{"id":222,"date":"2016-08-31T12:40:59","date_gmt":"2016-08-31T16:40:59","guid":{"rendered":"https:\/\/sites.bu.edu\/bu-i2b2\/?page_id=222"},"modified":"2019-06-21T15:14:10","modified_gmt":"2019-06-21T19:14:10","slug":"ontologies","status":"publish","type":"page","link":"https:\/\/sites.bu.edu\/bu-i2b2\/intro-to-i2b2\/ontologies\/","title":{"rendered":"Ontologies"},"content":{"rendered":"

BU-i2b2 has an extensive list of\u00a0ontologies to organize the extensive data in the system.<\/p>\n

\"Picture5\"<\/p>\n

Admissions<\/strong>: \u00a0This ontology uses the\u00a0DRG (Diagnostic Related Group) codes. \u00a0The DRG system classifies inpatient stays for the purposes of payment. Diagnoses are grouped into more than 20 major body systems and subdivided into almost 500 groups for the purpose of Medicare reimbursement. \u00a0More information about DRG codes can be found here<\/a>.<\/p>\n

Clinical Ontologies<\/strong>\u00a0are groups of codes mapped from diverse clinical data in the EHR to a standard set of codes in i2b2. \u00a0Currently the only clinical ontology supported in BU-i2b2 is tobacco smoking status within the “Substance Use” ontology. \u00a0We plan to expand the available ontologies in the future.<\/p>\n

Demographics<\/strong>: \u00a0This ontology organizes demographic concepts like race, ethnicity and gender. \u00a0The ontology also has a concept called “age” however it should be noted that the age used is the age at the time the data was last refreshed (i.e. the age the patient is now) so should be used with caution.<\/p>\n

Diagnoses (ICD 9\/10)<\/strong> \u2013 International Classification of Disease codes are used to classify diagnoses. \u00a0Between 2000 and 2015 the ICD9 codes were used. \u00a0Beginning in late 2015 coding was changed to ICD10. \u00a0In general ICD10 codes are more specific than ICD9 codes but both ICD9 and 10 codes can used in i2b2 queries. \u00a0In BU-i2b2 all concepts can have a beginning and end date as well as a value. \u00a0Diagnoses in BU-i2b2 have different values based on where the code came from. \u00a0ICD9\/10 codes from an EHR Problem List are assigned the value “Problem”, codes from billing systems (diagnoses made on a particular day) are assigned “Primary, Secondary, or Unknown” depending on the order of the diagnosis in the billing systems. \u00a0Diagnoses assigned to hospital admissions are assigned the value of “Admitting”. \u00a0\u00a0To learn more about ICD9\/10\u00a0click here<\/a>.<\/p>\n

Drug Products by VA Class –\u00a0<\/strong>This ontology organizes medications prescribed within the EHR. \u00a0RxNorm codes are used in this ontology. \u00a0RxNorm codes are a common standard for medication coding and are simpler to use than NDC codes. \u00a0For more information on RxNorm click here<\/a>.<\/del><\/p>\n

GE Centricity\/ New<\/strong>\u00a0– BMC and its affiliated health centers used the GE Centricity EHR between 2000 (BMC) and 2003 (CHCs) and 2015. \u00a0This EHR provided a library of concepts that could be used in form to capture structured data. \u00a0The codes (HDID codes) are unique to this vendor and not standardized. \u00a0However a rich set of data that includes labs, vital signs, answers to structured questions, and a wide variety of other data are available in HDID codes. \u00a0However, the codes are not standardized and are organized\u00a0in alphabetical order. \u00a0A complete list of HDID codes and definitions from the GE library for BU-i2b2 are available in an excel spreadsheet.<\/p>\n

GIS<\/strong> –\u00a0<\/strong>This ontology organizes the zip codes and census tract codes for patients at the time of visits. \u00a0The codes are organized by county and neighborhood.<\/p>\n

Immunizations (Epic)\u00a0<\/strong>– This ontology organizes immunizations using CVX codes. \u00a0CVX codes are the national immunization codes and are supported by the Centers for Disease Control. \u00a0For more information about CVX codes click here<\/a>.<\/p>\n

Insurance by Payer<\/strong> – This ontology organizes the insurances recorded at the time of visits. \u00a0Insurances are grouped by category\u00a0(Commercial, Medicaid, Medicare, etc) and type (Medical, Dental, Behavioral Health, etc).<\/p>\n

Laboratory Tests – Reference (LOINC) and LabsCommonName (Epic). \u00a0<\/strong>LOINC\u00a0(Logical Observations Identifiers, Names, Codes) is a\u00a0standard code system for reporting laboratory and other clinical observations. For more information on LOINC click here<\/a>.<\/span><\/p>\n

Procedures<\/strong>\u00a0(CPT) and Procedures (ICD) – These ontologies organize procedures done using CPT codes and ICD9\/10 procedure codes. \u00a0For more information about CPT codes and more information about ICD9\/10 procedure codes click here<\/a>.<\/p>\n

Services by Department and Services by Location<\/strong>\u00a0– This ontology organizes the visit location codes at each site using an ontology developed by researchers at BMC. \u00a0Inpatient, Observation, and Emergency Room visits are not independant of specialty involved while ambulatory visits (Outpatient (OP)) are organized by specialty. \u00a0The Services by Department ontology organizes all\u00a0services for a certain department regardless of location (for example, all visits to Family Medicine regardless of site). \u00a0The Services by Location ontology organizes services first by location and then by department (for example, all visits to Family Medicine at a particular site).<\/p>\n

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 <\/p>\n

Navigating\u00a0Ontologies<\/strong><\/p>\n

These ontologies can be explored, and concepts selected, in two ways. \u00a0The first way is to\u00a0use the folders to navigate\u00a0what it is you’re looking for in the Navigate Terms<\/strong> Tab. \u00a0Folders are expanded and concepts identified by “drilling down.” \u00a0The example below shows how a researcher could identify the “Asthma” diagnosis folder as well as individual diagnoses within that folder.<\/p>\n

\"navaigate<\/p>\n

 <\/p>\n

The second way involves using the\u00a0Find Terms<\/strong> tab. \u00a0concepts can be searched for by name using the Search by Names<\/strong> tab or by the actual code using the Search by Codes<\/strong> tab. \u00a0The example below shows how a user could find the diagnosis codes for asthma by name or ICD9 code.<\/p>\n

\"search<\/p>\n

 <\/p>\n

\"search<\/p>\n","protected":false},"excerpt":{"rendered":"

BU-i2b2 has an extensive list of\u00a0ontologies to organize the extensive data in the system. Admissions: \u00a0This ontology uses the\u00a0DRG (Diagnostic Related Group) codes. \u00a0The DRG system classifies inpatient stays for the purposes of payment. Diagnoses are grouped into more than 20 major body systems and subdivided into almost 500 groups for the purpose of Medicare […]<\/p>\n","protected":false},"author":11962,"featured_media":0,"parent":255,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/pages\/222"}],"collection":[{"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/users\/11962"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/comments?post=222"}],"version-history":[{"count":18,"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/pages\/222\/revisions"}],"predecessor-version":[{"id":544,"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/pages\/222\/revisions\/544"}],"up":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/pages\/255"}],"wp:attachment":[{"href":"https:\/\/sites.bu.edu\/bu-i2b2\/wp-json\/wp\/v2\/media?parent=222"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}