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The Path2Models branch of BioModels Database is not considered to be a frozen resource, and improved versions will be released as they are made available.
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The main difference to this study is that persistence to database was not considered in their study.
For calculations, drug target pairs that were only represented once in the database were not considered.
To avoid the possibility of sequencing errors in the EST database, the matches that were identified only once among the EST database were not considered.
For both MS and MS/MS, MASCOT scores falling below the 95% certainty criterion for the respective database were not considered significant.
Those variants, which do not cause any amino acid change and already reported as polymorphisms in databases, were not considered to be significant and were excluded from further analysis (data not shown).
Korean trials indexed in English-based databases were not considered.
Possible influences of different blast programs and the size of databases were not considered in setting the above E-value thresholds.
From the literature search, we found that there were substantial numbers of clinical trials on acupuncture in Korean literature, even though Korean trials indexed in English-based databases were not considered.
This was estimated by the fraction of peptides (from Type1_11-81aa set) having their best hits with a protein from a different (non-parental) KO-family, even when the members of their own KO-families were present in the reference database (self-hit is not considered).
In our subjective database, visible coding artifact is not considered by setting the quantization parameter (QP) to a certain smaller value.
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