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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







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