Codebook todo

[gurnoor1990]

• [x] Update Hl7 codes
• [x] Add Hl7 codes to all list
• [ ] Make Biocompare ontology and add code list id (Idea dropped for the current version of codebook, we first release and develop an ontology later )
• [x] Check format standardization
• [ ] AGB-code (Hospital codes) (Idea dropped)

[gurnoor1990]

-DUOrestricted list

[aderidder]

For the NULL-values: https://decor.nictiz.nl/medicatieproces/mp-html-20160602T152837/voc-2.16.840.1.113883.1.11.10609-2011-07-26T000000.html

[gurnoor1990]

@aderidder

Hi Sander,

We have the same list in the FAIRgenomes codebook, but different codes. We are using, https://bioportal.bioontology.org/ontologies/HL7 ontology.

Do you think that this code system is ok? In the Waardelijst NullFlavor 2011‑07‑26, codes are represented by spaces. I think we can use these codes based on the HL7 ontology

Thanks! Gurnoor

value_en	description_en	codesystem	code	description_code
NullFlavor	NoInformation	HL7	C1553727	The value is exceptional (missing, omitted, incomplete, improper). No information as to the reason for being an exceptional value is provided. This is the most general exceptional value. It is also the default exceptional value.
Invalid (INV, nullflavor)	invalid	HL7	C3245471	The value as represented in the instance is not a member of the set of permitted data values in the constrained value domain of a variable.
Derived (DER, nullflavor)	derived	HL7	C3245521	An actual value may exist, but it must be derived from the provided information (usually an EXPR generic data type extension will be used to convey the derivation expressionexpression .
Other (OTH, nullflavor)	other	HL7	C1556044	The actual value is not a member of the set of permitted data values in the constrained value domain of a variable.The actual value is not a member of the set of permitted data values in the constrained value domain of a variable. (e.g., concept not provided by required code system).
Negative infinity (NINF, nullflavor)	negative infinity	HL7	C1550695	Negative infinity of numbers.
Positive infinity (PINF, nullflavor)	positive infinity	HL7	C1550694	Positive infinity of numbers.
Un-encoded (UNC, nullflavor)	un-encoded	HL7	C3242590	The actual value has not yet been encoded within the approved value domain.
Masked (MSK, nullflavor)	masked	HL7	C1555580	There is information on this item available but it has not been provided by the sender due to security, privacy or other reasons. There may be an alternate mechanism for gaining access to this information.
Not applicable (NA, nullflavor)	not applicable	HL7	C1272460	Known to have no proper value (e.g., last menstrual period for a male).
Unknown (UNK, nullflavor)	unknown	HL7	C1609613	A proper value is applicable, but not known.
Asked but unknown (ASKU, nullflavor)	asked but unknown	HL7	C1548672	Information was sought but not found (e.g., patient was asked but didn't know)
Temporarily unavailable (NAV, nullflavor)	temporarily unavailable	HL7	C1549057	Information is not available at this time but it is expected that it will be available later.
Not asked (NASK, nullflavor)	not asked	HL7	C1548670	This information has not been sought. (e.g., patient was not asked)
Not available (NAVU, nullflavor)	not available	HL7	C0686905	Information is not available at this time (with no expectation regarding whether it will or will not be available in the future).
Sufficient quantity (QS, nullflavor)	sufficient quantity	HL7	C1699029	The specific quantity is not known, but is known to be non-zero and is not specified because it makes up the bulk of the material. e.g. 'Add 10mg of ingredient X, 50mg of ingredient Y, and sufficient quantity of water to 100mL.' The null flavor would be used to express the quantity of water.
Trace (TRC, nullflavor)	trace	HL7	C1552622	The content is greater than zero, but too small to be quantified.

[aderidder]

What do you mean with "codes are represented by spaces"?

Are you planning to include the table itself as a value list? Or will you be using items from this table to add null-values to the "normal" value lists?

As these are null-values they have to become "exception" tags in the xml. ART-DECOR actually validates this. I'm not sure whether it detects the "trace" or whether it detects "trc" or something else, but still it makes sense that these should be exceptions and not regular values. Currently, the codesystem in my conversion software that will turn it into an exception tag is "NullFlavour", which is also known as codesystem 2.16.840.1.113883.5.1008. I could add "HL7" to also trigger this effect, but it doesn't have a codesystem id, since ART-DECOR doesn't already know it. So it's probably possible, but I'd have to look into it.

[gurnoor1990]

There are spaces in the codes	Niveau/ Type	Code	Weergavenaam	Codesysteem	Omschrijving
0-S	NI	NoInformation	NullFlavor
1-S	INV	invalid	NullFlavor
2-L	DER	derived	NullFlavor
2-S	OTH	other	NullFlavor
3-L	NINF	negative infinity	NullFlavor
3-L	PINF	positive infinity	NullFlavor
2-L	UNC	un-encoded	NullFlavor
1-L	MSK	masked	NullFlavor
1-L	NA	not applicable	NullFlavor
1-S	UNK	unknown	NullFlavor
2-S	ASKU	asked but unknown	NullFlavor
3-L	NAV	temporarily unavailable	NullFlavor
2-L	NASK	not asked	NullFlavor
2-L	QS	Sufficient Quantity	NullFlavor
2-L	TRC	trace	NullFlavor