data2health/ehr2hpo.prj

Conversion of EHR data (such as LOINC) to HPO codes

ehr2hpo.prj's Issues

record how many HPO terms map to the first set of 7000 LOINC annotations

Implement synergy algorithm (test case)

Implement the algorithm described here and test it using artificial or genomic data as preparation for the CTSA analysis

Watkinson J, Wang X, Zheng T, Anastassiou D. Identification of gene interactions associated with disease from gene expression data using synergy networks. BMC Syst Biol. 2008;2:10.
Anastassiou D. Computational analysis of the synergy among multiple interacting genes. Mol Syst Biol. 2007;3:83.

Make tutorial page for LOINC2HPO project on HPO website

Add blog to HPO website

Add blog from npj

i2b2 tutorial

Documentation for HPO website

We will write up documentation that will live on the main HPO website that will explain LOINC and the LOINC2HPO project. This will be linked to the new pages on the HPO website. It will also use material from #9

Analysis of reasons for mapping failures on real data

Can we make a list of LOINC terms that were not mapped at one real-life CTSA, and look at the most common ones to identify any potential systematic reasons for failure? That is, if we are expecting the wrong codes or something like that, then the failure might not be because of incomplete curation (we know about that) but because of a logic problem in our code that we are not aware of. This analysis will try to figure that out by looking at the top 250 most common failures. If possible, it would be good to share this in a de-identified way with the entire team.

Test MI algorithm on Asthma data

Determine most likely group of participating CTSAs

We should try to identify at least 2 CTSAs (and better 3-5) that would be willing to implement a LOINC2HPO analysis project

• Determine contact people
• Determine whether the centers can use FHIR
• Determine what level of data sharing will be possible

Submit revised version to Digital Medicine

test issue :-0

Develp ingest pipeline for the LOINC annotation data into the HPO web database

Automatic ingest script.

Design look and feel for LOINC data on HPO website

One possibility is to add a "tab" on HPO term pages (next to the disease and gene tabs) and call it "Test"
Link out to LOINC like this: https://s.details.loinc.org/LOINC/2345-7.html?sections=Comprehensive

• We will probably want to indicate if the test is directly related to the HPO term or if it is an inherited (true path rule) association.

• Ask Julie for advice about look and feel.

Additional biocuration to fill gaps identified when using HPO on FHIR in production

Radlex and gamut ontologies

Examine current status of these ontologies with respect to HPO mappings

• Quality control of mappings from https://academic.oup.com/jamia/article-abstract/26/2/149/5280856
• Make concrete plan for collaboration

Implement HPO on FHIR at OHSU "live"

Can we move this to a production environment, keeping all of the data within the firewall, as a next step?

Improve evaluation plan

right now the eval plan is largely the same as the deliverables. It would be good to have some evaluation measures.
What functionality will there be and how will you know the app has achieved it?
How will you measure user satisfaction or query answering capabilities?
What constitutes success?

Here is a simple example of an evaluation plan with more of these sorts of items, you could copy the template: https://github.com/data2health/Operational-architecture/blob/master/evalulation.md

Demo needs clarification on scope / privacy

Here on the demo linked from labs, https://octri.ohsu.edu/hpo_on_fhir/, the language needs to change to either:

• clarify that the data is simulated/synthetic OR
• state explicitly (with IRB number) that the data is real but can be shared. #6 says it is test data, which implies it is synthetic, but isn't crystal clear, especially in the demo.

Write implementation protocol

• draft by Peter
• revisions by Amy Yates and Justin Ramsdill: implementation in FHIR/Epic system
• discuss with Chris Chute.

Demo needs prepopulated examples and better functionality

• Prepopulate examples

The text in the header is easy to miss. Needs to be more Plug-and-Play whether hyperlink (eg. https://hpo.jax.org/app/ or button eg. https://alpha.monarchinitiative.org/)

• Phenotype search

Moreover, searching by patient is the least interesting form of what the LOINC2HPO makes possible. We should be able to search by phenotype, preferably one shared by a bunch of patients. Ultimately this should be possible using autocomplete, however, for now, some hardcoded examples (prepopulated per above) would be fine.

Make slide for LOINC "show-and-tell" session

Begin work on DREAM ontology mapping

Not funded by CD2H but related.
The HPO team has been contacted by a European radiology project with lots of data on radiology findings with the goal of ammping this to HPO Terms

Ask the LOINC team about license issues

Is it allowable for us to add the LOINC mappings to the HPO website? Ask Daniel V exactly how we need to show the license

Determine goal of multi-CTSA project

In the original project, we looked at a cohort that was enriched in but not exclusively composed of asthma patients. This type of cohort would be good to have for a larger project.

• Determine areas of medical interest and opportunity among the chosen CTSA sites
• Determine method for assigning a patient to a diagnosis or excluding the diagnosis (e.g., ICD codes, or some other means offered by existing CTSA technologies such as OMOP)
• Analyze our current LOINC2HPO annotations and try to ensure that all tests relevant to the disease of interest as included in our library.
• If possible, design some test as to whether we are correctly identifying our diagnosis of interest in the cohort, for instance, by manual inspection of 100 charts.

reconcile RPPR outcomes with milestones

the RPPR doc https://github.com/data2health/ehr2HPO.prj/blob/master/RPPR.md
isn't consistent with the milestones and deliverables on the ReadMe.
Also please add dates to the timeline.
thx.

Revised figure 1 of Loinc paper

• Determine new authors list

• Finish revising text

• Finish response letter

• test

naming and privacy

should this repo/project be renamed ehr2HPO rather than HPO2ehr?
And any reason it is private? the tracking repos must be public. Ideally the code is too ;-).

Report on usage of LOINC2HPO at a CTSA site

We will write up a report with an analysis of the performance of the HPO on FHIR app at OHSU and diseminate it on the CD2H website.

Documentation for use of Mutual Information algorithm at the CTSA sites