tag:blogger.com,1999:blog-90257503794846877222024-02-07T16:35:45.866-08:00EMR's to OMOPRogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.comBlogger11125tag:blogger.com,1999:blog-9025750379484687722.post-67968387716041117682022-02-22T21:46:00.001-08:002022-02-22T21:46:13.237-08:00Clair Blacketer: CDM 5.4 Workshop Part 1<div class="WordSection1"> <p class="MsoNormal">This is good overview of CDM with some practical hints.<o:p></o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><a href="https://www.youtube.com/watch?v=wVtEH7QXyvk&t=2135s">https://www.youtube.com/watch?v=wVtEH7QXyvk&t=2135s</a><o:p></o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEicbH1i4ewuaVK9Q0DTw7qpMfwgZRKBW9LO40u61TNFdBD0DUP7G22MuoiEjMxGlV-lZ6i3ddam_Dg8qbDEub8En7GOjbcjrhh8bxidUU1CjEd1oFhhYB49-A5uZMWEjfz7S4qM3cIlB--MDnkEM4klWWee2pq2XzVDpu1LNG4F5cP3PlnKLR0iHCQ2"><img src="https://blogger.googleusercontent.com/img/a/AVvXsEicbH1i4ewuaVK9Q0DTw7qpMfwgZRKBW9LO40u61TNFdBD0DUP7G22MuoiEjMxGlV-lZ6i3ddam_Dg8qbDEub8En7GOjbcjrhh8bxidUU1CjEd1oFhhYB49-A5uZMWEjfz7S4qM3cIlB--MDnkEM4klWWee2pq2XzVDpu1LNG4F5cP3PlnKLR0iHCQ2=s320" border="0" alt="" id="BLOGGER_PHOTO_ID_7067777454209552354" /></a><o:p></o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><o:p> </o:p></p> </div> Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-77120544893928206432022-02-08T21:45:00.000-08:002022-02-08T21:46:10.968-08:00Clair Blacketer OMOP ETL tips and tricks<div class="WordSection1"> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#333333;border:none windowtext 1.0pt;padding:0cm">Clair Blacketer gives a great overview of practical aspects of the OHDSI ETL process here:</span><o:p></o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><a href="https://www.youtube.com/watch?v=wVtEH7QXyvk&t=3670s" title="https://www.youtube.com/watch?v=wVtEH7QXyvk&t=3670s"><span style="color:#0563C1">https://www.youtube.com/watch?v=wVtEH7QXyvk&t=3670s</span></a><o:p></o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#333333;border:none windowtext 1.0pt;padding:0cm">Clair Blacketer,</span><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#333333"> <span style="border:none windowtext 1.0pt;padding:0cm">Manager, Epidemiology Analytics</span>, <span style="border:none windowtext 1.0pt;padding:0cm">Janssen Research & Development\</span></span><o:p></o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhwPakFmuhX3gxqPuhL-yH1FCJCZNK2ev3-IqpT50Y7MEB1XY2SEp-j8a2cG23z6W85PotA2rXpa4OukrtkVsW4M9Eo4wGUYC47kUOagKKpIH34pbNu3OoBXRV0eOv4oIDS979PlzVXMLkKjVErupt1Ni-nNdP8E2YKbeV6OrL7bxXDreA1wE_lxm-3"><img src="https://blogger.googleusercontent.com/img/a/AVvXsEhwPakFmuhX3gxqPuhL-yH1FCJCZNK2ev3-IqpT50Y7MEB1XY2SEp-j8a2cG23z6W85PotA2rXpa4OukrtkVsW4M9Eo4wGUYC47kUOagKKpIH34pbNu3OoBXRV0eOv4oIDS979PlzVXMLkKjVErupt1Ni-nNdP8E2YKbeV6OrL7bxXDreA1wE_lxm-3" border="0" alt="" id="BLOGGER_PHOTO_ID_7062582251991127906" /></a><o:p></o:p></p> <p class="MsoNormal"><o:p> </o:p></p> </div> Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-15158398145227792172021-11-17T15:04:00.000-08:002021-11-23T17:48:57.791-08:00The University of Queensland OMOP Dataset<div class="WordSection1"> <p class="MsoNormal">The University of Melbourne and The University of Queensland have signed an agreement to work on the conversion Queensland Health Cerner data to the OMOP common data model. Analysts are currently working on establishing a pilot extract load transform process (ETL) with synthetic Cerner data.</p> <p class="MsoNormal">A community of practice is also being established to share expertise and support EMR conversions in other states.<o:p></o:p></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><o:p></o:p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjsSVAeMdTVEmv-39gwlRdx315Exw3QMgrNODW0uw1EhZQ0ubZj8rqeLfGoYLoaAFCFAlqnedwgxv0_S4wIhBHH7N02woPM8f7B0hk_Eq7wHAg5Pblc8uYdQMxDS20_y7liywioHC6OAdJdixDZsmc7nY91wUuyUBGnWNp62bB135uLvUtC8oKyS9RN=s856" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="570" data-original-width="856" height="266" src="https://blogger.googleusercontent.com/img/a/AVvXsEjsSVAeMdTVEmv-39gwlRdx315Exw3QMgrNODW0uw1EhZQ0ubZj8rqeLfGoYLoaAFCFAlqnedwgxv0_S4wIhBHH7N02woPM8f7B0hk_Eq7wHAg5Pblc8uYdQMxDS20_y7liywioHC6OAdJdixDZsmc7nY91wUuyUBGnWNp62bB135uLvUtC8oKyS9RN=w400-h266" width="400" /></a></div><br /><br /><p></p> <p class="MsoNormal"><br /><o:p></o:p></p> </div> Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-83068741743043378582021-08-01T22:05:00.001-07:002021-08-01T22:05:17.922-07:00Steering committee<div class="WordSection1"> <p class="MsoNormal">We had our first steering committee meeting on the 14<sup>th</sup> July. Industry representation was high on the agenda. A co-chair was proposed and we had nominations of Nicole Pratt and David Bunker. A decision will be confirmed at the next steering committee meeting. </p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbdbj1kX8Xw9O8xWxtl3grpKeL69zAXmVCDvPC_EwexXyb4e27f8PBfP3VAazKsGWRxfP5gtKNl3aoNyeDAftUIjcPiaQpr5WiGi7BOBvp3vAJC5H5UnPag87znpn0vxHb1RXWpbyfoVA/s1600/image001-717929.png"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbdbj1kX8Xw9O8xWxtl3grpKeL69zAXmVCDvPC_EwexXyb4e27f8PBfP3VAazKsGWRxfP5gtKNl3aoNyeDAftUIjcPiaQpr5WiGi7BOBvp3vAJC5H5UnPag87znpn0vxHb1RXWpbyfoVA/s320/image001-717929.png" border="0" alt="" id="BLOGGER_PHOTO_ID_6991694446179625922" /></a></p> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><o:p> </o:p></p> </div> Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-78087667529970824772021-06-28T21:18:00.001-07:002021-06-28T21:18:42.057-07:00Technical Meetings<p>We had our first EMR's to OMOP technical meeting today with colleagues from Queensland and NSW. </p><p>We had demonstration of the OMOP ETL tool <a href="https://www.omop.link/" style="color: #954f72; font-family: Helvetica; font-size: 9pt;">https://www.omop.link</a> and a demonstration of Atlas. </p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNaFUZkg93FHvzIDB0sbD7OKsLJhTwNcrHvsoSNR6UerWSMoqOodREPu3EBQmfuCN-Ue0CtoaWfi28rtf6UL5pL-xp6Iu9OGTUuSFoA-48_s33RSadT9a0OWOnNRBiHQbmYS1hzQjUdL0/s878/Screen+Shot+2021-06-29+at+11.26.19+am.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="378" data-original-width="878" height="173" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNaFUZkg93FHvzIDB0sbD7OKsLJhTwNcrHvsoSNR6UerWSMoqOodREPu3EBQmfuCN-Ue0CtoaWfi28rtf6UL5pL-xp6Iu9OGTUuSFoA-48_s33RSadT9a0OWOnNRBiHQbmYS1hzQjUdL0/w400-h173/Screen+Shot+2021-06-29+at+11.26.19+am.png" width="400" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><br /></div><br /><p><br /></p><p><br /></p><p><br /></p><p><br /></p><p class="p2" style="font-family: Helvetica; font-size: 9pt; margin: 0cm 0cm 0cm 36pt;"><o:p></o:p></p>Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-47604003238003942622021-06-16T18:05:00.000-07:002021-06-16T18:05:02.417-07:00Extract, Transform, Load Framework for the Conversion of Health Databases to OMOP<p>Congratulations to our colleagues in UNSW on the publication of their paper on conversion methods for OMOP.</p><p>"Extract, Transform, Load Framework for the Conversion of Health Databases to OMOP"</p><p>Link:</p><p><a href="https://www.medrxiv.org/content/10.1101/2021.04.08.21255178v2">https://www.medrxiv.org/content/10.1101/2021.04.08.21255178v2</a></p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgvv5NIrDPhMgczynXEiU1wa6wXcsE5a2A3YrKxvtWvp76SHQ8gqNDeZGDYfqVfOYQ0ABwKO4eVeEaMM6Li9SUqhGJACIQ_y7r1AZVqKem_SxBJ476BemeEC6SOeqhhboUJ6Xj5Gx3L5_0/s2222/Screen+Shot+2021-06-17+at+11.02.42+am.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1060" data-original-width="2222" height="306" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgvv5NIrDPhMgczynXEiU1wa6wXcsE5a2A3YrKxvtWvp76SHQ8gqNDeZGDYfqVfOYQ0ABwKO4eVeEaMM6Li9SUqhGJACIQ_y7r1AZVqKem_SxBJ476BemeEC6SOeqhhboUJ6Xj5Gx3L5_0/w640-h306/Screen+Shot+2021-06-17+at+11.02.42+am.png" width="640" /></a></div><br /><p><br /></p>Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-47053801276923776902021-06-16T17:58:00.004-07:002021-06-16T17:58:44.780-07:00EMR's to OMOP Progress<p>We are advancing work with two centres in Victoria and Queensland. Atlas is being set up in each centre with Synthetic CDM data to get researchers familiar with the structure of OMOP. All those R skills are going to come in handy!</p><p><a href="https://www.ohdsi.org/atlas-a-unified-interface-for-the-ohdsi-tools/">https://www.ohdsi.org/atlas-a-unified-interface-for-the-ohdsi-tools/</a></p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidWTQzjLKuga8-Io9Ji8NwTb36IojfD8jrhkEMBM8gxkyrHQgwSu2_CiEAyNbc39O4vnGg0y025y0YRa37-_mPNFZPgf0ZJeq6sqdgwKJTOS9jO8_6PQ02pvG7Ixx4Rg-7GBVyVGDNNno/s402/687474703a2f2f7777772e6f686473692e6f72672f7765622f77696b692f6c69622f6578652f66657463682e7068703f63616368653d266d656469613d646f63756d656e746174696f6e3a736f6674776172653a6c6f676f5f776974686f75745f746578742e706e67.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="402" data-original-width="330" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidWTQzjLKuga8-Io9Ji8NwTb36IojfD8jrhkEMBM8gxkyrHQgwSu2_CiEAyNbc39O4vnGg0y025y0YRa37-_mPNFZPgf0ZJeq6sqdgwKJTOS9jO8_6PQ02pvG7Ixx4Rg-7GBVyVGDNNno/s320/687474703a2f2f7777772e6f686473692e6f72672f7765622f77696b692f6c69622f6578652f66657463682e7068703f63616368653d266d656469613d646f63756d656e746174696f6e3a736f6674776172653a6c6f676f5f776974686f75745f746578742e706e67.png" /></a></div><br /><p><br /></p><p><br /></p><p><br /></p><p><br /></p><p><br /></p>Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-42851712496994994322021-04-28T17:13:00.003-07:002021-04-28T17:13:28.573-07:00Metadata is key to success<p>We had a really interesting meeting with Melanie Barlow and Julia Martin from the ARDC about metadata and Research Data Australia. We are planning how to describe the OMOP datasets. Fortunately OMOP already has a metadata table included in the CDM. </p><p><a href="https://ohdsi.github.io/CommonDataModel/cdm531.html#Metadata_Tables" style="color: #0563c1; font-family: Calibri, sans-serif; font-size: 14.666666984558105px;" title="https://ohdsi.github.io/CommonDataModel/cdm531.html#Metadata_Tables">https://ohdsi.github.io/CommonDataModel/cdm531.html#Metadata_Tables</a></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVqUP0_eN3OnExvZoS7nX6oYGopTQX-dgHrsxQu0pxxdAnC1B0Q7yWiQYNIipJMRACKaqnO31KX81zqnF0D6blXnoD04jBhyphenhyphenuEuDmNoaag7hxh2IOKS2LNohHlNanAA651YtX_8JqMpJ4/s2306/Screen+Shot+2021-04-29+at+10.11.22+am.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="940" data-original-width="2306" height="260" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVqUP0_eN3OnExvZoS7nX6oYGopTQX-dgHrsxQu0pxxdAnC1B0Q7yWiQYNIipJMRACKaqnO31KX81zqnF0D6blXnoD04jBhyphenhyphenuEuDmNoaag7hxh2IOKS2LNohHlNanAA651YtX_8JqMpJ4/w640-h260/Screen+Shot+2021-04-29+at+10.11.22+am.png" width="640" /></a></div><br /><p><br /></p>Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-23772661248227130332021-04-28T17:03:00.004-07:002021-04-28T17:03:33.440-07:00ARDC Workshop<p>It's been a busy week on the EMR's to OMOP project. On Tuesday we had a workshop with ARDC to discuss sharing EMR to OMOP mappings in the future. Dr Daniel Capurro facilitated and we had a lively discussion of the issues. We are collating the results at the moment and will share the outcomes.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg0NIteWKytK6o3TmmxSJ6ogVJhg8qxJ2NRZ3h62q6xWvn5ktlSqRmzaCyLHxxmIcFKKs61U3yyRe9E_uEj-ls-unRk55QdrZH2vblbi1QQrKjnOeYuGiIPgw1LK6FfMO6oMXCO3lotTPo/s1516/Screen+Shot+2021-04-29+at+10.00.19+am.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="892" data-original-width="1516" height="376" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg0NIteWKytK6o3TmmxSJ6ogVJhg8qxJ2NRZ3h62q6xWvn5ktlSqRmzaCyLHxxmIcFKKs61U3yyRe9E_uEj-ls-unRk55QdrZH2vblbi1QQrKjnOeYuGiIPgw1LK6FfMO6oMXCO3lotTPo/w640-h376/Screen+Shot+2021-04-29+at+10.00.19+am.png" width="640" /></a></div><br /><p><br /></p>Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-88803855048332000962021-04-06T21:41:00.006-07:002021-04-06T21:42:22.876-07:00The Challenge<p> Hospital EMR to OMOP </p><p>These are the OMOP tables. Our challenge is map Cerner and Epic tables to these tables. </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIboLfAd2Ssb06REvDzeYl9VR1RAcez4JEmLLSoZaNYdETsy-zXRdXqkVoXDChTEDWwK1COLjDqo5y6r1N-R-K9yINggfxq9Nj5rBoVit3MTYZhhvWxkccz8cL1DcrCP4RHMrZuNJ82FY/s2048/cdmDiagram.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1614" data-original-width="2048" height="315" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIboLfAd2Ssb06REvDzeYl9VR1RAcez4JEmLLSoZaNYdETsy-zXRdXqkVoXDChTEDWwK1COLjDqo5y6r1N-R-K9yINggfxq9Nj5rBoVit3MTYZhhvWxkccz8cL1DcrCP4RHMrZuNJ82FY/w400-h315/cdmDiagram.png" width="400" /></a></div><br /><p><br /></p>Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0tag:blogger.com,1999:blog-9025750379484687722.post-24002867366542792722021-03-30T17:11:00.000-07:002021-11-23T17:48:42.460-08:00EMR's to OMOP<p><span style="box-sizing: border-box; caret-color: rgb(33, 37, 41); color: #212529; font-family: "Proxima Nova"; font-size: 14px;">EMR's to OMOP is ARDC funded project that runs from 2021 - 2023. </span><a href="https://ardc.edu.au/project/electronic-medical-records-as-a-national-data-asset/" style="color: #954f72; font-family: Calibri, sans-serif;" target="_blank"><span style="font-size: x-small;">https://ardc.edu.au/project/electronic-medical-records-as-a-national-data-asset/</span></a></p><p><span style="box-sizing: border-box; caret-color: rgb(33, 37, 41); color: #212529; font-family: "Proxima Nova"; font-size: 14px;">Hospital EMR data as a National Data Asset for Research (10.47486/PS014): </span><span style="background-color: white; caret-color: rgb(33, 37, 41); color: #212529; font-family: "Proxima Nova"; font-size: 14px;">This project aims to establish a national, research ready hospital electronic medical record (EMR) Data Asset that will enhance data accessibility for rapid interrogation and evidence generation. Data will be transformed to an international gold standard Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). </span></p><br style="box-sizing: border-box; caret-color: rgb(33, 37, 41); color: #212529; font-family: "Proxima Nova"; font-size: 14px;" /><span style="background-color: white; caret-color: rgb(33, 37, 41); color: #212529; font-family: "Proxima Nova"; font-size: 14px;">Tools, mappings and experience gained will be made openly available, and a community of practice and a roadmap for continued national implementation will be built. The Data Asset will significantly improve the quality, accessibility and feasibility of EMR data warehouses by streamlining data governance, consent and ethics. The project’s outcome is a CDM platform, converting three Cerner-based data warehouses: Queensland Health ( State Public Health Hospital EMR), Austin Health and Western Health (Melbourne EMR). Learnings from the Cerner conversions will then be applied to the conversion of other data warehouse platforms including the EPIC EMR system which will be investigated in collaboration with the Peter MacCallum Cancer Centre.</span>Rogerhttp://www.blogger.com/profile/07960546644568096753noreply@blogger.com0