Hi All,
The following is a link to the NIST Automated Security Assessment Tool.
For OpenEHR one tool will be insufficient. Something similar is feasible for
the
low-level (network/system) OpenEHR project.
-Thomas Clark
Hi,
I had problems wth my membership with the list for a while so I could not
catch up with recent stuff but during this time I had some time to examine
openEHR documents posted on the website. As a person who had previously been
involved with bioinformatics and especially human genomic databases, some
part in my mind still reminds me of the fact that one day all these
information shall be integrated. Also personally, I believe the approach
taken in openEHR shall form the baseline for future of EHR systems. So I
would like this issue to be considered during these discussions. Enough of
good wishes, here is my question:
Is there a specific way to represent genomic data of a patient (Either
Nucleic Acid sequences or protein sequences) in the Reference Models or is
the general purpose text data type is thought to be the solution? I think it
could be wise to create a new class with its own attributes, methods and
constraints right into the RM because with this speed of biologic evolution
I don't think the genetic code and concepts are going to change for a couple
million years!
Best regards,
Koray Atalag
Korag
This may well be the way to go soon - but I would think that an external
datatype would be better for the moment as the representation will probably
not be uniform (and openEHR should not impose uniformity in such a domain).
Also, we would see the genome as only forming part of the genetic record -
as there will need to be a lot of other information present to make
healthcare work.
What do you think?
Cheers, Sam Heard
Korag and Sam,
As you may know, we have recently initiated a new SIG at HL7 called
Clinical-Genomics, focusing on the use of genomic data in clinical
scenarios. In particular I've been working on the usecase of tissue typing
where more and more genomic data are being used to make the new methods of
bone marrow transplantation more successful. In that SIG we have other
people working on usecases in the areas of genomic-based diagnostics and
clinical trials. in the later, patients are being tested for their genetic
profile and conclusions are made accordingly so that inappropriately
prescription could be avoided.
In all these usecases we are trying to find the commonalities in the data
representations (e.g., the representation of allele and its SNPs) and then
come up with a domain information model using the HL7 tooling. I agree with
you that genomic data are not just different data types and they do need
special attention.... 
I would be very happy to share this work or even collaborate with OpenEHR
members of are interested in this domain and use the OpenEHR tools.
At IBM Research we have been working intensively with a research center in
Canada (iCapture) where mass clinical and genomic data were correlated to
explore lung and hurt diseases (see InfoWorld article at
http://www.infoworld.com/article/03/03/26/HNicapture_1.html).
Thanks,
Amnon.
Dear Amon
I have switched this to the clinical list as I think this is where it should
live in the first instance - although I know people are rushing to the
genetic material out there!
Thank you for this. I am very interested in this as well. I have already
developed an archetype outline for genetic problem (optionally coded) - this
is a specialisation of problem but is not a diagnosis (requires coded label)
as terminology services are not up to speed in this area and may well not be
for the foreseeable future.
There is a real issue - as we have seen with Cystic Fibrosis - that simple
gene presence, absence or damage is not sufficient to determine the
phenotype - and the phenotype is usually the important expression to
consider (except in pre-natal work).
I have worked with CHIME in London on this to a minor extent. The critical
issues to get into the EHR that were specific to the genetic diagnosis
seemed to be:
- If the person was a carrier only - we have this as a Boolean - as most
carrier states do not have specific names
- Compatible DNA findings - ie the genetic material that pointed to this
Date of onset, diagnostic criteria etc all come from problem....
Cheers, Sam
Dear All,
I think what Amnon offers is a very valuabe contribution and a good starting
point. I have mentioned about this subject in my previous message because I
had recently received an email asking for collaboration in determination and
standardization of phenotypic data but unfortunately deleted this message;
but the main idea was that the genomic society is in a good position in
modelling and representation of genetic data (Sequence, Proteins,
Chromosomes, Primers, Genetic Linkage-maps, functional genomics and etc) but
do not know what to do with the "phenotypic" or the clinical/medical part. I
think they underestimate the domain they are facing :))
In my message, regarding representation in RM, I was specifically talking
about DNA/RNA sequences and protein sequences. Of course other genomic data
might be very complex and hence difficult to represent and probably out of
scope in openEHR.
I will try to provide input on this subject if discussion continues in the
list.
I am continuing to examine and understand the concepts mentioned in the
openEHR documents. I have decided and will try to implement a small clinical
information system based on openEHR archetypes and RM as part of my Ph.D.
thesis so I will probably start asking lots of questions in near future!
Friendly regards,
koray
Dear Koray,
[...] I have decided and will try to implement a small clinical
information system based on openEHR archetypes and RM as part of my Ph.D.
thesis [...]
Any chance you will be allowed to open source it ?
Thanks,
Karsten Hilbert, MD