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The noticeable differences between patent and journal extractions in Table 2 are that the later produce fewer compounds but more sequence identifiers.
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Notably, among the 9673 HPRD identifiers involved in PPIs, 119 were identified to correspond to obsolete nucleotide sequence identifiers, 4 corresponded to non protein-coding RNAs, while 16 were replaced by new nucleotide sequence identifiers; due to this updating, in three cases, two HPRD identifiers were assigned to the same nucleotide sequence identifier.
The reasons for less total sequence identifiers in patents are not only the target class restriction but also because activity data against non-human proteins is more commonly included in journal articles than patents.
These keys pointed to a list of template sequence identifiers.
(sequence identifiers can be found in Table S2).
Problems incurred by sequence alignment on long descriptions as sequence identifiers are also resolved.
Sequence identifiers without assigned GO terms were discarded.
In HPRD, the interactor identifier dictionary is used to update the nucleotide sequence identifiers to their currently active entries.
Only the primary one-to-one correspondence of the HPRD identifiers to nucleotide sequence identifiers was considered.
The different kinds of sequence identifiers included in the database are shown in Figure 3. Performing in-house annotations allowed us to discard any probe that could be associated with more than one gene.
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