1) develop use cases decide how we want the functions to work
For the second part a very important consideration to keep in
mind (and link to at the appropriate place) are Richard's
design documents. He already has detailed and extensive
descriptions written up on how he wants those function
I suspect it would just throw an error if it can't match to a patient.
(this is proably rarer than it would be in Australia)
Yes.
I'm not sure why we have to have a two-step process. The importer
can insert directly into lab_result if it finds a match, and
unmatched_results when it doesn't.
Therefore results would need to be written into unmatched results *not
only* if the patient cannot be uniquely identified, but also if the
test_org cannot be identified.
I disagree here. If the patient matches we should import so it becomes
available straightaway.
That sounds reasonable,
gmPatient.py... should have been gmPerson.py.
That is the reason why gmPatient.gmPerson is
named like that: it is a person, not a patient. It only
becomes a patient when you start requesting clinical data from
it (eg. after the first request of get_clinical_record()).
I thought the above
I (think I) understand you, but remain unclear how foreign key
dependencies for test_type, test_org and test_org's identity would
work.
On surface, people may think it *should* not happen that a test_org
is encountered for the first time during an import.
I don't think that. I check for
I was thinking that a data clearinghouse might, in place of 'BC
Biomedical Laboratories, simply have BC Bio in a field but this
abbreviation seems enough to stick into org on a temporary basis.
I agree. Plus notify the user.
Should the fact that a new org needed to be created appear in a
That needs updating. The automatic updating still chokes on
wxPython to which no one apparently has an answer.
If the API is worth updating manually (until it can run
automatically) what frequency would you suggest it be done manually?
Once a week?
Once a week.
Once a month? What is
1. can fully serve their clinical and administrative (billing etc) EMR needs
2. can serve a partial solution, able to be integrated with other EMRs for
the other parts (billing, scheduling)
3. partial solution that integrates *incompletely* (or not at all) i.e.
requires some
Is this useful to gnumed?
http://ncicb.nci.nih.gov/download/downloadhl7.jsp
Preferably we would want something accessible from Python.
Nonetheless, yes, any HL7 parser that can be made to
connect to PG is potentially useful.
Karsten
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- vendors will crap (is this term used outside N America?) on FOSS
Nothing we can do about that.
They will either
- - view it as a possible solutionabout which some users /
clinics / centres remain enthusiastic which may cause these
decision-makers to give preference to this known,
I'm fine with moving the metadata from config-definitions to
backend tables. Will have a look on that this week.
Good. *That* is the real point worth considering in this
debate (it's not important where to move things but it *is*
useful to make things simpler/clearer).
Karsten
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As I mentioned before, I don't believe that learning the
table structure of config data is something an admin will want
to do.
Yes, but now is not the time to worry about that.
So I don't see why anybody should have to edit gmConfigData.sql.
They serve entirely different domains.
That certainly gave me pause. A pilot for the anticoagulation clinic
is almost certainly more achievable (less work yet to do / shorter
time frame) than to have a web app developed, yes?
Hm, given a dedicated and skilled web programmer it might take
less time. It might. There's the rub.
Ref_source is meant to hold coding systems, so is test_type meant to
have an fk constraint?
No. ref_source lives in a different service (reference).
Also, if you don't mind, how is test_norm meant to be used? (I could
find nothing in the gnumed-devel archive)
No clear vision on how to use
Can we activiate the Patch Manager feature on savannah, so there's a
proper place to keep controversial patches
Does gnumed/test_area/ not do ?
Karsten
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more to keep
- Forwarded message from USM Bish [EMAIL PROTECTED] -
On Thu, Feb 24, 2005 at 01:21:05PM +, rob challen wrote:
Sorry to add my thoughts after the discussion has died down.
Actually, yours is the first concrete proposal towards the
issue of gestational
It would be nice to be able to have test builds where one can run a client
with a test feature running in it, instead of it running in some
isolated unit tester.
If you want to test some GUI part that does not change the
basic workings you can simply write a notebook plugin for the
initial
Hallo Christoph,
I loaded the gm-schema-dump.sql with Emacs and replaced 95
character varying with varchar. The explanation is, that if you use
varchar and dump the db, pg_dump writes character varying, no matter
wether you have used character varying oder varchar.
Aha, that makes sense !
a regular update is impossible for free. I played arround a bit with the
gnumed schema in dezign for databases. It will need several hours, to
optimize the tables on the display in a reasonable way. This is a nice game
to learn about how the tables in gnumed are organized, but to do this on
If someone were to set up MoinMoin I would happily invest what time I
can to get a bit more familiar with it. If someone deciphered its
directory structure (maybe creating a Gnumed web within it) it could
be tried copying the existing pages from TWiki and we could see what
results.
I
I got one consistent way of stopping a block.
If I edit DevelRefMisc from the web page, and then view processes with
ps -A
there is no new processes.
When I try to save it , and it blocks, a process called oops appears
on doing ps -A in ssh.
there is a perl(?) program called oops in
Christoph,
thanks a lot ! I added that as a baseline for our table. The
idea is to run a script every night to update that table from
the names actually in use in the demographics database.
@all: Mini Project:
- Python script that attaches to the database
- per firstname compile gender freqency
Here in Thailand Mims seems to be a preffered source of information as well.
I remember when I was there they got a new hospital
information system from AU.
Karsten
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Yeah it's pretty crappy. Looks like they had a hard time adapting it to CMUs
need. There is all kind of wierdness all over the program.
Well, the first weirdness I noted was that two people died
because requests for blood conserves couldn't be entered
somehow (of course it was the hospital's
just hard to know because we are rather Balkanized (is that term
used/understood in DE?)
yes
So in Canada we do not have electronic requests except:
a) inside *some* hospitals, for inpatient and hospital clinic tests and
b) one lab is wedded to the idea of coaxing people to enter requests
MediNet provided info about their uncoded ASCII reports (see below)
and are mailing me their paper HL7 documentation. While I await what
type of server-based connection they might enable, I am thinking to
download their Windows-only visual basic client for the clinic.
If that client
Mar 2005 11:23 pm, Sebastian Hilbert wrote:
Yeah it's pretty crappy. Looks like they had a hard time adapting it to
CMUs need. There is all kind of wierdness all over the program.
On Monday 28 February 2005 18:01, Karsten Hilbert wrote:
Here in Thailand Mims seems to be a preffered source
My public health/community medicine reflexes make me recoil somewhat
from the depictions of what look like Big Expensive Hi-Tech Hospitals,
hence I like the top right ;-)) as it does *not* depict a
hospital
in fact, depicting a hospital would be misleading in scope
but the overall sense of
Ian, do you think it an acceptable solution for now to add a
flag is_blob (or similar) to test_result
IMHO display can be inferred by length.
Fine by me. I was just attempting to make some concessions
to lure you into the trap ;-)
If it is a few chars, it can
be displayed in Sebastian's
Just find on and use it. If a wiki was written
in COBOL, and if it was the best, then we should use it.
if everyone adopted that type of logic, then why don't we all become
real estate agents.
Well, if all carpenters adopted the opposite logic they would
all be out tending forests and
- the code was not very well, if at all, documented
well :-)
- what I do know about it involves
- - a connection method that used to be IPsec but has since changed to SSH
VPN.
as long as we can use their code...
- - instead of downloading a file, the fetcher queries the service
My idea is for split viewer, with a listbox at the top listing the
transmissions.
(so FBE such a date, UE the next, and so on), when you click, it is
shown:
either a textbox for blobs, or the grid view for granular numeric results.
Well, this is what we would do with profiles -
At 10:59 PM +0100 3/2/05, Karsten Hilbert wrote:
Our widget allows for signing off groups, btw.
Please elaborate
per item tickboxes: [_] reviewed
button: [mark all as reviewed]
button: [sign off]
Karsten
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by line are you referring to the line that describes which
user(s) viewed a particular result? Would this have application to
regions where privacy requirements dictate that viewing must be
tracked?
Tracking who apparently has viewed something does not really
add that much hard value to
I like the bottom-left. This would go great with a new website. ;-)
It looks way too much like lofty high-flying US health care
for my taste, but hey, that's just me.
Flatly the flying leaves don't appeal to me. I won't argue
against it, however, if that's what people want. It's still
heaps
How do you/would you display per-number tracking results?
Not.
In our hospital system, we have something like this:
With all due respect you are at the wrong level of care here.
But you knew that.
FBE: | 3/3/05 |
---++
Hb | 83|
MCV| 86.2 |
WCC| 15.1 |
I've fed back all the comments to Tim with a new brief. Let's see what the
feedback look brings. We will have to acknowlege his work on our help if we
use this stuff as the 'graphic designer' for gnuMed.
Why, of course !
Karsten
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What do people think:
Should editing (eg intending to change) a progress
note previously entered by another user result in ...
... a new progress note being generated and the old one being
textually marked as modified, see ...
... the original progress note being changed to the new
whatsoever that those that are transmitted are forming a
natural group.
Ok, that makes sense.
This is also why (I assume) you want to be able to mark the eariler results
as reviewed, but still display them all as logical groups when they all
arrive.
Yep.
Karsten
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MediNet provided info about their uncoded ASCII reports (see below)
and are mailing me their paper HL7 documentation. While I await what
type of server-based connection they might enable, I am thinking to
download their Windows-only visual basic client for the clinic.
If that client can
FBE: | 3/3/05 |
---++
Hb | 83|
MCV| 86.2 |
WCC| 15.1 |
---++
Viewed by:
Ward 4W at 19:04 3/03/05
Pharmacist Joe Bloggs at 19:10 3/03/05
Ian Haywood at 20:32 3/03/05
a) we aren't tracking who's seen something in the
The above appears to be a list of users who have accessed the
results via a certain method (there cannot be any assurance as
to whether they have physically seen and cogitated it so
there's no real value in the information). What we are
tracking is who was the last person modifying the
IMHO having any sort of results/documents handling without a tracking
mechanism is worse than useless.
Well, the commercial systems I know here in Germany (I don't
know all of them) don't even bother with tracking. That does
not render them entirely useless, either.
Karsten
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what specific sorts of tracking is needed?
tracking of who took responsibility and what their decision
was (technically_abnormal/clinically_relevant).
What is the workflow for taking responsibility ?
Signing off.
I'm wondering if receiving ,(application )acknowledging, displaying
results
Ian, were you thinking that incoming communications like letters,
consultation reports would also go here (i.e. not just the results of
Yes, all external (asynchronous) communications, which then need to be
followed up.
That makes sense.
The idea is a single Inbox tab which looks like an
The reason I wanted the savannah patch manager is putting patch files
into the CVS tree you are patching is seriously strange.
This sounds right at first sight. But with CVS we aren't
patching trees (eg there is no changeset support that I know)
but are keeping revisions of individual files.
Some non-doctors that
I know who built a lab interface for an open source emr built their
schema to exactly accommodate a single lab data provider. They
asserted that when a second lab data provider comes online, an import
table should be built exactly around *those* data. And
at work , the secretary showed me a stack of paper to be scanned
in about 15 cm high each day. 50 x 5 x 15 = 25 metres a year.
I can see why one might want to a separate service for blobs.
How we (my parents, that is) do it:
Scan the documents at a local workstation into a queue
directory on
I don't think there is. Richard himself once entertained the
idea of formalizing the scratchpad content more. His original
design had a scratchpad AND a patient inbox.
scratchpad is like a precursor to natural language processed
structured TODOs /plan items?
Oh, I was thinking of adding
However MSH.sending_application is useful for figuring out which HL7 dialect
is being used.
True !
observation_identifier:2000-8 Sodium LN
This is actually 2000-8^Sodium^LN, a field with 3 components,
Even better ! Hence we can parse it.
LN is LOINC, 2000-8 is the code which can then be
I don't think there is. Richard himself once entertained the
idea of formalizing the scratchpad content more. His original
design had a scratchpad AND a patient inbox. He once wondered
whether they could be merged. I would agree they can.
... which might make the scratchpad a special type
On account of our having clin_root_item we cannot simply change the
patient to whom the record is linked (we wouldn't want to, anyway)
We sure can. Just link it to the proper episode/encounter, et
voila.
Adding a note to the EMR of the wrong patient can be done but
is not really necessary, IMO
For any one test_result, only a single .narrative would be stored, is
this a preferred place in which a secretary's input Phoned to Dr X,
2:45pm could be stored?
It would work.
Is it better for the secretary to enter a Soap item relating to the
health_issue (visit) in which the labs were
Working quietly I am spending many hours a day to make 0.1 happen. Am I
...
This is the work of a release guy.
Thanks.
As hard as it seems we simply cannot (IMHO) have Richard's GUI in 0.1.
That's what I've been saying all along. As much as I admire
his GUI and even believe in their
Absolutely. For the time being our only chance it to put info in the Wiki on
what works and what does not. Users need to know before they start and end up
in frustration.
Functionality-wise or what you need to install how ?
BTW, the AddWindow wx2.5 issue is fixed I just need to check it
in.
Last week Richard and I had a phone conversation about his frustration with
the adding more structure on the *backend* and not getting closer to having
this working with the GUI.
a) no one is bound by the backend not being available
- propose the needed changes yourself
- or proceed
What about a view layer ontop of the middleware , like a facade pattern
specific for Richard's gui. Has no wxwindows code in it, but Richard's
gui calls this facade which translated to middleware calls.
Not a bad idea.
This is a sort of a intermediate step for connection, and
may reduce the
I think Karsten [does not]
...
plan to spend much (if any time) on the backend on post-0.1
issues until 0.1 is done.
Correct. The one thing I try to do with the backend, however,
is to not make post-0.1 changes excessively difficult if we
already have some idea of how things should be changed
Ian,
please document this in the code.
Karsten
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One thing taking up a some of the focus at the moment is sorting out
labs. Maybe I have been part of the problem if I spawned (or helped
enable) ongoing threads concerning results tracking. To the degree
that results tracking can be split from (or added afterward to) lab
fetching /
how do you get docs into the emr?
by the scan/import process I described recently
Karsten
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Also there is in BC a project looking at the feasibility of improving
the information value of our medicare's prescription payment system
which is accessible online to doctors and pharmacists but provides
nothing but a chronologic display of filled prescriptions. So if a
patient gets
Here is some information that might be useful to the Gnumed coders.
I am running Suse 9.2 which has been out for almost 6 months now.
It ships with wxGTK 2.5.2.8 (unicode compiled) as well as python-wxGTK 2.5.2.8
Trying to set up the menu with a translation for About (= Über):
[PANIC]
Richard,
thanks for your analysis.
1) The Inbox should be a general not pertaining to single patient inbox.
This is like you 'in tray'. It should contain an amalgam of things - eg
patient results for review (This in itself brings up the concept of should be
auto-file in the patient
Yes, of course, scratch pad comments should be seen by anybody.
That's why I thought the scratchpad would act like a patient
inbox. It would hold messages directed at anyone
(with proper credentials) accessing that patient's EMR. Or, to
be picky, it would be an EMR inbox.
Karsten
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And then make a release, with *only* these five modules (currently gnumed
loads *23* modules, mostly non-functional)
Fine by me. It only loads 23 modules if configured to load
them. No coding needed, just reconfiguration.
Oh, and your comment prompted me to define a workplace called
Release
I ask because in any surveys of local doctors who lack ANY EMR (they
just have appointment scheduling and billing) their first desire
would be to have a system to look after
- the filing, organization, storage and retrieval of test results and/or
fairly easy
- prescription (medication)
Functionality-wise or what you need to install how ?
No. No istallation instruction. Just say Suse 6.3 with wx and python xyz
works
for me
Suse 7.2
- Python 2.2.1
- wxPython 2.4.2.4
- PostgreSQL 7.1
- pyPgSQL 2.4
works for me.
Karsten
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however would get out of sync of the doctor reviewed some but not all.
The method you would propose (to have the inbox query the data) would avert
this problem. I was just saying that if it was the importer that had tallied
80
results for a patient into the inbox, that number should be
All design credits go to Richard ! I just followed his specs.
Well, not quite.
Correct.
Where did the extra listbox come from in gnuMed which seems
to contain 'schedules'. Of what?
Vaccination schedules the patient is configured to be on.
I have not yet reached the level of sophistication
I would think it desirable that whenever one logs in, a person would
log into a general/ status area which would display numbers of
messages etc.
That surely sounds reasonable.
I had believed it was already suggested overall that
when one logs in, it may be safer to NOT automatically
1.) every widget related to a specific patient has a function
OnPatientActivated(id) which it registers with the message dispatcher for
the PatientActivated event.
Same here.
2.) until it receives a PatientActivated event, it displays a default state
Same here.
Karsten
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On Thu, Mar 10, 2005 at 12:51:53AM -0800, Jim Busser wrote:
At 5:18 PM +1100 3/10/05, Richard Terry wrote:
PS: Seems I'm the only one who routinely adds my name to the bottom of the
comments. As the headers on a reply are sometimes snipped, I wish others
would do it as I have difficulty seeing
On Fri, Mar 11, 2005 at 09:39:35AM +0100, Hilbert, Sebastian wrote:
I have found some time to whip up some Wiki content
You will find it starting with installation instructions, main via CVS.
Please do me a favor and read it.
No. You'll have to structure this differently or else I don't
know
I was thinking it might be acceptable to do a first cut of Richard's inbox
using a draft business interface for messaging and add it as a tab for
the client.
Well, you are free to do so.
Karsten
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If there is no objection, can the list of remembered patients be
retained (not deleted) between logins/sessions?
Technically it can. You can list it as a todo item for
post-0.1.
Also, if a single user can have the same userid and password logged
into two or more instances of gnumed (using
There we are, folks, a concrete and no-risk offer from Horst.
No-risk ?
Karsten
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On Sat, Mar 12, 2005 at 12:52:01PM +1100, Tim Churches wrote:
I think that dispassionate outsiders may want to take a knife to at
least some of the code in an effort to reign in the complexity.
They may very well have a point - or not. Either way I should
definitely like to know where what why.
On Sat, Mar 12, 2005 at 06:46:30AM -0800, Jim Busser wrote:
Some people indicated they may want to run multiple instances of
gnumed concurrently on the same desktop. What you say above suggests
that to do so, they would each require a separate copy of the client
to be installed?
Of course
On Sat, Mar 12, 2005 at 09:38:08AM +1100, Tim Churches wrote:
Horst wrote:
If you check the available code, you'll see that gnumed doesn't really need
that much work any more to become fully functional.
functional != usable by Joe User, MD.
I have been monitoring the GnuMed email list for
On Sun, Mar 13, 2005 at 10:34:13AM +1100, Syan Tan wrote:
Q. is usability a matter of taste?
I would think yes.
Karsten
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On Sun, Mar 13, 2005 at 12:01:39AM -0800, Jim Busser wrote:
So the list of tracked patients, within each instance, is stored only
in memory?
yes
And if it were desired to re-access that list in the next session,
the list would have to be written from memory to a disk file or into
a
Anyone care to comment on the current state of family history
tables/views ?
-
create table clin_hx_family (
pk serial primary key,
fk_narrative integer
unique
not null
references
So, do we need to store the source timezone for our timestamps ?
Absolutely.
But I was uynder the impression that a postgrs data type timestamp does
that
anyway.
The postgresql data type timestamp is not in the least
equivalent. It does not even preserve *any* time zone
information, eg it
On Mon, Mar 14, 2005 at 07:34:40PM +1100, Syan Tan wrote:
BTW i had to directly update the cfg_string row which had value
status_quo to terry or somesuch. Is there another way of setting
which gui gets loaded?
run the status_quo gui and change it with Hilmar's config registry
Karsten
--
On Mon, Mar 14, 2005 at 07:40:29PM +1100, flotsamjetsom wrote:
Personally I thnk that a full GUI interface, which is the path Gnumed is
taking, is a better long-term bet for everyday use, but having a fully
featured Web interface to allow easy remote access (from home, nursing
homes,
On Mon, Mar 14, 2005 at 06:40:02PM +1100, Ian Haywood wrote:
I agree with your comments about the sash windows, its a bad idea,
but I'm sure the changeover to using tabs will be straightforward.
It is.
Carlos and Karsten just want to get something working out the door first,
Yes.
If Carlos
On Mon, Mar 14, 2005 at 02:05:30PM +1100, Richard wrote:
spending more than 20 seconds on a progress notes - of course - thats where
the SOAP style editor comes into play. You can write as many lines as you
want in each of the SOAP or whatever lines. My only quibble about the current
On Sun, Mar 13, 2005 at 11:22:00PM -0800, Jim Busser wrote:
Moreover if gnumed 0.1 is possible with only a rudimentary GUI, is
Richard's concern that if 0.1 is built that way, the die will be cast
and gnumed will never acquire the sophistication Richard advocates?
Can anything dissuade
On Sun, Mar 13, 2005 at 10:38:47PM +1100, Syan Tan wrote:
if it's gnumed, I might put in some money to get to 0.1 and beyond quickly.
Not sure if someone independent needs to act as the client stakeholder
though,
otherwise the main developers could be still using up time changing
/fine
the schema changes frequently
yes
and sometimes it's not available on the cvs
yes
can a cron job be run to do a pg_dump of the database on salaam,
yes, however, the database on salaam is only updated after the CVS tree has
been synced to salaam which means the changes are in CSV, too...
On Wed, Mar 16, 2005 at 12:34:54PM +0100, Hilmar Berger wrote:
PS: I modified the DrugBrowser to work again ( at least with AMIS), but as
this is probably post-0.1 stuff I won't check it in right now.
Please do. It'll simply not be included with the release.
Unless it changes *core* stuff - in
On Wed, Mar 16, 2005 at 09:23:51AM +0100, Hilbert, Sebastian wrote:
What I meant was to ignites some discussion about the ConfigEditor itself.
Mainly the structure and what should be configured where. Suppose I want to
add a new lab to the list of labs I send my specimen to. Where do I do
gnuMed config is better (though I find the existing gnuMed one confusing as
to where to find things - and it certainly is a sysadmin config tool, not
user config tool)
That's precisely the intended scope for it right now. Admin
config tool.
Karsten
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If the receiver send is wrapped in
a try, catch block, and the exception is caught and logged in the
dispatcher, then the dispatcher will work as expected,
Fixed but with a lower impact fix. Explanation in the code.
Karsten
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On Thu, Mar 17, 2005 at 09:11:40AM +1100, Syan Tan wrote:
regetMixin is using the paint event to refresh the view when the model
changes, by polling the model.
Correct.
the dispatcher is supposed to notify receivers
Correct.
by pushing model change to the receivers,
Wrong. It notifies
The dispatcher.send() shouldn't be wrapped in a try: catch block as a hacky
sacrifice to impatient module writers,
No, wait, I do think you have a point there. I do think it is
OK to catch those exceptions, report them and try to continue.
because release modules should not
be throwing
On Thu, Mar 17, 2005 at 02:57:53PM +0100, Hilbert, Sebastian wrote:
You once told me that some stuff like document types for the Archive do not
go in there. Which I never understood.
So where is this stuff to be configured/changed in case the admin wants to
add some document types?
On Thu, Mar 17, 2005 at 03:09:33PM +0100, Hilbert, Sebastian wrote:
to make it run on Horstspace or RichardSpace where are we going to develop
those files.
If so something smells really fishy. It may not be solvable
but needs a good hard look.
I don't understand. Are you saying that one file
Richard et al,
more input sought.
There are two conceputally conflicting design goals (that I am aware of).
1) family history item integrated into a patient's EMR
- searching a patient's EMR for family history narrative is easy
- a condition of my grandparents can be of significance to
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