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Requirements for a General Nomenclature Validation Service
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.
Here is a list of functional requirements for such a service:
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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)
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ability to validate with version (e.g. 3.33.0) or “current” version (result may change over time)
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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)
| 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 |
This could possibly be built quickly my making a swagger-ized version of pyARD (which calls MAC) HPE: looks good to me. I am not aware of any HLAcore features that are not present here.