#158: usable view of LOINC lab terms
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Reporter: rwaitman | Owner: dconnolly
Type: enhancement | Status: accepted
Priority: major | Milestone: data-domains3
Component: data-stds | Resolution:
Keywords: | Blocked By:
Blocking: 241, 285 |
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Comment (by ngraham):
One thing we ran in to when implementing at KUMC is that there seem to be
terms that don't have parents. I don't know that i2b2 cares (other than I
think the terms won't show up) but some our ETL code that counts
patients/facts makes sure that every term has parents. We filled in the
missing parents for our production release.
An example path that I think is an orphan:
{{{
\i2b2\Laboratory Tests\Microbiology\Microorganism\Bacteria\Yersinia
sp\Yersinia pestis\Yersinia pestis Ab\Yersinia pestis Ab | Bld-Ser-Plas\Y
pestis AbTitr Ser EIA\
}}}
I found 63 missing parents using attachment:missing_parents.py run against
the .dsv from comment:34. Maybe this isn't something that needs
addressed, but I wanted to document what we found in case someone else
runs in to it.
Also, it seems that the CDT file linked in comment:34 only has 48,943 rows
rather than the 71,000 noted in comment:34. Maybe I'm looking at the
wrong file?
{{{
wc -l GPC_LOINC_HIERARCHY.dsv
48943 GPC_LOINC_HIERARCHY.dsv
...
md5sum ./GPC_LOINC_HIERARCHY.dsv
9d07adf37a04efe319324a36dcc48e12 *./GPC_LOINC_HIERARCHY.dsv
}}}
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:36>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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