Semantic Data Platform for Healthcare
Contents
1. JS at orm included amp edited Structure 2 gt project oo baal ID following formats it editing 3 u 2 C3 using left additional different c gt V E fie C concept dh format mar ked E 2 25 d window t Ao U T Ss Dutch import suppor d n S E i dictionary area 2 D ge os exact Y SEU Sous patient type Add m gt c rm S CT attributes em node iem CY Op opo2 D dialogue D B d O mining t 7 1 http www wordle net Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition OOOO MM Dissemination level Public S e C e Author C Riede Averbis J Kors EMC Version 1 1 Final 1 Introduction The research project SEMCARE aims to build a semantic data platform to support case identification for clinical studies and to facilitate clinical decision making based on patient level criteria e g age gender diagnosis indication symptoms lab results Most patient level data can be found in unstructured text documents Text mining tools will be used to extract and convert relevant data These text mining tools require multilingual terminologies in English German and Dutch to standardize and address specific idiosyncrasies of medic2. Semantic Data Platform for Healthcare ICT 611388 Lead beneficiary EMC amp Averbis D4 2 Terminology Management Platform Date 09 01 2015 WP4 Terminological resource acquisition Nature Prototype vO a ane Dissemination level PU D4 2 Terminology management platform WP4 Terminological resource acquisition 1 Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final TABLE OF CONTENTS DOCUMENT INFORMATION cuore pug sur aieo ou ve vd EUG vs CUL eue aU or oEvU sp Sut uva ELiemuE ui un au aUo RE CDs aiak 3 DOCUMENT HISTORY d e en 3 Py m sy n M I caboencuee 4 EXECUTIVE SUMMARY 5 KEY WORDS WORDLE STYLE scssi EE iiS aaa 6 1 INITRODUC MON ass ecto tet EEE E E 7 2 TERMINOLOGY MANAGEMENT PLATFORM cccccsesseeecessseeseenseeeeenseeeeensseeseenseeseoanees 7 25 PROTOTYPE DA ENORMES 7 22 AVAILABLE TERMINOLOGIES saison open Ide tlutam o dp dire ole Rd adr phu dat c Mattb cdd 7 MENU bo ol aL 5 107 n 9 3 1 USER INTERFACE Mc 9 3 2 SEARO e E E E T E E O 10 3 3 HIERARCHICAL NAVIGATION ccccsccccesscecessseceesseecesseecessseecesseecensaeecenseecessseeeesaeeceneeceesaeeeenas 11 3 4 CONCEPT DETAI anren e E E E A a 12 3 5 EDITING EXISTING TERMINOLOGIES ssc
3. Management Platform especially terminologies covering the medication in the different countries D4 1 Initial multilingual biomedical terminology Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 OOOO f MM Y Semcare 3 User Manual D4 2 Terminology management platform WP4 Terminological resource acquisition Dissemination level Public Author C Riede Averbis J Kors EMC Version 1 1 Final The terminology management platform offers both reading and editing functions Terminologies can be exported in different formats e g OBO or SKOS 3 1 User Interface aD Export Admin Show Logs About logged in as seccam click to logout averbis TS RET Perrrmnokogues zm i Herarciey SEICARE 10 ry Search results 1 o AHA ZUM Modam Olas Concept Labal Terminology o Labor 20 oll ame i in SERC 10 5 SEMCARE 10 Laie mom coronary anter i 1 JQ semcare 10 7 ai iria B semCare Modder 10 al Of Cinca edeg ERSHOMED2QUIT adi Family tatpry of dapedar GISNOMED 30M 00 1 d TS Deseevable entity Gus sEMCARE 10 7 ull Gd Cardona obont Ciromi ampogram eleseeable Comaary atenes P Ethocandiogram observable c PHElecimcandeognam oaea 1 1 yon 1 Ergebressen TS MRI observable Do Vitel Seye Concepl delats CARE 1 0 ipa o Procedure Pr
4. resource acquisition OOOO MM Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final 5 Details of the concept An area can be faded out in order to enlarge the disposable space for the remaining areas by clicking on top right 3 2 Search A basic functionality of the Terminology Platform is the possibility to search terms via a free text search in different terminologies All terminologies which are marked in the left area Terminologies are included into the search The search covers all synonyms of a concept Search box The search box allows a free text search During the entry of the word the AutoSuggest function helps to find the desired term Search Llimit25 Ischemia SNOMED 2014 02 52674009 Ischemia UMLS SEMCARE 1 0 C0022116 Ischemia disorder SNOMED 2014 02 52674009 Ischemia disorder UMLS SEMCARE 1 0 C0022116 Ischemia and infarction of kidney UMLS SEMCARE 1 0 C0495064 Ischemia Anoxia Brain UMLS SEMCARE 1 0 C0752306 Ischemia Anoxia Cerebral UMLS SEMCARE 1 0 C0752307 ischemia bowel UMLS SEMCARE 1 0 C0156149 Ischemia bowel UMLS SEMCARE 1 0 C2004435 ischemia brain UMLS SEMCARE 1 0 C0007786 Ischemia cerebral UMLS SEMCARE 1 0 C0917798 Ischemia cerebrovascular UMLS SEMCARE 1 0 C0917798 Figure 2 Example of the AutoSuggest function Search results The search results are listed on the ri
5. tabs Linked Data Images and Settings can be used in prospective versions to display information form external sources or images 3 5 Editing existing terminologies Import Users with the appropriate rights can import additional content into an existing terminology under the menu item Admin aP Export Admin Show Logs About logged in as lt th Import Terminology ey Em pty delete Terminology Figure 9 Import Terminology Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC D4 2 Terminology management platform WP4 Terminological resource acquisition Version 1 1 Final In the opening dialogue window the target terminology and the source file have to be chosen Additionally the existing terminology can be emptied before import Allowed import formats are csv and OBO PUT piatom OOOO o Import content into a terminology Please choose a OBO or CSV file The values will get appended to the chosen terminology Choose target SEMCARE 1 0 xz v Empty terminology before import Choose source file obo nosy Me wtjlmportt Stop Close bo s sa Figure 10 Dialogue window
6. 8 ES Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s D4 2 Terminology management platform WP4 Terminological resource acquisition A OOOO MM Dissemination level Public S e C e Author C Riede Averbis J Kors EMC Version 1 1 Final DEFINITIONS e Partners also named as beneficiaries of the SEMCARE Consortium are referred to herein according to the following codes AVERBIS Averbis GmbH Germany Coordinator EMC Erasmus Universitair Medisch Centrum Rotterdam Netherlands Beneficiary MUG Medical University of Graz Austria Beneficiary SGUL Saint George s University of London UK Beneficiary SYNAPSE Synapse Research Management Partners S L Spain Beneficiary e Project The sum of all activities carried out in the framework of the Grant Agreement e Consortium The SEMCARE Consortium conformed by the above mentioned legal entities e AEP Averbis Extraction Platform text analysis tool to extract information units such as facts and relations from unstructured text e EHR Electronic health record clinical data record of a patient e Terminology General term for information artefacts that provide controlled terms for a domain identifiers of meaning and semantic relations e g SNOMED ICD 10 MeSH e Term Browser Tool provided by Averbis to load view modify and export terminologies It can also be used to cre
7. EMCARE F 2014 01 4 Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388
8. F EXPORT MODES s essstsitie PERS VERS UES TUERI PORE PRU G M OUR IUE REEF Un M TIR PS SEVERE TN anes ENNE I MUR UTI E 20 FIGURE 20 AVERBIS CONCEPT MAPPER EXPORT isses Senat riu UR UR FEX ES PAX DUK RERUMAESN OR SERE RUE OEE ERE R QN DONE SRU UU REETA 21 Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition 3 Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final DOCUMENT INFORMATION Grant Agreement ICT 611388 SEMCARE Number Full title Semantic Data Platform for Healthcare EU Project officer Saila Rinne Saila Rinne ec europa eu Deliverable Terminology management platform Work package Terminological resource acquisition Delivery date Contractual 31 12 14 09 01 2015 Status Version V1 1 Final Drat O Final M Nature Report O Prototype M Other O Dissemination Level Public M Confidential O Authors Partner C Riede Averbis J Kors EMC Claudia Riede Claudia riede averbis com Responsible Author Partner AVERBIS Phone 49 761 203 97690 DOCUMENT HISTORY NAME DATE VERSION DESCRIPTION X Wang SQUL J Kors EMC Seventh Programme for research technological development and demonstration under grant agreement No 61138
9. GNO MetrFier Y GNO Uederspeched Terms Gua S SEMCARE 10 Fiter fio ambiguity check v ICD ipon Ambiguous Direct Hypenmyms Of Unspecited Terms EE SNOUED 2004 Y dgrore oll ignore Ambigoos Tees PND spec v SWDGEO specific v SWDspec amp 9 UnderspecisedTermsFiter ii Show Logs O Close dialog Figure 18 Export filters After closing the export dialogue window clicking on Close dialog at the bottom of the window the export mode of a term or a concept can be set Concept details SEMCARE 1 0 xyz PF9ItOW QRS duration DEFAULT O Terms Synonyms 4 A Relatives 1 0 EB Attributes 0 lt Xrefs 2 Linked Data 9 Images Settings Pref Label Xrefs Attributes Type wd Dict mode 2 QRS complex duration DEFAULT QRS duration DEFAULT QRS Komplex Dauer DEFAULT QRS duur DEFAULT DEFAULT EXACT IGNORE Figure 19 Manual setting of export modes Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition 1 OOOO MM Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final By setting the export mode to IGNORE the term or concept will not be included into an export The IGNORE mode can be extend
10. Import 6 5 The fields of a source file in csv format must be separated by The following fields are expected Table 1 Import fields ConceptlD TermLabel TermType parentConceptlDs MappingForms ID of the label of type of identification concept ID of the mapping concept the term the term code of the feed parent concept forms of the if empt language term term ie ia E de cr optional type 0 no optional default E uen Manual editing Terminologies can be edited manually provided that the terminology is editable and that the user has write permission Concepts With a right mouse click on the concept in the hierarchical view the concept can be deleted its hierarchy 6 if a homonym term has an additional specification which will not be found in a text e g note finan and note mus the text analytics pipeline can use the mapping form e g note Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 Dissemination level Public NANNAN sel e Y C are e Author C Riede Averbis J Kors EMC D4 2 Terminology management platform OOOO WP4 Terminological resource acquisition 6 Version 1 1 Final can be edited or a new child can be added Below the hierarchical tree there is also a Button to add new concept
11. Remove selected profile eel Add entres to Prole 3 Store Prose Fee evaluation all inheeted terms ate incloded E Show Loge D Cose aio Figure 17 Choose Profile Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition OOOO MM Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final For each export profile at least one terminology has to be allocated There are several predefined filters which can be applied e g the Default Filter English identifies all terms containing acronyms and stop words and sets them to the EXACT modus for the export Using the Averbis Concept Mapper format for the export the term or concept will then be written into a separate dictionary see below The results of a filter can be downloaded as csv file for evaluation instead of applying the filter directly O Erse af medications cos proble H Terminology AbstrciConceptsFite 8 General MCD 10 AHA 2014 9 Aciauiseiiotes Caster Custom Advanced v DetautF iter English 7O suci 10 F DehyutFitar German Y DetsutF iter No Numbers semCare Moater 1 0 ONG ignore Short Orscer20 Synonyms v ONB PND Kucrwert GB SNOMED 2014 02 Yv
12. Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition 8 Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final Terms The terms of a concept can be edited in the Concept details area Concept details SEMCARE 1 0 xyz L2AqQkS ST segment 233 p e tQ P E S Pref Label Xrefs Attributes Type ala ECG ST segment imported from A umls_semcare ala Electrocardiogram ST segment pon NM iF umls_semcare ala electrocardiogram ST segment imposiad um iF umls_semcare elektrocardiogram ST segment impariad Som iF umls_semcare 9 Elektrokardiogramm ST Strecke imposed kom umls_semcare aia segment st imported fom 4 umls_semecare za segments st imported from A umls_semcare E ST z Ei S ST seament Figure 15 Editing terms to delete the term E to search for synonyms in the terminologies available in the Terminology Platform i to edit the term Additional synonyms can be entered by clicking on the amp Button at the bottom right 3 6 Export of terminologies Users with the appropriate rights can export a terminology under the menu item Export amp pD Export Admin Show Logs About logged in as it Quick export E Export profile settings Quick export With the Quick export function terminol
13. a ST segment imported from umls semcare y ala ST Elektrokardiogramm ST Strecke imported from umls semcare sla Electrocardiogram ST segment imported from umls semcare ala ECG ST segment imported from umls_semcare i Figure 6 Concept details for ST segment In the first tab Terms Synonyms all terms or synonyms of the concept are listed For each term the language the type and possible attributes are specified In each language a preferred term can be defined this is indicated in the column Pref Term attributes provide additional information in a typified format where types can be defined by the user E g common typing errors can be added to a concept as synonyms and can be marked by the attribute typing error In the second tab Relatives the direct relatives of the concept within the terminology are listed Concept details SEMCARE 1 0 xyz WRTfyMb Electrocardiogram observable S XS 0 Terms Synonyms 4 pO Relatives 1 8 BB Attributes 0 Xrefs 0 C9 Linked Data 6 Images Settings Type Label Concept ID Type Label Concept ID is a Cardiovascular tZ6GLKZ 9 is a ST segment L2AqQkS Q m is a QT interval f2DnPA8 Q9 duration is a PR Interval VGzKgzj Q Duration is a Q wave 1MXCUKY Q is a T wave Sov P Kf Q is a ST segment 3J3UgVk Q duration is a Q wave height EtfqNCt Q is a QRS duration PFSitOW Q Figure 7 Concept details Relatives Copyright 2014 2015 SEMCARE Consortium This project
14. al language The SEMCARE Terminology Management Platform is using the Averbis Terminology Platform called Term Browser It provides software services to support the management of the terminologies used for the SEMCARE text analytics pipeline It is possible to import terminologies into the platform to browse easily the terminologies to add and modify concepts and terms The modified terminology can be exported for utilisation in the text mining platform 2 Terminology Management Platform 2 1 Prototype Data The prototype is available via the internet with the URL http www termbrowser de Username and password will be sent on request please send a message via the SEMCARE homepage http semcare eu contact 2 2 Available Terminologies The partners of the SEMCARE project have agreed on an initial use case Risk Stratification and Differential Diagnosis of Patients suffering from transient loss of consciousness Based on the topic of interest as defined in deliverable D3 2 Requirement specification a distinct SEMCARE terminology has been created Further terminologies are used to enrich the SEMCARE terminology but are also needed to cover laboratory data medication and diagnosis The following terminologies are currently available in the Terminology Management Platform D3 2 Requirements Specification chapter 2 1 3 Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European U
15. ate new terminologies e UMLS Unified Medical Language System metathesaurus e OBO OBO formatis the text file format used by OBO Edit the open source platform independent application for viewing and editing ontologies e SKOS Simple Knowledge Organization System SKOS is part of the Semantic Web family of standards e LOINC Logical Observation Identifiers Names and Codes LOINC was initiated in 1994 by the Regenstrief Institute and provide a universal code system for tests measurements and observations e SNOMED CT systematically organized computer processable collection of medical terms e UIMA Unstructured Information Management Architecture framework by Apache enabling the generation of analysis pipelines for arbitrary content such as text image or video data Seventh Programme for research technological development and demonstration under grant agreement No 611388 ERES Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s D4 2 Terminology management platform WP4 Terminological resource acquisition D OOOO MM Dissemination level Public S e C e Author C Riede Averbis J Kors EMC Version 1 1 Final EXECUTIVE SUMMARY The aim of the Terminology Management Platform is to provide a user friendly software which can support the management of terminologies needed within the SEMCARE project This document presents a user manual explaini
16. cccssscccesseecesseecessseecenseecessseecenseecenssecessseecessesessseeeenas 14 3 6 EXPORT OF TERMINOLOGIES ccccccccccssseccesseeeceseecesseeccesaeecenseecccsueecenseececsseceesaeecenseeseesaneeenes 18 Seventh Programme for research technological development and demonstration under grant agreement No 611388 ERES Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s D4 2 Terminology management platform WP4 Terminological resource acquisition 2 Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final TABLE OF FIGURES gc zu US E INTERA E e C 9 FIGURE 2 EXAMPLE OF THE AUTOSUGGEST FUNCTION ssssuxsetpeseu e eoru FExEEF HEXREREPXMAEEERCE RYE FER ENTERRE KU xn YPF Nea F QUEE ERE KRRAR 10 FIGURE 3 SEARCH RESULT FOR ST SEGMENT scccsseccccessccccnscsceensceccesecscescececsceseeussssseueceseueseseussssseneceseeusseseusessenesess 10 FIGURE 4 SEARCH RESULT USING THE WILDCARD CHARACTER IN ISCHEM sssseccccceesccccceeesecceeceeseecceeeeseeseseegeeceetsaeneseeses 11 FIGURE 5 PART OF THE HIERARCHY OF THE SEMCARE TERMINOLOGY scccsccecceecseceecceccecceecesccscssececeeceecssceseeseeeceeeeeeees 12 FIGURE 6 CONCEPT DETAILS FOR ST SEGMENT sssccccsssscccnscccecnsccceesssescuscesecnsseseeeesscseussesecusseseussssseusseseoussesenesessen
17. cept SEMCARE 1 0 Child of Vital Signs Concept ID Preferred term label Weight Language English v Suggest synonyms v Qok Cancel Figure 13 Add concept The concept ID can be entered manually otherwise the ID is generated automatically By ticking the box Suggest synonyms all synonyms from terminologies that were marked as selected in the left area of the Terminology Platform are proposed The terms can be selected individually The checkmark on concept level inserts an XREF to the referencing terminology Proposed synonyms qeseeseseseeeeeeeoeee0Pe00P000000009900000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 0000000 000000000000 000000000004 Deselect all C0043100 WEIGHT UMLS SEMCARE 1 0 xyz EE WEIGHT VEE WEIGHT Ila Weight mala weight v amp la weighted Mala weighting Mala Weights m v amp la weights v amp la Weights qualifier value Seen eee oseee eee eese eese ees eess ese ees eee eee 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 000029 n Qo Deselect all 3 C0005910 Body Weight UMLS SEMCARE 1 0 xyz v ala bodies weight v amp la Body Weight TSE Andu waoinht D Add selected cance Figure 14 Proposing synonyms Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s
18. ed to subordinate concepts if the tick box on the right side of the drop down menu on concept level is marked By setting the export mode to EXACT the term or concept is exported into a separate dictionary The text mining pipeline will use the terms from this exact dictionary only in this exact form and allows no variations like differing lower or upper case or grammatical inflections For the export the following formats are available Averbis Concept mapper Format Averbis MSI Format Averbis Lemmatizer Format OBO SKOS and csv The text analytics pipeline expects the Averbis Concept mapper Format which considers all three export modes Please choose the coecepts annotation type the concepts shall be tagged with include Teemisctogy Comcegt Type ces Lasgeage Term languag O secure F German v ngish Netertand OQDovssiecas 10 jo anemia extraction types Concept ront nsceched e By chching on OK a new dictionary wil be crested it wil replace the old one in the currert folder Figure 20 Averbis Concept Mapper export In the dialogue window the concept type and the language s can be defined The resulting dictionary is stored automatically in a defined data folder in the Averbis file system but its current version can be downloaded in the register Choose Profile b Show al modied terms Erase all modifications E Choos Profle Choose Terminologies amp Ftor 4T Exper Profile label Created S
19. emi HN normed coronary arborea o 5ubsianca Tenson 0 ERIS SSRN NMC SLAIN IN HiRape HE Pref Label refs Amitus type imi O coronaire mader apai Fi iaire a coronasmvales pmo emm ieri eH enronaries mut 43 S Coronary arteries afit za coronary arteries inne ieee zu Coronary arigry infi o Herziranrgetahe Satan Koronasarterien s u Kranulagnden era Fu Engish T imga T umi pg QE Selecta Q Deselect al Apta iiag Platon 3 2 17 Tueety sadi D Aba mbH 2210 2074 Figure 1 User Interface Description of the areas 1 List of the available terminologies The terminologies to be used in the search can be selected by ticking the box before the name of the terminology By clicking on the name of the terminology this terminology can be browsed in the area rightwards 2 The hierarchical structure of a selected terminology The result of a free text search will be shown here in its hierarchical position 3 The search box which allows a free text search 4 List of the search results OBO Flat File Format http oboformat googlecode com svn trunk doc GO format obo 1 4 html Simple Knowledge Organization System http www w3 0rg 2004 02 skos Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological
20. g Neurological finding Respiratory system finding Family history of disorder Observable entity Procedure Substance English Sibling limit 25 v Hide IDs E Add root concept Figure 5 Part of the hierarchy of the SEMCARE terminology If the selected terminology is multilingual the language can be selected below By default the concept IDs are not visible this can be changed by removing the tick besides Hide IDs The classical view is only available for monolingual terminologies 3 4 Concept Details For each concept there is additional information available called Concept details which are displayed in the lower right area Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition 3 OOOO MM 1 Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final Concept details SEMCARE 1 0 xyz L2AqQkS ST segment ib 0 Terms Synonyms 12 A Relatives 1 0 BB Attributes 0 9 Xrefs 2 C9 Linked Data 6 Images Settings Pref Label Xrefs Attributes Type o ala electrocardiogram ST segment imported from umls_semcare E 9 ST segment imported from umls semcare ST Strecke imported from umls semcare sl
21. ght hand side ST segment Q Search M Limit 10 v Search results 2 ConceptlD Label Terminology e C0429029 segment st UMLS SEMCARE 1 0 L2AqQkS ST segment SEMCARE 1 0 1 2 von 2 Ergebnissen Figure 3 Search result for ST segment Displayed are the ID and preferred term of the concepts and the name of the corresponding terminology By clicking on one of the search results more details of the selected concept are shown in the area Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 OOOO MM Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC D4 2 Terminology management platform WP4 Terminological resource acquisition 1 Version 1 1 Final below and additionally the hierarchical tree structure of the terminology is expanded to show the position of the concept The asterisk can be used as a wildcard character to expand the search ischem Q Search Limit25 Search results 52 ConceptlD Label Terminology e 14 ischemic semCare Modifier 1 0 IBq1eOR Ischemic Heart Disease SEMCARE 1 0 10076004 Ischemic muscular atrophy disorder SNOMED 2014 02 129611009 Ischemic peripheral neuropathy disorder SNOMED 2014 02 13026000 Ischemic stricture of intestine disorder SNOMED 2014 02 13954005 Ischemic u
22. has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition N OOOO MM Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final The direct parents are listed in the left table and the direct children are listed in the right table With a click on the pin symbol next to a concept ID it is possible to switch to the corresponding concept Concept Attributes can be used for specifying additional information on concept level e g describing the scope of the concept Ejection fraction MRI only to be used when the ejection fraction is measured by a MRI In the tab Xrefs the relations with concepts in other terminologies are listed The relationship between the concept and the referenced terminology can be described by the type If no type is specified the terminology is containing the same concept Concept details SEMCARE 1 0 xyz L2AqQkS ST segment j KA Type Label ID in target Namespace o relatedTo depressed elevated 27 semCareModifier 9 segment st C0429029 umls_semcare 9 Figure 8 Concept details Xrefs If the referenced terminology is part of the Terminology Management Platform it is possible to go directly to the referenced concept by clicking on the pin symbol The
23. lcer disorder SNOMED 2014 02 140911000119109 Ischemic stroke with coma disorder SNOMED 2014 02 m 1 10 von 52 Ergebnissen E33 81 Figure 4 Search result using the wildcard character in ischem 3 3 Hierarchical Navigation Besides searching for a specific term it is possible to navigate through the hierarchic structure of a terminology By clicking on the name of a terminology in the left area Terminologies this terminology is displayed in the area Hierarchy opening the highest level of the hierarchical tree More detailed sub trees can be opened by clicking on the symbol before the appropriate superordinate concept Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition 2 OOOO CY Y Y 1 Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final Hierarchy SEMCARE 1 0 xyz Modern Classical E3SEMCARE 1 0 3 Clinical finding Atrial fibrillation Bradycardia Brugada syndrome Bundle Branch Block Electrocardiogram finding Heart Failure Ischemic Heart Disease Myocardial infarction Pulmonary Hypertension Stenosis Sudden cardiac death Syncope Ventricular Dysfunction H 3 Metabolic findin
24. ng how to import terminologies into the platform how to browse the terminology how to add or modify terms and how to export the terminology for usage in the text analytics pipeline and the integrated search platform Besides the SEMCARE terminology which has been developed especially for the use case further terminologies which are also used for the text analytics pipeline or support the refinement of the SEMCARE terminology are additionally available in the Terminology Management Platform They are described shortly in this document Seventh Programme for research technological development and demonstration under grant agreement No 611388 ERES Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s D4 2 Terminology management platform OOOO WP4 Terminological resource acquisition f NNAN __ Dissemination level Public S Mm C ci Author C Riede Averbis J Kors EMC Version 1 1 Final t referenced 12 case xact SKOS Manual of E CORSO allows KEY WORDS Wordle style Once listed German symbol P Search platform ee text downloaded o 2 setting name possible 3 4 laboratory results version LLJ appropriate ssi qm language Clicking right 2 g Averbis selected x E g Selecte JIO Isynonyms C5 a rights information gx A gt details c tf children sea rC
25. nion s Seventh Programme for research technological development and demonstration under grant agreement No 611388 O f Se OOO Y Y Y D4 2 Terminology management platform WP4 Terminological resource acquisition Dissemination level Public C e Author C Riede Averbis J Kors EMC Version 1 1 Final e UMLS SEMCARE multilingual terminology provided by EMC SEMCARE terminology created for the defined use case The UMLS SEMCARE terminology has been used to enrich the vocabulary Additional concepts and terms have been added based on the free text phrases found in the test documents The terminology is multilingual for all concepts English German and Dutch terms are included e SemCare Modifier list of descriptive and evaluative qualifiers which are linked to the corresponding concepts in the SEMCARE terminology by cross references The terminology is multilingual for all concepts English German and Dutch terms are included e Labor 2 0 terminology for laboratory parameters developed by Averbis Its hierarchical structure is based on the hierarchy used in LOINC The terminology is multilingual for all concepts English German and Dutch terms are included e SNOMED CT English version from 2014 e ICD AHA 2014 German version of ICD 10 GM 2014 enriched by Averbis with further synonyms in order to use it for text mining purposes Further terminologies can be imported into the Terminology
26. ogies can be exported in the data formats OBO SKOS and csv The export in csv format includes only the fields that were accepted when the terminology was imported see Table 1 Import fields Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition O Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final Averbis Terminology Platform Export terminology Choose terminology SEMCARE 1 0 xyz Full or subtree Full Restrict to subtrees Output format Successfully exported terminology You can download it using this link Download 4222322 MA 22222 22 Figure 16 Quick export The exported terminology can be downloaded directly in the dialogue window Export profile settings For the export of terminologies into a ConceptMapper dictionary which is used in the text mining pipeline the Export profile settings modus is required First an export profile has to be defined or an existing profile has to be selected The name of the selected profile is displayed at the top of the window Ernie af modifications cess profin Created 7041 14 2014 05 08 2014 10 07 Que selected profile Add new proble pre selected probe 6
27. s Le Electrocard E Electrocardiograes chad PR Interval D m A Edit hierarchy Q wave heigh Ri ERES Remove QRS duration QT interval duration ST segment ST segment duration T wave H MRI observable 7 Vital Signs EA Procedure E3 Cardiovascular procedure Angioplasty m Sibling limit 25 Hide IDs Add root concept Figure 11 Concept hierarchy Manual changes e Editing concept hierarchy Edit concept hierarchy Concept ID tfY6RG4 Preferred term label Heart Rate Current parents bCahZp2 Vital Signs x Add parent Bra Add Bradycardia 6d24xJc Current children Bundle Branch Block g223G1B Add child Add OK amp Close Figure 12 Editing concept hierarchy Both parents and children can be added In the fields after Add parents and Add child any term of the desired concept can be entered The system will suggest applicable concepts Existing parent or children relationships can be deleted by clicking on the red X Copyright 2014 2015 SEMCARE Consortium This project has received funding from the European Union s Seventh Programme for research technological development and demonstration under grant agreement No 611388 D4 2 Terminology management platform WP4 Terminological resource acquisition f OOOO MM Dissemination level Public S e mMm C ci e Author C Riede Averbis J Kors EMC Version 1 1 Final e New concepts Add con
28. ssess 13 FIGURE 7 CONCEPT DETAILS RELATIVES eceeeeeeeee eene nennen nnn nne nne ne tes ia nasse see se sea ea esses eese sea ea ee ee sees sea sean 13 FIGURE S CONCEPT DETAI dc arene 14 FIGURE 9 IMPORT TERMINOLOGY ccscceccssccecceccesceecceesseeeeeaeeeeeeeeseeseeeeseeeeeeeeeeeeseesseseeceeceeceeesaesaeseeceeeeeceeeseeaesaeeeeeees 14 FIGURE 10 DIALOGUE WINDOW IMPORT cceeeeeeeeeeeneenne nennen nenne nennen tna esee see se sea ea nasse sees ses sea ea ee see sse sess ea sena 15 FIGURE 11 CONCEPT HIERARCHY MANUAL CHANGES ssccccessccccesececeesecccesceceuseceeeuseceseeecesseecessuscesseneceteuaeseseuecetseneeets 16 FIGURE 12 EDITING CONCEPT HIERARCHY eceeeeee eene eene nnne see see se ses ea ea ea eese ses ea ee esses stes ses ee esses ste stessa euns 16 FOET ADD OE erc c 17 FIGURE 14 PROPOSING SYNONYMS sscccccssecccessccccesecceeesececeuecceeeeceesuseceseeeceseueceseueeeeeeceseeeceseuecessenecessueeessuecesseneeets 17 FIGURE Ee EDITING TERIS vases ae tiratnnnaaspitronseo sen NN E E saunas ewnecaan V Du E E es OMNE 18 PRE TE GOUF 7 0 t D cs be cit artes ese moans 19 ies S eec di el e 19 FIGURE FE PORT IL TIES o a ie hu pebrdd bue dox DN epIUPU deu VEMM x M NO eRUDK Du MM NNNM non eDS REEF DOMNUM E 20 FIGURE 19 VIANUAL SETTING O
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