https://www.ohdsi.org/web/wiki/ 2026-04-24T12:26:17+0000 https://www.ohdsi.org/web/wiki/ https://www.ohdsi.org/web/wiki/lib/exe/fetch.php?media=wiki:favicon.ico text/html 2015-03-18T11:31:29+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:data_sources&rev=1426678289&do=diff Data sources The incoming data is being present as the vocabularies, which should be imported into the OMOP. Vocabularies can be stored in csv-files, xlsx-files, database dumps or they can be retrieved from external system via API. text/html 2015-03-18T10:17:44+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:domain_analysis&rev=1426673864&do=diff Domain Analysis. Process incoming source vocabulary and alter it to standard structure, described in OMOP, then transfer data from source to OMOP. The source vocabulary can be delivered in: csv-files, xlsx-files, XML format, sql-dump. It’s structure and data can change freely from version to version, so every next update could require structure and data analysis to be made. text/html 2015-03-27T12:18:18+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:entities&rev=1427458698&do=diff Short description of entities involved in the business processes. text/html 2015-03-30T11:03:01+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:entity_concept&rev=1427713381&do=diff Concept is a central entity, some kind of a hub, which binds and defines the roles of all other entities. Every entity present in the model, should be defined as a Concept. Requirements: * must have name * must belong to Domain * must be declared in text/html 2015-03-18T11:40:41+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:import_data_from_umls&rev=1426678841&do=diff Import data from UMLS UMLS(Unified Medical Language System) contains the selection of vocabularies which should be imported into OMOP. The list of vocabularies: * CPT4 * HCPCS * ICD10 * ICD9CM * LOINC * MeDRA * RxNorm * SNOMED UMLS consist of three modules: Metathesaurus(contains data about Concepts), Semantic Network(contains data about Types and Relations), SPECIALIST(NLP-module). Detailed info about UMLS: text/html 2015-04-02T04:30:02+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:import_snomed&rev=1427949002&do=diff I would build the logic slightly differently: 1. Concepts. - We have one authoratitative source: SNOMED international in combination with SNOMED UK. Other components might follow later (DM+D, other country-specific versions). - We get a stream of concepts from them: text/html 2015-03-18T10:29:59+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:problem_description&rev=1426674599&do=diff Problem description Two kinds of changes, which will require source adaptation, can be distinguished. Changes in the structure * New column added. * Column was removed. * Column data type changed. * Column name changed. * New relation appeared. text/html 2015-04-01T07:52:45+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:sidebar&rev=1427874765&do=diff Automated Terminology Harmonization, Extraction and Normalization for Analytics - ATHENA Preliminary analysis * Statement of problem. * Domain Analysis * Problem description * Solution * The Implementation and technology stack. Application Design * Data sources * Import Data from UMLS * Import Data from SNOMED * Entities * Concept * Concept Ancestor * Concept Class * Concept Relationship * Concept Synonym * Domain * Drug Strength * Relationship … text/html 2015-03-18T10:34:48+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:solution&rev=1426674888&do=diff Solution To successfully adapt a new version of the source vocabulary we need to perform these tasks: * Analyze the structural and data changes. * Alter the migration algorithm. Our goal is to develop an application, which will do: * Parse data from: XML, csv, xlsx, db-table or db-dump text/html 2015-03-18T10:17:18+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:statement_of_problem&rev=1426673838&do=diff Statement of Problem. Design and develop the system for automated or semi-automated vocabulary upload. text/html 2015-03-30T12:10:35+0000 Anonymous (anonymous@undisclosed.example.com) https://www.ohdsi.org/web/wiki/doku.php?id=documentation:athena:the_implementation_and_technology_stack&rev=1427717435&do=diff The implementation and technology stack. Suggested implementation of the ATHENA project is a web-application. The advantages of this solution are: * Faster development speed, rather than developing the desktop app. * The ability to deploy it local PC, local network, open or private www-segment.