Nate It sounds like Jeff and Aaron are addressing my question. I may be overly dense when trying to reapply Shawn's example. Does it work that the Concept_dimension entry below returns the age of the patient in days with concept code LOINC:30525-0 at query time WITHOUT an observation_fact being loaded for the patient age?
Jim <concept> <level>3</level> <c_fullname>\PCORI\Demographics\Age\</c_fullname> <c_name>Age</c_name> <visualattributes>LA</visualattributes> <c_basecode>LOINC:30525-0<c_basecode> < facttablecolumn>patient_num</facttablecolumn> < tablename>patient_dimension</tablename> < columnname>Birth_date</columnname> < columndatatype>Integer</columndatatype> < operator>=</operator> < dimcode>(sysdate-Birth_date)*365.24</dimcode> <tooltip>PCORI\Demographics\Age</tooltip> <\concept> ________________________________ From: Apathy,Nate [[email protected]] Sent: Tuesday, July 29, 2014 10:01 PM To: Murphy, Shawn N.; Campbell, James R; Phillip Reeder; Phillips, Lori C. Cc: [email protected]; Munns, Michael B; Jeffrey Klann; Meyer,Aaron Subject: Re: i2b2 Queries For what it痴 worth, Jeff Klann and Aaron Meyer worked on building this age demographics ontology table to accommodate pediatric clients and dynamically calculate age at the time of query execution from the birth date (shifted birth date for de-identified data). I知 not sure if this specifically addresses the question at hand, but it might be valuable for additional approaches or at least some context. User beware, though, we are all still finalizing our production deployment of this ontology, so it isn稚 live with Cerner clients or in any non-dev environments to my knowledge. I still figured it would be worth sharing for this conversation. Nate Apathy Program Manager, Cerner Research From: <Murphy>, "Shawn N." <[email protected]<mailto:[email protected]>> Date: Tuesday, July 29, 2014 at 10:25 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, Phillip Reeder <[email protected]<mailto:[email protected]>>, Lori Phillips <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "Munns, Michael B" <[email protected]<mailto:[email protected]>> Subject: RE: i2b2 Queries Hi Jim In the demo data instance we calculate it dynamically from birth_date, that is not what you want? Thanks, Shawn. From: Campbell, James R [mailto:[email protected]] Sent: Tuesday, July 29, 2014 11:23 AM To: Phillip Reeder; Murphy, Shawn N.; Phillips, Lori C. Cc: [email protected]<mailto:[email protected]>; Munns, Michael B Subject: RE: i2b2 Queries That was not precisely my question Phillip. I was wondering if we could avoid loading Observation_fact for age since it is a dynamic variable, changing daily, and define a function to calculate age at time of query submission. Hubert and I have come to the conclusion that is not supported by i2b2 and so Hubert rolled out the observation fact as a numeric value with metadataxml for conversion between days/months/years depending upon the requirements of the researcher. It looks good and would answer a question that Michael Kahn had posed some time ago about the different units of age needed by the pediatric researcher Jim ________________________________ From: Phillip Reeder [[email protected]<mailto:[email protected]>] Sent: Monday, July 28, 2014 1:02 PM To: Murphy, Shawn N.; Campbell, James R; Phillips, Lori C. Cc: [email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:gpc-dev%40listserv.kumc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=71ebd848b61b30510efd6f668ed69d502fba22df0d849f95523b35e6f006e79f>; Munns, Michael B Subject: Re: i2b2 Queries This message was sent securely using ZixCorp.<https://urldefense.proofpoint.com/v1/url?u=http://www.zixcorp.com/get-started/&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=34eee81585c9db37cd270526257609f48ecc94b872b55bdd5e741b12fbf60a86> Jim, Are you asking about doing a query by value based on a birthdate calculation? So you would, for example, Search for patients > 90 days old using the query by value option in i2b2, and then it would calculate the age, compare it to 90 days, and return the patient set? I think the query by value assumes that numeric values are in the nval_num columns so I知 not sure if it would be possible. But it would probably be useful, especially for age. Phillip From: <Murphy>, "Shawn N." <[email protected]<mailto:[email protected]>> Date: Monday, July 28, 2014 at 6:20 AM To: "Campbell, James R" <[email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:campbell%40unmc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=a94b021b1accc11679ffc9afd7b21866916b060741346735f20887506d5f18d1>>, "Phillips, Lori C." <[email protected]<mailto:[email protected]>> Cc: "[email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:gpc-dev%40listserv.kumc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=71ebd848b61b30510efd6f668ed69d502fba22df0d849f95523b35e6f006e79f>" <[email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:gpc-dev%40listserv.kumc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=71ebd848b61b30510efd6f668ed69d502fba22df0d849f95523b35e6f006e79f>>, "Munns, Michael B" <[email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:mike.munns%40unmc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=2d52506d223edd711e06ee0b4e1eaee21d7b52c6e13c2aa697178b1008227bcf>> Subject: RE: RE: Hi Jim, I知 not exactly sure I understand what you mean Jim? Thanks, Shawn. From: Campbell, James R [mailto:[email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:campbell%40unmc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=a94b021b1accc11679ffc9afd7b21866916b060741346735f20887506d5f18d1>] Sent: Sunday, July 27, 2014 1:16 PM To: Murphy, Shawn N.; Phillips, Lori C. Cc: [email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:gpc-dev%40listserv.kumc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=71ebd848b61b30510efd6f668ed69d502fba22df0d849f95523b35e6f006e79f>; Hickman, Hubert B; Munns, Michael B Subject: RE: RE: Thanks Shawn, however one clarification please. I see from your examples that the formalism can be used to identify a subset of patients or providers for a folder view access, and I assume that I can select a Patient_dimension attribute an rename it as a variable in the first example below (leaf attribute). But can you also recompute a result such as in the second example below where I compute age from Patient_dimension.Birth_date? Jim <concept> <level>3</level> <name>Birth date</name> <visualattributes>LA</visualattributes> <facttablecolumn>patient_num</facttablecolumn> <tablename>patient_dimension</tablename> <columnname>Birth_date</columnname> <columndatatype>Date</columndatatype> <operator>=</operator> <dimcode>\PCORI\Demographics\Birthdate\</dimcode> <tooltip>PCORI\Demographics\Birthdate</tooltip> </concept> <concept> <level>3</level> <name>Age</name> <visualattributes>LA</visualattributes> <facttablecolumn>patient_num</facttablecolumn> <tablename>patient_dimension</tablename> <columnname>Birth_date</columnname> <columndatatype>Integer</columndatatype> <operator>=</operator> <dimcode>(sysdate-Birth_date)*365.24</dimcode> <tooltip>PCORI\Demographics\Age</tooltip> <\concept> ________________________________ From: Murphy, Shawn N. [[email protected]<mailto:[email protected]>] Sent: Saturday, July 26, 2014 8:14 PM To: Campbell, James R; i2b2 Academic Forum ([email protected]<mailto:[email protected]>); Hickman, Hubert B; Karthik Tumu; Munns, Michael B Subject: RE: RE: Hi Jim, It is here: https://community.i2b2.org/wiki/display/DevForum/Query+Building+from+Ontology<https://urldefense.proofpoint.com/v1/url?u=https://community.i2b2.org/wiki/display/DevForum/Query%26%2343%3BBuilding%26%2343%3Bfrom%26%2343%3BOntology&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=2c652b2fd845d462e3a7ff0a890bc1fc7b661f14fab868afb066bce4a10f62e2> Thanks, Shawn. From: Campbell, James R [mailto:[email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:campbell%40unmc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=a94b021b1accc11679ffc9afd7b21866916b060741346735f20887506d5f18d1>] Sent: Friday, July 25, 2014 7:48 AM To: Murphy, Shawn N.; i2b2 Academic Forum ([email protected]<mailto:[email protected]>); Hickman, Hubert B; Karthik Tumu; Munns, Michael B Subject: RE: Shawn Is the deployment of this documented in any i2b2 reference? Jim ________________________________ From: Murphy, Shawn N. [[email protected]<mailto:[email protected]>] Sent: Thursday, July 24, 2014 9:06 PM To: Campbell, James R; i2b2 Academic Forum ([email protected]<mailto:[email protected]>) Subject: RE: Hi Jim, It computed off of the birth_date column in the patient dimension. For example, here is the XML associated with the 10-17 y/o folder (from the demo demographics ontology): <concept> <level>3</level> <key>\\i2b2_DEMO\i2b2\Demographics\Age\10-17<file:///\\i2b2_DEMO\i2b2\Demographics\Age\10-17> years old\</key> <name> 10-17 years old</name> <synonym_cd>N</synonym_cd> <visualattributes>FA </visualattributes> <totalnum xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance<https://urldefense.proofpoint.com/v1/url?u=http://www.w3.org/2001/XMLSchema-instance&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=4778eec22b046474c4106f51daabf2b698a49c0865ebeedc33c40bcfdfca45f9>" xsi:nil="true" /> <facttablecolumn>patient_num</facttablecolumn> <tablename>patient_dimension</tablename> <columnname>birth_date</columnname> <columndatatype>N</columndatatype> <operator>BETWEEN</operator> <dimcode>sysdate - (365.25*18) AND sysdate - (365.25*10) </dimcode> <tooltip>Demographics \ Age \ 10-17 years old</tooltip> </concept> Thanks, Shawn. From: Campbell, James R [mailto:[email protected]<https://urldefense.proofpoint.com/v1/url?u=http://mailto:campbell%40unmc.edu&k=PmKqfXspAHNo6iYJ48Q45A%3D%3D%0A&r=7jqROYnRJZ%2FRUK29eXLgd84I9Ih235HbTh2w98KlP4I%3D%0A&m=pDdvQD%2Biwpb1alvTBMP8roYfCDj%2BfTL8t4gdGC2pkoo%3D%0A&s=a94b021b1accc11679ffc9afd7b21866916b060741346735f20887506d5f18d1>] Sent: Thursday, July 24, 2014 7:57 PM To: i2b2 Academic Forum ([email protected]<mailto:[email protected]>) Subject: At the Boston meeting I saw a formulaic rendition of patient age from birthdate data in the Patient Dimension. I may have been confused about context but I assume it was either an Observation fact load utility or, better yet, a computable datatype definition for patient age. Can anyone clarify my uncertainty and direct me to resources? Jim Campbell The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. 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