always provide sufficient detail to describe the severity as well as symptom presence but this can be addressed by using an additional qualifier code (mild, moderate or severe) to fully express the specific, observed sign or symptom. This is illustrated for the iFAAM oral food challenge record where symptoms have been classified and coded with both the symptom code and the terms, mild, moderate or severe using the approach of Sampson \u003csup\u003e36\u003c/sup\u003e (Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). This shows, for example, if a patient experienced one episode of diarrhoea this would be coded as the SNOMED-CT code for diarrhoea and the code of mild severity and paired in a structure to indicate one episode of diarrhoea: 62315008\u0026ndash;255604002.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab4\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eEncoding severity alongside symptoms and signs using SNOMED-CT.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"5\"\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eSymptom\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eSNOMED- CT code\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c5\" namest=\"c3\"\u003e \u003cp\u003eDescription for relevant severity grade (SNOMED-CT code)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eMild\u003c/b\u003e (255604002)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cb\u003eModerate\u003c/b\u003e (6736007)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003eSevere\u003c/b\u003e (24484000)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003ePruritus\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e418363000\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026bull; Occasional scratching\u003c/p\u003e \u003cp\u003e\u0026bull; Continuous scratching for \u0026gt;\u0026thinsp;2\u0026nbsp;min at a time\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026bull; Hard continuous scratching leading to excoriations\u003c/p\u003e \u003cp\u003e\u0026bull; Scratching of palms, soles, genitals, scalp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eErythema\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e247441003\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u0026bull; Few areas of faint erythema\u003c/p\u003e \u003cp\u003e\u0026bull; Areas of erythema (\u0026thinsp;\u0026lt;\u0026thinsp;=\u0026thinsp;50%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneralised marked erythema (\u0026gt;\u0026thinsp;50%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eUrticarial rash (wheal)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e247472004\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eUp to 10 new hives\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneralised involvement (\u0026gt;\u0026thinsp;10 new hives)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eAngioedema\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e41291007\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMild lip oedema\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026bull; Significant lip oedema\u003c/p\u003e \u003cp\u003e\u0026bull; Whole face oedema\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eRhinitis\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e70076002\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026bull; Rare bursts, occasional sniffing\u003c/p\u003e \u003cp\u003e\u0026bull; \u0026lt;\u0026thinsp;10 bursts, frequent sniffing or intermediate rubbing of nose;\u003c/p\u003e \u003cp\u003e\u0026bull; Long bursts, persistent rhinorrhoea or continuous rubbing\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eOcular\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eIntermittent rubbing of eyes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContinuous rubbing, periocular swelling, reddening\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eWheezing\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e56018004;\u003c/p\u003e \u003cp\u003e272040008\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026bull; Expiratory wheezing to auscultation\u003c/p\u003e \u003cp\u003e\u0026bull; Inspiratory and expiratory wheezing to auscultation\u003c/p\u003e \u003cp\u003e\u0026bull; Use of accessory muscles or audible wheezing\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eGastrointestinal pain\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003eNausea\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e21522001\u003c/p\u003e \u003cp\u003e422587007\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026bull; Complaints of nausea or abdominal pain\u003c/p\u003e \u003cp\u003e\u0026bull; Frequent complaints of nausea or pain with abnormal activity\u003c/p\u003e \u003cp\u003e\u0026bull; Notably distressed due to GI symptoms with decreased activity\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eEmesis\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e422400008\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026bull; 1 episode of emesis\u003c/p\u003e \u003cp\u003e\u0026bull; \u0026gt;\u0026thinsp;1 episode of emesis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eDiarrhoea\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e62315008\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026bull; 1 episode of diarrhoea\u003c/p\u003e \u003cp\u003e\u0026bull; \u0026gt;\u0026thinsp;1 episode of diarrhoea\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"5\"\u003eSigns and Symptoms recorded in the iFAAM challenge record [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e] were classified and coded as to their severity using a combination of the approach of Sampson \u003csup\u003e36\u003c/sup\u003e as being either mild (Sampson grade 1), moderate (Sampson grades 2 and 3) or severe (Sampson grades 4 and 5) and then encoded using SNOMED-CT.\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003c/div\u003e "},{"header":"Discussion","content":" \u003cp\u003eThe results demonstrate the complexity required to encode food allergy information and each terminology has a different way of classifying an allergic reaction. Furthermore, each terminology varies in the system used to classify and organise concepts, which depend on the primary purpose of the classification system. The analysis showed that SNOMED-CT encoded all of the key terms and provided the conceptual coverage required to maximise the representation and classification of food allergy data for public health purposes aimed at food allergen management. In addition, SNOMED-CT provides a classification scheme that relates specific and more general concepts and that considers food as the trigger of an allergic reaction which is clinically relevant. Therefore, it was chosen as the most appropriate terminology to code data relating to food allergies collated within the ThRAll project. Additionally, SNOMED-CT also provides severity code, allowing for more precise, qualified records of reactions.\u003c/p\u003e \u003cp\u003eAlthough FoodEx2, SNOMED-CT, MeSH, LanguaL and AGROVOC all provide terms for foods, FoodEx2 provided the greatest conceptual coverage including species of origin and food processing methods. Consequently, FoodEx2 was selected to code the foods that initiate an allergic reactions, enabling analysis to be undertaken to identify how factors, such as food processing, may influence eliciting dose threshold and reaction severity.\u003c/p\u003e "},{"header":"Conclusion","content":" \u003cp\u003eThe ThRAll study has determined that SNOMED-CT and FoodEx2 are presently the most competent terminologies for the representation of clinical knowledge relating to food allergy, the former delivering encodings for observed symptoms or signs and the latter representing eliciting foods (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). This combined set of terminologies provides not only complete conceptual coverage, but a depth of granularity providing a structured flexibility to encoding a given required level of detail, via symptom severity in SNOMED-CT, and facets for food matrices and processing techniques in FoodEx2.\u003c/p\u003e \u003cdiv id=\"Sec19\" class=\"Section2\"\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eIt is expected that by defining a coding system for the ThRAll oral food challenge database will increase accessibility through standardisation. This will in turn extend the usefulness of these data into the future. Furthermore, the approach taken could also be expanded in future to encompass data from other clinical studies and registries of food anaphylaxis such as the network of severe allergic reactions (Network for Online-Registration of Anaphylaxis, NORA) \u003csup\u003e37\u003c/sup\u003e. The proposed pairing of codes to qualify severity of reaction is supported in HL7\u0026rsquo;s FHIR (Fast Healthcare Interoperability Resource), a standard for exchanging healthcare information electronically. This system represents data as a set of related hierarchical elements and values into resources. For the purpose of capturing data relating to allergic reactions, it is possible to record a symptom element, a severity element and a food element within the same resource meaning that there is a standard definition of the relationships between the codes. Using the proposed approach to coding within this standard could further increase the future utility of these data making for a promising approach for recording and storing reusable datasets. The coding approach is also applicable to representing an individual\u0026rsquo;s food allergy information in a standardised way in their electronic health records by including other metadata, such as diagnostic certainty (e.g. whether the data was a self-reported, negative, possible, probable or confirmed allergy) which could ensure correct interpretation across medical systems.\u003c/p\u003e \u003c/div\u003e "},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no competing interests in relation to the published work.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis project has received financial support from the European Food Safety Authority (EFSA), Grant GP/EFSA/AFSCO/2017/03. The present article, however, is under the sole responsibility of the authors. The positions and opinions presented in this article are those of the authors alone and do not necessarily represent the views/any official position or scientific works of EFSA. EFSA guidance documents and other scientific outputs of EFSA, can be found in the EFSA website: \u003ca href=\"http://www.efsa.europa.eu\"\u003ehttp://www.efsa.europa.eu\u003c/a\u003e. The ThRAll project is also co-funded by the UK Food Standards Agency FS101209. This work was partly funded by the European Union through the iFAAM project: Integrated Approaches to Food Allergen and Allergy Risk Management (Grant Agreement N\u0026deg; 312147) and the Medical Research Council Health eResearch Centre, Farr Institute (MR/K006665/1).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors' contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePC and ENCM were responsible for the original concept and design of the work and have overall supervision of its execution. CF, BJ, BG and S L-T were responsible for its execution.MM, AK, T-ML, AS, SD, NdJ, BB-W, MF-R and KB were involved in providing clinical oversight and revision of the work. The manuscript was drafted by CF, BJ, ENCM and PC and all authors were involved in its review and revision and final approval.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eSchoemaker AA, Sprikkelman AB, Grimshaw KE, et al. 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Evaluating standard terminologies for encoding allergy information. \u003cem\u003eJ Am Med Inform Assoc. \u003c/em\u003e2013;20(5):969-979.\u003c/li\u003e\n\u003cli\u003eGrimshaw KE, King RM, Nordlee JA, Hefle SL, Warner JO, Hourihane JO. Presentation of allergen in different food preparations affects the nature of the allergic reaction--a case series. \u003cem\u003eClinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology. \u003c/em\u003e2003;33(11):1581-1585.\u003c/li\u003e\n\u003cli\u003eMackie A, Knulst A, Le TM, et al. High fat food increases gastric residence and thus thresholds for objective symptoms in allergic patients. \u003cem\u003eMolecular nutrition \u0026amp; food research. \u003c/em\u003e2012;56(11):1708-1714.\u003c/li\u003e\n\u003cli\u003eEller E, Muraro A, Dahl R, Mortz CG, Bindslev-Jensen C. Assessing severity of anaphylaxis: a data-driven comparison of 23 instruments. \u003cem\u003eClinical and translational allergy. \u003c/em\u003e2018;8:29.\u003c/li\u003e\n\u003cli\u003eMuraro A, Fernandez-Rivas M, Beyer K, et al. The urgent need for a harmonized severity scoring system for acute allergic reactions. \u003cem\u003eAllergy. \u003c/em\u003e2018;73(9):1792-1800.\u003c/li\u003e\n\u003cli\u003eSampson HA. Anaphylaxis and emergency treatment. \u003cem\u003ePediatrics. \u003c/em\u003e2003;111(6 Pt 3):1601-1608.\u003c/li\u003e\n\u003cli\u003eWorm M, Moneret-Vautrin A, Scherer K, et al. First European data from the network of severe allergic reactions (NORA). \u003cem\u003eAllergy. \u003c/em\u003e2014;69(10):1397-1404.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Ontology, Terminology, Vocabulary standards, Data harmonisation, Food Allergy, Hypersensitivity, ThRAll","lastPublishedDoi":"10.21203/rs.3.rs-118179/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-118179/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground: \u003c/strong\u003eCollation of clinical\u003cstrong\u003e \u003c/strong\u003edata on IgE-mediated food allergies is essential to provide evidenced-based approaches to managing and treating food allergies and prevent accidental reactions. However, this can be a time consuming and difficult process due to the heterogeneous way in which studies collect such data. In order to facilitate data harmonisation a set of standardised terminologies have been identified and a consensus technique established to code food allergy data.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eMethods: \u003c/strong\u003eDifferent terminologies to encode the most common signs, symptoms and problematic foods associated with IgE-mediated food allergies were identified. Their suitability for classifying and coding information about the signs and symptoms of food allergic reactions, causative foods and reaction severity of was assessed. The assessment included existing conceptual coverage and data descriptions, classification schemes and additional relevant information.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eResults: \u003c/strong\u003eAll of the terminologies reviewed included classification schemes, allowing broader concepts to be related to those that are more specialised. Additional information was often present such as equivalence. Of the clinical coding systems assessed, the Systemized Nomenclature of Medical Clinical Terms (SNOMED-CT) provided the most complete coverage with options to code symptom severity. Only food coding systems, such as FoodEx2, provided comprehensive conceptual coverage of the food terms.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConclusions: \u003c/strong\u003eUtilising SNOMED-CT and FoodEx2 standards together will support the harmonisation of data regarding food allergy from diverse sources, providing a transparent and effective way to collate relevant data required for effective food allergen management in the future.\u0026nbsp;\u003c/p\u003e","manuscriptTitle":"Classification and Coding of Data About IgE-mediated Food Allergic Reactions","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2020-12-07 21:42:34","doi":"10.21203/rs.3.rs-118179/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"03d3a59a-4dca-4bee-a616-852b946c60a3","owner":[],"postedDate":"December 7th, 2020","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":1371188,"name":"Translational Medicine"},{"id":1371189,"name":"Allergy \u0026 Immune Disorders"}],"tags":[],"updatedAt":"2020-12-11T14:25:17+00:00","versionOfRecord":[],"versionCreatedAt":"2020-12-07 21:42:34","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-118179","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-118179","identity":"rs-118179","version":["v1"]},"buildId":"-HB7Z8yhvgn0wM9Nzuekk","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}