Changes between Initial Version and Version 101 of HERON

Remember: No patient names, identifiers, or other PHI


Ignore:
Timestamp:
May 17, 2018 11:25:54 AM (2 years ago)
Author:
mwennberg
Comment:

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  • HERON

    v1 v101  
     1[[PageOutline]]
     2== Accessing HERON ==
     3
     4The main HERON page is at https://heron.kumc.edu/heron. This can be accessed from KUMC network or via the KUMC VPN. For any questions about HERON, please contact `heron-admin@kumc.edu.`
     5
     6== HERON Information ==
     7
     8The Healthcare Enterprise Repository for Ontological Narration (HERON) is a method to integrate clinical and biomedical data for translational research.
     9
     10 * HERON cohort discovery queries can span the [http://en.wikipedia.org/wiki/Electronic_medical_record EMR] from [http://www.kumed.com/ The University of Kansas Health System (TUKHS)]  and an increasing list of other sources for [http://en.wikipedia.org/wiki/Retrospective_cohort_study retrospective studies].
     11 * HERON queries can give you hard data on how many patients come through TUKHS that meet the criteria of your next [http://en.wikipedia.org/wiki/Prospective_cohort_study clinical trial].
     12 * Combined with the Frontiers participant registry, HERON can even give you contact information to support recruitment directly.
     13
     14To get started, see [http://www.kumc.edu/miea/medical-informatics/heron.html HERON Training Materials].
     15
     16Or if you're a returning HERON user, proceed directly to:
     17
     18 * [https://heron.kumc.edu/ HERON]
     19 * Please note: To access HERON, you must be on the KUMC campus or connected via the VPN.
     20
     21Questions? Please contact `heron-admin@kumc.edu`
     22
     23== Citing HERON ==
     24
     25Please cite us as:
     26
     27    -  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.
     28
     29== Progress, History, and Plans ==
     30[[BlogList(category=HERON,recent=10)]]
     31
     32... see [[HERONAnnouncements]] for the full list.
     33
     34The [/roadmap roadmap] is our main concrete planning tool, but we also use HeronProjectTimeline for brainstorming.
     35
     36== Training and Support == #support
     37
     38[[HERONIndependentStudy]]
     39
     40* Ask the Clinical Informatics Coordinator for help via the [https://redcap.kumc.edu/surveys/?s=3SBkPg&tool=1 feedback form]
     41
     42* The FrontiersInformaticsClinic meets every other week. [https://redcap.kumc.edu/surveys/?s=L72oqA Register] in advance if possible but drop-ins are welcome.
     43
     44== Data Sources and Monthly Update Process ==
     45Our 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.
     46
     47 * Data Sources
     48   * [[HospitalEpicSource]]
     49   * [[ClinicIdxSource]] (including HICTR)
     50   * [[UHCSource]] (billing diagnoses and DRGs)
     51   * KUH TumorRegistry for NCI designation
     52   * [[BiospecimenRepository]] (#517)
     53   * ... things like CRIS, CoPath, GME, and biospecimens will follow; April [[DROCMeetingMinutes]] has a list:
     54     * SMS (lower priority; UHC data meets most of the relevant needs)
     55     * !CoPath
     56     * CRIS/REDCap (clinical trial enrollment and registries)
     57     * Read only Chronicles Access for Content not included in Clarity #20
     58 * HeronLoad monthly update process
     59   * UpdateValidation
     60   * HeronReleaseNotes - features, changes, updates
     61
     62
     63== Architecture ==
     64[[Image(heron-arch2.png, 800px)]]
     65
     66Bring-up and some configuration notes on the machines are in:
     67
     68 * #80 - bring up identified server hardware, os
     69 * #82 - bring up de-identified database server
     70 * #43 - bring up virtual server for production web services
     71
     72See also:
     73
     74 * HeronSizingGrowth
     75 * [[HERONsecuritynotes]]
     76 * HeronPerformance
     77 * HeronStatsPlugins
     78
     79=== Open Source ETL Code === #open-source-etl-code
     80
     81The [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!
     82
     83[http://www.kumc.edu/miea/presentations.html Our presentation materials] may help with the bigger picture; in particular:
     84
     85 - [http://www.kumc.edu/Documents/eami/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
     86
     87=== Terminology Mapping ===
     88 * [[FlowsheetMapping]]
     89 * [[DiagnosisMapping]]
     90 * [[SmartNotes]]
     91 * [[MedMapping]]
     92 * [[LabDiscussion]] January 31, 2011
     93 * [[LabDiscussion2]] February 11, 2011
     94 * [[MedDiscussion]] March 7, 2011
     95 * [[LoincMapping]] largely obsolete as of #311 milestone:heron-apr-update
     96 * MedicalTerminologyMarketplace
     97
     98
     99=== Leveraging NIH funded i2b2 framework === #i2b2-nih
     100Per 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:
     101
     102  User access, activity logs,  and project management for the de-identified repository is managed via  the i2b2 framework ...
     103
     104This involves [[Using I2B2]]. We've had a further discussion on overall security for i2b2, other applications, oracle and the operating systems: [[HERONsecuritynotes]].
     105
     106 * [[Using I2B2]]
     107   * [[i2b2 security]]
     108 * [[HERONsecuritynotes]]
     109
     110== Governance (DROC), Privacy (De-identification), and Security == #governance
     111Governance 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.
     112
     113 * [[DROCMeetingMinutes]] and oversight issues
     114
     115The main usage scenarios for milestone:system-access was PatientCountStory, which demonstrates Data Request Oversight Mechanisms and Frequency of Review.
     116
     117See 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:
     118
     119 * [attachment:L0017227FinalElectronicHeronCopyFromLisaH09092010.docx Final legal agreement for HERON with System Access Agreement]
     120 * [attachment:HERONAgreementSigned.pdf:wiki:GroupOnly Signed master agreement for medical data sharing]
     121 * [attachment:HERON_Repository_HSC_IRB_Protocolv1_1.docx HERON IRB protocol original 2010-2011]
     122 * [attachment:HERON_Repository_HSC_IRB_Protocolv2_1final.pdf HERON IRB protocol revised for 2011-2012]
     123
     124Another design consideration is de-identification of data and then what's kept on blue HERON. See DeIdentificationStrategy.
     125
     126 * [[HERONsecuritynotes]]
     127 * DeIdentificationStrategy
     128
     129== Acknowledgements ==
     130
     131This 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://www.kufrontiers.org/ Frontiers: University of Kansas Clinical and Translational Science Institute] # UL1TR002366 (formerly # UL1TR000001 and #UL1RR033179). The contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH, NCRR, or NCATS.
     132