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Requirements for a General Nomenclature Validation Service

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Michael Halagan edited this page Jul 18, 2018 · 8 revisions

Background

In order to provide validation of inputs and validation of "resolution" of inputs, we want PHYCuS to be able to reference a general nomenclature validation service.

Requirements

Here is a list of functional requirements for such a service:

  • ability to validate any HLA input string and determine if its is “valid"

    • accept WHO nomenclature (HLA-A*01:01:01:01)
    • accept shortening of names (HLA-A*01:01:01 or HLA-A*01:01)
    • accept shortening of loci (A*01:01:01:01)
    • accept MAC designations (HLA-A*01:AB)
    • accept GL strings (HLA-A*01:01:01:01/HLA-A*01:01:01:02+HLA-A*03:01:01:01)
    • accept G and P codes
    • accept WMDA codes (XXXX, NNNN, POS, NEG)

  • ability to validate with version (e.g. 3.33.0) or “current” version (result may change over time)

  • after establishing the validity, the service should have the ability to validate that any HLA input string is at the stated resolution

    • 1,2,3,4-field
    • G, g-NMDP, g-DKMS
    • P (only with version)
    • Serology

g-NMDP is nucleotide sequence based: a 2-field version of the corresponding G-group.

g-DKMS is amino acid sequence based: a P-group with nulls put back in.

In most cases these are the same.

HLA-C*02:10 is an example where the encoding is different. NMDP uses g-NMDP for frequency analysis but then converts to g-DKMS for the purpose of matching (C*02:10 is ARD match to C*02:02)

pyARD current functionality

Type Functionality pyARD
Validate HLA accept WHO nomenclature (HLA-A*01:01:01:01) yes
Validate HLA accept shortening of names (HLA-A01:01:01 or HLA-A01:01) yes
Validate HLA accept shortening of loci (A*01:01:01:01) yes
Validate HLA accept MAC designations (HLA-A*01:AB) yes
Validate HLA accept GL strings (HLA-A01:01:01:01/HLA-A01:01:01:02+HLA-A*03:01:01:01) yes
Validate HLA accept G and P codes no - It can create G groups, but doesn't check whether a provided G group is valid or not. This would be easy to add.
Validate HLA accept WMDA codes (XXXX, NNNN, POS, NEG) no
Validate Resolution 1,2,3,4-field yes
Validate Resolution G yes
Validate Resolution g-NMDP yes - Should double check that it's exactly as we defined it
Validate Resolution g-DKMS no
Validate Resolution With user defined mapping no
Validate Resolution P (only with version) yes
Validate Resolution Serology no
Validate with version Ability to validate HLA and resolution with specific IMGT/HLA DB versions yes

Discussion

This could possibly be built quickly my making a swagger-ized version of pyARD (which calls MAC)

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