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[Gnumed-devel] re: concrete mappings of v2.3 messages onto gnumed measur
From: |
sjtan |
Subject: |
[Gnumed-devel] re: concrete mappings of v2.3 messages onto gnumed measurements. |
Date: |
Sun, 06 Mar 2005 01:15:44 +1100 |
User-agent: |
Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.5) Gecko/20041231 |
Below is an output from the oscar pathnet hl7 parser on a part of
Richard's test hl7 message.
I'm optimistic that hl7 version2.3 is a bit interoperable after all!
I think work should be done on mapping to and fro to the gnumed
measurements schema
from such V2.3 messages.
MSH.sending_facility test_org.fk_org
MSH.sending_application test_org.internal_name
OBR
filler_order_number:00-49828852-1
universal_service_id:S00.46 BIOCHEM dlabsys
requested_date_time:200109120000
observation_date_time:200109121000
results_report_status_change:200109122225
quantity_timing: 200109120000
filler_order_number -> lab_request.lab_request_id
lab.request.request_status
-> ? F , if all child OBX have observation_result_status: F
requested_date_time -> lab_request.lab_rxd_when
observation_date_time -> ? a field for lab_request.test_done_when ? (*
not in schema)
results_report_status_change -> lab_request.results_reported_when
universal_service_id : ? -> ? lab_request.lab_dept_id ? ( * not in schema)
OBX
value_type:FT ? FT - full text? NM - numerical
observation_identifier:2000-8 Sodium LN
observation_results:139 or a description with
internal delimiter characters
(
\\.nf (?new form), \\.br (lineBReak) ) in
value_type is FT
units:mmol/L
reference_range:135-145
observation_result_status:F ? F=finished
maps as
observation_identifier: test_result . fk_type
observation_results: test_result. val_num or val_alpha
units : test_result. val_unit
reference_range test_result.val_normal_range,
test_result.val_norm_min, val_norm_max
The ORC fields weren't used in Richard's examples, and seem to overlap
with the OBR data.
"order_control",
"placer_order_number1",
"filler_order_number",
"placer_order_number2",
"order_status", ---> this could map
to lab_request.request_status
"response_flag",
"quantity_timing",
"parent",
"date_time_of_transaction",
"entered_by",
"verified_by",
"ordering_provider", ---->
lab_request.fk_requestor
"enterer_location",
"callback_phone_number",
"order_effective_date_time",
"order_control_code_reason",
"entering_organization",
"entering_device",
"action_by"
=================================================================
gnumed tables
--------------------------------
gnumed=> \d test_org
Table "public.test_org"
Column | Type |
Modifiers
----------------+--------------------------+---------------------------------------------------------------
pk_audit | integer | not null default
nextval('public.audit_fields_pk_audit_seq'::t
row_version | integer | not null default 0
modified_when | timestamp with time zone | not null default
('now'::text)::timestamp(6) with time zone
modified_by | name | not null default
"current_user"()
pk | integer | not null default
nextval('public.test_org_pk_seq'::text)
fk_org | integer | not null
fk_adm_contact | integer |
fk_med_contact | integer |
internal_name | text |
comment | text |
Indexes:
"test_org_pkey" primary key, btree (pk)
"test_org_fk_org_key" unique, btree (fk_org)
"test_org_internal_name_key" unique, btree (internal_name)
Foreign-key constraints:
"$1" FOREIGN KEY (fk_adm_contact) REFERENCES
xlnk_identity(xfk_identity) ON UPDATE CASCADE ON DELETE RE
"$2" FOREIGN KEY (fk_med_contact) REFERENCES
xlnk_identity(xfk_identity) ON UPDATE CASCADE ON DELETE RE
------------------------------
gnumed=> \d lab_request
Table "public.lab_request"
Column | Type
| Modifiers
-----------------------+--------------------------+---------------------------------------------------------------------
pk_audit | integer | not null default
nextval('public.audit_fields_pk_audit_seq'::text)
row_version | integer | not null default 0
modified_when | timestamp with time zone | not null default
('now'::text)::timestamp(6) with time zone
modified_by | name | not null default
"current_user"()
pk_item | integer | not null default
nextval('public.clin_root_item_pk_item_seq'::text)
clin_when | timestamp with time zone | not null default
('now'::text)::timestamp(6) with time zone
fk_encounter | integer | not null
fk_episode | integer | not null
narrative | text |
soap_cat | text | not null default
'p'::text
pk | integer | not null default
nextval('public.lab_request_pk_seq'::text)
fk_test_org | integer | not null
request_id | text | not null
fk_requestor | integer |
lab_request_id | text |
lab_rxd_when | timestamp with time zone |
results_reported_when | timestamp with time zone |
request_status | text |
is_pending | boolean | not null default true
Indexes:
"lab_request_pkey" primary key, btree (pk)
"lab_request_fk_test_org_key" unique, btree (fk_test_org, request_id)
"idx_lreq_encounter" btree (fk_encounter)
"idx_lreq_episode" btree (fk_episode)
Check constraints:
"clin_root_item_soap_cat" CHECK (lower(soap_cat) = 's'::text OR
lower(soap_cat) = 'o'::text OR lower(soap_cat) = 'a'::text OR
lower(soap_cat) = 'p'::text)
"lab_request_request_id" CHECK (btrim(request_id) <> ''::text)
"lab_request_request_status" CHECK (request_status =
'preliminary'::text OR request_status = 'partial'::text OR
request_status = 'final'::text OR request_status IS NULL AND is_pending
IS TRUE)
Foreign-key constraints:
"$1" FOREIGN KEY (fk_test_org) REFERENCES test_org(pk)
"$2" FOREIGN KEY (fk_requestor) REFERENCES
xlnk_identity(xfk_identity) ON UPDATE CASCADE ON DELETE RESTRICT
-----------------------------------------------------------------------------------------
gnumed=> \d test_result
Table "public.test_result"
Column | Type
| Modifiers
-----------------------+--------------------------+---------------------------------------------------------------------
pk_audit | integer | not null default
nextval('public.audit_fields_pk_audit_seq'::text)
row_version | integer | not null default 0
modified_when | timestamp with time zone | not null default
('now'::text)::timestamp(6) with time zone
modified_by | name | not null default
"current_user"()
pk_item | integer | not null default
nextval('public.clin_root_item_pk_item_seq'::text)
clin_when | timestamp with time zone | not null default
('now'::text)::timestamp(6) with time zone
fk_encounter | integer | not null
fk_episode | integer | not null
narrative | text |
soap_cat | text | not null default
'o'::text
pk | integer | not null default
nextval('public.test_result_pk_seq'::text)
fk_doc | integer |
fk_type | integer | not null
val_num | numeric |
val_alpha | text |
val_unit | text |
val_normal_min | numeric |
val_normal_max | numeric |
val_normal_range | text |
val_target_min | numeric |
val_target_max | numeric |
val_target_range | text |
technically_abnormal | text |
norm_ref_group | text |
note_provider | text |
material | text |
material_detail | text |
reviewed_by_clinician | boolean | not null default false
fk_reviewer | integer |
clinically_relevant | boolean |
Indexes:
"test_result_pkey" primary key, btree (pk)
"idx_tres_encounter" btree (fk_encounter)
"idx_tres_episode" btree (fk_episode)
Check constraints:
"clin_root_item_soap_cat" CHECK (lower(soap_cat) = 's'::text OR
lower(soap_cat) = 'o'::text OR lower(soap_cat) = 'a'::text OR lower(soap_ca
t) = 'p'::text)
"test_result_val_num" CHECK (val_num IS NOT NULL OR val_alpha IS NOT
NULL OR val_num IS NULL AND val_alpha <> ''::text AND val_alpha IS NOT
NULL)
"test_result_technically_abnormal" CHECK (reviewed_by_clinician IS
FALSE OR reviewed_by_clinician IS TRUE AND technically_abnormal IS NOT N
ULL)
"test_result_fk_reviewer" CHECK (reviewed_by_clinician IS FALSE AND
fk_reviewer IS NULL OR fk_reviewer IS NOT NULL)
"test_result_clinically_relevant" CHECK (reviewed_by_clinician =
false AND clinically_relevant IS NULL OR clinically_relevant IS NOT NULL)
Foreign-key constraints:
"$1" FOREIGN KEY (fk_type) REFERENCES test_type(pk)
"$2" FOREIGN KEY (fk_reviewer) REFERENCES xlnk_identity(xfk_identity)
=================================================
HL7 data
address@hidden
seperator:None
encoding_characters: ~\\&
sending_application:dhm
sending_facility:dlabsys
receiving_application:UNK
receiving_facility:UNK
date_time_of_message:200109122234
security:
message_type:ORU
message_control_id:06160
processing_id:D
version_id:2.3
sequence_number:
continuation_pointer:
accept_acknowledgment_type:NE
application_acknowledge_type:AL
country_code:AU
character_set:None
principal_language_of_message:None
address@hidden
set_id:1
external_id:
internal_id:JN1033482
alternate_id:49828852
patient_name:PENSIONER TESS MS
mother_maiden_name:
date_of_birth:19640717
sex:F
patient_alias:
race:
patient_address:26 MAIN ROAD ANYWHERE UNK
country_code:None
home_number:None
work_number:None
language:None
marital_status:None
religion:None
patient_account_number:None
ssn_number:None
driver_license:None
mother_identifier:None
ethnic_group:None
birth_place:None
multiple_birth_indicator:None
birth_order:None
citizenship:None
veteran_military_status:None
nationality:None
patient_death_date_time:None
patient_death_indicator:None
address@hidden
address@hidden
set_id:1
placer_order_number:
filler_order_number:00-49828852-1
universal_service_id:S00.46 BIOCHEM dlabsys
priority:
requested_date_time:200109120000
observation_date_time:200109121000
observation_end_date_time:
collection_volume:
collector_identifier:
specimen_action_code:
danger_code:
relevant_clinical_info:
specimen_received_date_time:
specimen_source:
ordering_provider:
order_callback_phone_number:
placers_field1:
palcers_field2:
filler_field1:
filler_field2:
results_report_status_change:200109122225
charge_to_practice:
diagnostic_service_sect_id:
result_status:F
parent_result:
quantity_timing: 200109120000
result_copies_to:None
parent_number:None
transportation_mode:None
reason_for_study:None
principal_result_interpreter:None
assistant_result_interpreter:None
technician:None
transcriptionist:None
scheduled_date_time:None
number_of_sample_containers:None
transport_logistics_of_collected_sample:None
collector_comment:None
transport_arrangement_responsibility:None
transport_arranged:None
escort_required:None
planned_patient_transport_comment:None
address@hidden
set_id:1
value_type:NM
observation_identifier:2000-8 Sodium LN
observation_sub_id:
observation_results:139
units:mmol/L
reference_range:135-145
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:2
value_type:NM
observation_identifier:14631-6 Bilirubin LN
observation_sub_id:
observation_results:14
units:umol/L
reference_range:0-20
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:3
value_type:NM
observation_identifier:2823-3 Potassium LN
observation_sub_id:
observation_results:5.7
units:mmol/L
reference_range:3.5-5.6
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:4
value_type:NM
observation_identifier:6769-4 ALP(Alk Phos) LN
observation_sub_id:
observation_results:76
units:U/L
reference_range:30-115
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:5
value_type:NM
observation_identifier:2075-0 Chloride LN
observation_sub_id:
observation_results:102
units:mmol/L
reference_range:99-108
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:6
value_type:NM
observation_identifier:2324-2 GGT(Gamma GT) LN
observation_sub_id:
observation_results:14
units:U/L
reference_range:0-45
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:7
value_type:NM
observation_identifier:1963-8 Bicarbonate LN
observation_sub_id:
observation_results:27
units:mmol/L
reference_range:23-33
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:8
value_type:NM
observation_identifier:2532-0 LD LN
observation_sub_id:
observation_results:142
units:U/L
reference_range:100-225
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:9
value_type:NM
observation_identifier:1920-8 AST LN
observation_sub_id:
observation_results:21
units:U/L
reference_range:0-40
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:10
value_type:NM
observation_identifier:22664-7 Urea LN
observation_sub_id:
observation_results:2.9
units:mmol/L
reference_range:2.1-9.0
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:11
value_type:NM
observation_identifier:1742-6 ALT LN
observation_sub_id:
observation_results:22
units:U/L
reference_range:0-40
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:12
value_type:NM
observation_identifier:2160-0 Creatinine LN
observation_sub_id:
observation_results:0.08
units:mmol/L
reference_range:0.06-0.13
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:13
value_type:NM
observation_identifier:2885-2 T-Protein LN
observation_sub_id:
observation_results:79
units:g/L
reference_range:60-80
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:14
value_type:NM
observation_identifier:2000-8 Calcium LN
observation_sub_id:
observation_results:2.48
units:mmol/L
reference_range:2.10-2.60
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:15
value_type:NM
observation_identifier:1751-7 Albumin LN
observation_sub_id:
observation_results:41
units:g/L
reference_range:38-55
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:16
value_type:NM
observation_identifier:18281-6 Corrected Ca LN
observation_sub_id:
observation_results:2.45
units:mmol/L
reference_range:2.10-2.60
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:17
value_type:NM
observation_identifier:10834-0 Globulin LN
observation_sub_id:
observation_results:38
units:g/L
reference_range:20-32
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:18
value_type:NM
observation_identifier:14879-1 Phosphate LN
observation_sub_id:
observation_results:1.08
units:mmol/L
reference_range:0.80-1.40
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:19
value_type:NM
observation_identifier:3084-1 Uric Acid LN
observation_sub_id:
observation_results:0.19
units:mmol/L
reference_range:0.15-0.36
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:20
value_type:NM
observation_identifier:14647-2 Cholesterol LN
observation_sub_id:
observation_results:5.4
units:mmol/L
reference_range:3.9-5.5
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
address@hidden
set_id:21
value_type:NM
observation_identifier:14927-8 Triglycerides LN
observation_sub_id:
observation_results:0.8
units:mmol/L
reference_range:0.5-1.7
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
---------------------
address@hidden
seperator:None
encoding_characters: ~\\&
sending_application:dhm
sending_facility:dlabsys
receiving_application:UNK
receiving_facility:UNK
date_time_of_message:200109122254
security:
message_type:ORU
message_control_id:06163
processing_id:D
version_id:2.3
sequence_number:
continuation_pointer:
accept_acknowledgment_type:NE
application_acknowledge_type:AL
country_code:AU
character_set:None
principal_language_of_message:None
address@hidden
set_id:1
external_id:
internal_id:AMN1032577
alternate_id:51911788
patient_name:EZKYOWNER ALF MR
mother_maiden_name:
date_of_birth:19600627
sex:M
patient_alias:
race:
patient_address:26 MAIN ROAD ANYWHERE UNK
country_code:None
home_number:None
work_number:None
language:None
marital_status:None
religion:None
patient_account_number:None
ssn_number:None
driver_license:None
mother_identifier:None
ethnic_group:None
birth_place:None
multiple_birth_indicator:None
birth_order:None
citizenship:None
veteran_military_status:None
nationality:None
patient_death_date_time:None
patient_death_indicator:None
address@hidden
address@hidden
set_id:1
placer_order_number:
filler_order_number:00-51911788-1
universal_service_id:HEPS.5 HEPATITIS SEROLOGY dlabsys
priority:
requested_date_time:200109120000
observation_date_time:200109120745
observation_end_date_time:
collection_volume:
collector_identifier:
specimen_action_code:
danger_code:
relevant_clinical_info:
specimen_received_date_time:
specimen_source:
ordering_provider:
order_callback_phone_number:
placers_field1:
palcers_field2:
filler_field1:
filler_field2:
results_report_status_change:200109122248
charge_to_practice:
diagnostic_service_sect_id:
result_status:F
parent_result:
quantity_timing: 200109120000
result_copies_to:None
parent_number:None
transportation_mode:None
reason_for_study:None
principal_result_interpreter:None
assistant_result_interpreter:None
technician:None
transcriptionist:None
scheduled_date_time:None
number_of_sample_containers:None
transport_logistics_of_collected_sample:None
collector_comment:None
transport_arrangement_responsibility:None
transport_arranged:None
escort_required:None
planned_patient_transport_comment:None
address@hidden
set_id:1
value_type:FT
observation_identifier:22034-3 REPORT LN
observation_sub_id:
observation_results:\\.nf\\ HEPATITIS SEROLOGY\\.br\\
\\.br\\ Hepatitis B Surface Ag Not Detected\\.br\\
Hepatitis C Ab Not Detected\\.br\\No evidence of current
hepatitis B infection (acute or chronic). Hepatitis
C\\.br\\seroconversion may be delayed and repeat testing up to 6 months
post exposure\\.br\\or clinical illness may be required to exclude
infection.\\.br\\\\.br\\
units:
reference_range:
abnormal_flags:
probability:
nature_of_abnormal_test:
observation_result_status:F
date_last_normal_value:None
user_defined_access_checks:None
observation_date_time:None
producer_id:None
responsible_observer:None
observation_method:None
- [Gnumed-devel] re: concrete mappings of v2.3 messages onto gnumed measurements.,
sjtan <=
- Re: [Gnumed-devel] re: concrete mappings of v2.3 messages onto gnumed measurements., Karsten Hilbert, 2005/03/05
- Re: [Gnumed-devel] re: concrete mappings of v2.3 messages onto gnumed measurements., Karsten Hilbert, 2005/03/05
- Re: [Gnumed-devel] re: concrete mappings of v2.3 messages onto gnumed measurements., Karsten Hilbert, 2005/03/05
- Re: [Gnumed-devel] re: concrete mappings of v2.3 messages onto gnumed measurements., Karsten Hilbert, 2005/03/05
- Re: [Gnumed-devel] re: concrete mappings of v2.3 messages onto gnumed measurements., Ian Haywood, 2005/03/05