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Table 2 Features of the ROG assignment score and their corresponding character representations.

From: iRefIndex: A consolidated protein interaction database with provenance

Character Description of feature (when the value is 1). Frequency1
P The interaction record's primary (P) reference for the protein was used to make the assignment. 79.196
D The source database (D) listed in the interaction record is different than what is expected for the given accession for the protein. In specific cases, this difference is tolerated and the assignment is made. 3.167
T The taxonomy (T) identifier for the protein (as supplied by the interaction record) differed from what was found in the protein sequence record. This discrepancy was tolerated and the assignment was made. 16.134
M The protein reference listed by the interaction record was a typographical modification (M) of a known accession. In specific cases, this variation is tolerated and the assignment is made. 0.289
V The protein reference listed by the interaction record contained version (V) information that was ignored. For example, RefSeq accession.version NP_012420.1 was listed but treated as RefSeq accession NP_012420. 0.591
Q The protein reference used to make the assignment was of the type "see-also". See PSI-MI Path: entrySet/entry/interactorList/interactor/xref/primaryRef/refType = "see-also". 0.003
U The protein reference listed in the interaction record and used to make the assignment was a secondary UniProt accession and was updated (U) to a primary UniProt accession in order to make the assignment. 2.817
E The protein reference was a retired NCBI Identifier. NCBI's eUtils (E) were used to retrieve the current accession and/or sequence. 1.537
I The protein reference used was an NCBI GenInfo Identifier (I). 1.741
G The interaction record's reference for the protein was an EntrezGene (G) identifier. The corresponding products of the gene were used to make the assignment. 0.581
S One of the interaction record's secondary (S) references for the protein was used to make the assignment. 20.804
+ More than one possible assignment is possible (+). This case may arise in one of three ways. 1) The reference supplied by the interaction record requires updating but more than one possibility exists. For example, Q7XJL8 was found to be a secondary accession in three separate UniProt records (Q3EBZ2, Q6DR20, and Q8GWA9). 2) The secondary references supplied by the interaction record point to more than one unique protein sequence. 3) An EntrezGene identifier is provided in the interaction record as a protein reference. This identifier points to more than one protein product. An attempt is made to resolve this ambiguity as indicated by ROG score features O, X or L (see below). 1.296
O More than one possible assignment is possible (see + above). The assignment chosen has a SEGUID that is identical to the SEGUID of the original (O) sequence provided in the interaction record. 0.469
X More than one possible assignment is possible (see + above). The assignment chosen has the same taxonomy (X) identifier as listed in the interaction record. 0.002
L More than one possible assignment is possible (see + above). The assignment with the largest (L) SEGUID is arbitrarily chosen (see Methods). 1.259
N The protein reference, taxonomy identifier and sequence for the protein as provided in the interaction record are used to make a new entry in the SEGUID table. The protein interactor is assigned the newly (N) generated ROG identifier. 2.024
  1. 1Total number of assignment scores where this occurs expressed as a percentage of all assignments (774,086).