Changes between Initial Version and Version 90 of HERON


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Timestamp:
01/28/15 15:53:21 (3 years ago)
Author:
rwaitman
Comment:

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  • HERON

    v1 v90  
     1[[PageOutline]]
     2
     3The Healthcare Enterprise Repository for Ontological Narration (HERON) is a method to integrate clinical and biomedical data for translational research.
     4
     5 * HERON cohort discovery queries can span the [http://en.wikipedia.org/wiki/Electronic_medical_record EMR] from [http://www.kumed.com/ KUH]  and an increasing list of other sources for [http://en.wikipedia.org/wiki/Retrospective_cohort_study retrospective studies].
     6 * HERON queries can give you hard data on how many patients come through KUH that meet the criteria of your next [http://en.wikipedia.org/wiki/Prospective_cohort_study clinical trial].
     7 * Combined with the Frontiers participant registry, HERON can even give you contact information to support recruitment directly.
     8
     9To get started, see [http://frontiersresearch.org/frontiers/HERON-introduction HERON Training Materials].
     10
     11Or if you're a returning HERON user, proceed directly to:
     12
     13 * [https://heron.kumc.edu/ HERON]
     14
     15== Citing HERON ==
     16
     17Please cite us as:
     18
     19    -  Waitman LR, Warren JJ, Manos EL, Connolly DW. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243191/ Expressing Observations from Electronic Medical Record Flowsheets in an i2b2 based Clinical Data Repository to Support Research and Quality Improvement]. AMIA Annu Symp Proc. 2011;2011:1454-63. Epub 2011 Oct 22.
     20
     21== Progress, History, and Plans ==
     22[[BlogList(category=HERON,recent=10)]]
     23
     24... see [[HERONAnnouncements]] for the full list.
     25
     26The [/roadmap roadmap] is our main concrete planning tool, but we also use HeronProjectTimeline for brainstorming.
     27
     28== Training and Support == #support
     29
     30[[HERONIndependentStudy]]
     31
     32* Ask the Clinical Informatics Coordinator for help via the [https://redcap.kumc.edu/surveys/?s=3SBkPg&tool=1 feedback form] or at 5-7470.
     33
     34* The FrontiersInformaticsClinic meets every other week. [https://redcap.kumc.edu/surveys/?s=L72oqA Register] in advance if possible but drop-ins are welcome.
     35
     36*  Send a question to the !HERON-USERS@LISTSERV.KUMC.EDU or review the [http://listserv.kumc.edu/cgi-bin/wa?A0=HERON-USERS mailing list archive].
     37
     38== Data Sources and Monthly Update Process ==
     39Our initial approach is to get dumps from the source systems,  wipe out our store in nightHERON for i2b2 and reload it all, reassigning i2b2 internal patient, provider, visit ids.
     40
     41 * Data Sources
     42   * [[HospitalEpicSource]]
     43   * [[ClinicIdxSource]] (including HICTR)
     44   * [[UHCSource]] (billing diagnoses and DRGs)
     45   * KUH TumorRegistry for NCI designation
     46   * [[BiospecimenRepository]] (#517)
     47   * ... things like CRIS, CoPath, GME, and biospecimens will follow; April [[DROCMeetingMinutes]] has a list:
     48     * SMS (lower priority; UHC data meets most of the relevant needs)
     49     * !CoPath
     50     * CRIS/REDCap (clinical trial enrollment and registries)
     51     * Read only Chronicles Access for Content not included in Clarity #20
     52 * HeronLoad monthly update process
     53   * UpdateValidation
     54   * HeronReleaseNotes - features, changes, updates
     55
     56
     57== Architecture ==
     58[[Image(heron-arch2.png, 800px)]]
     59
     60Bring-up and some configuration notes on the machines are in:
     61
     62 * #80 - bring up identified server hardware, os
     63 * #82 - bring up de-identified database server
     64 * #43 - bring up virtual server for production web services
     65
     66See also:
     67
     68 * HeronSizingGrowth
     69 * [[HERONsecuritynotes]]
     70 * HeronPerformance
     71 * HeronStatsPlugins
     72
     73=== Open Source ETL Code === #open-source-etl-code
     74
     75The [source:heron_load/README.rst heron_load] open source codebase consists of ~20KLOC of SQL along with a set of python scripts that control the HeronLoad ETL process. Share and enjoy!
     76
     77[http://frontiersresearch.org/frontiers/kumc_bmi_presentations Our presentation materials] may help with the bigger picture; in particular:
     78
     79 - [http://frontiersresearch.org/frontiers/sites/default/files/frontiers/heron-pydata-neutral-theme.pdf Using Python and Paver to Control a Large Medical Informatics ETL Process] presented at PyData Silicon Valley May 3, 2014
     80
     81=== Terminology Mapping ===
     82 * [[FlowsheetMapping]]
     83 * [[DiagnosisMapping]]
     84 * [[SmartNotes]]
     85 * [[MedMapping]]
     86 * [[LabDiscussion]] January 31, 2011
     87 * [[LabDiscussion2]] February 11, 2011
     88 * [[MedDiscussion]] March 7, 2011
     89 * [[LoincMapping]] largely obsolete as of #311 milestone:heron-apr-update
     90 * MedicalTerminologyMarketplace
     91
     92
     93=== Leveraging NIH funded i2b2 framework === #i2b2-nih
     94Per section ''C.2.2.  Implement cost effective, researcher-centric solutions while preserving  patient privacy and respecting community trust among disparate  participating organizations by leveraging open source and existing NIH  funded initiatives'' of the [[CTSA]] grant application:
     95
     96  User access, activity logs,  and project management for the de-identified repository is managed via  the i2b2 framework ...
     97
     98This involves [[Using I2B2]]. We've had a further discussion on overall security for i2b2, other applications, oracle and the operating systems: [[HERONsecuritynotes]].
     99
     100 * [[Using I2B2]]
     101   * [[i2b2 security]]
     102 * [[HERONsecuritynotes]]
     103
     104== Governance (DROC), Privacy (De-identification), and Security == #governance
     105Governance is provided by an executive committee and the Data Request Oversight Committee (DROC).  All three contributing organizations: the University of Kansas Medical Center, the University of Kansas Hospital and the University of Kansas Physicans Incorporated are represented and contribute to making this initiative possible.
     106
     107 * [[DROCMeetingMinutes]] and oversight issues
     108
     109The main usage scenarios for milestone:system-access was PatientCountStory, which demonstrates Data Request Oversight Mechanisms and Frequency of Review.
     110
     111See section ''C2.1. Develop repeatable business agreements, policies,  data use agreements and oversight for organization inclusion'' in ''KUMC  HICTR CTSA outline'' for more scenarios.  For reference:
     112
     113 * [attachment:L0017227FinalElectronicHeronCopyFromLisaH09092010.docx Final legal agreement for HERON with System Access Agreement]
     114 * [attachment:HERONAgreementSigned.pdf:wiki:GroupOnly Signed master agreement for medical data sharing]
     115 * [attachment:HERON_Repository_HSC_IRB_Protocolv1_1.docx HERON IRB protocol original 2010-2011]
     116 * [attachment:HERON_Repository_HSC_IRB_Protocolv2_1final.pdf HERON IRB protocol revised for 2011-2012]
     117
     118Another design consideration is de-identification of data and then what's kept on blue HERON. See DeIdentificationStrategy.
     119
     120 * [[HERONsecuritynotes]]
     121 * DeIdentificationStrategy
     122
     123== Acknowledgements ==
     124
     125This work was supported by a CTSA grant from NCRR and [http://www.ncats.nih.gov/ NCATS] awarded to the University of Kansas Medical Center for [http://frontiersresearch.org/ Frontiers: The Heartland Institute for Clinical and Translational Research] # UL1TR000001 (formerly #UL1RR033179). The contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH, NCRR, or NCATS.
     126