What's the difference between these two filtering alternatives when looking for all proteins available for a selected organism in NCBI? I get the double of proteins in 'noexp' case!
The reason for that seems to be that if you use [Organism:noexp], you get only those proteins linked directly to that taxonomy ID (Haemophilus parasuis without explicit strain designation). With [Organism:exp], this is expanded to include all associated tax IDs, so for all of the strains listed under
http://www.ncbi.nlm.nih.gov/taxonomy/?term=txid738[Subtree].
So with [Organism:noexp] you get only those entries that have the modifier
/db_xref="taxon:738" in their "source" feature, while [exp] also gets you things like
/db_xref="taxon:1322346" and so on that are grouped below 738.
Hope that helps a bit
Agreed with Christian. Also [Organism:exp] points to the data shown at column "Subtree links" in table listing "Entrez records" for each taxid entry on taxonomy database, on the other hand [Organism:noexp] points to the data shown at column "Direct links".
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