Congruence¶

SeroTools evaluates multiple levels of congruence for comparisons between serovar designations.

exact¶

Exact matches must meet one of the following criteria:

Two serovar designations are the identical string:

Corvallis                  Corvallis
I 8,[20]:z4,z23:[z6]       I 8,[20]:z4,z23:[z6]

Every antigenic factor (required or optional) matches:

Corvallis                  I 8,[20]:z4,z23:[z6]
I 8,[20]:z4,z23:[z6]       I 8,20:z4,z23:z6
I 1,3,10,19:f,g,t:1,(2),7  I 1,3,10,19:f,g,t:1,2,7

Neither serovar designation includes any antigenic factors, and the subspecies designations match:
```
I ::                       I –:–:–
II :                       II –:
```

congruent¶

Congruent matches must meet the following criteria:

The subspecies field must be present for both serovars or neither.

All required antigenic factors match. For example:

I 6,7,14:g,m,s:–          I 6,7,[14],[54]:g,m,[p],s:–
I 6,7:g,m,s:–             I 6,7,[14],[54]:g,m,[p],s:[1,2,7]
Amager var. 15+           Amager
I 3,15:y:1,2:[z45]        I 3,{10}{15}:y:1,2:[z45]
6,7:k:[z6]                6,7:k:–

minimally congruent¶

Minimally congruent matches must meet the following criteria:

Every antigen of at least one serovar can be considered a formal subset of the corresponding antigen (no direct conflicts). For example:

I 6,7,14,[54]:g,m,[p],s:–     6,7,[14],[54]:g,m,[p],s:–
I                             I 6,7,8,[14],[54]:g,m,[p],s:–
I 7:g:–                       I 6,7:g,m,s:–
Gallinarum                    Enteritidis

Note - the empty set (–) is a subset of every set

The minimally congruent designation is unique to SeroTools and is useful for distinguishing between two scenarios:

Serovars which differ due to sample misannotation (incongruent)
Serovars derived from correctly annotated samples with variation based solely on missing information. When comparing serovar designations, minor differences may be expected due to method-specific irregularities, for example reagent variation for laboratory-based techniques or the presence of nonproductive genomic data when comparing antigenic agglutination to in silico-based techniques. Our assumption is that these minor method-specific differences are more likely manifested as missing data (e.g. all but one of the correct factors were detected) than direct conflicts.

incongruent¶

Any comparison which is not minimally congruent. For example:

I                             II
I 1:                          1 2:
Javiana                       Saintpaul
I 7,8:g,m,s:–                 I 6,7,[14],[54]:g,m,[p],s:[1,2,7]
I 4,5:a,b:6,7                 I 5:a,b,c:6,7