Blog of Andrés Aravena

2. Entrez query

09 November 2022

The key idea here is that [orgn:exp] will match entries associated with the given taxon and entries associated with taxa located under the given taxon in the taxonomy tree. In this case the taxon is a species, and the expanded taxa are subspecies and strains.

In contrast, using [orgn:noexp] will result in entries associated with the given taxon, and nothing more.

Student 1 100

Escherichia coli[orgn:exp] entrez in the protein database will give us all the proteins of all the E. coli strains have in the protein database. The entrez Escherichia coli[orgn:noexp] will give us the proteins that only Escherichia coli has. For example, first query shows us the proteins from Escherichia coli K-12, which is a strain of E. coli. So, the second entrez is more advanced in the manner of limiting; it only shows us the E. coli proteins, not the other proteins belonged to the strains of E. coli.

Student 2 30

When the query changes to Escherischia coli [orgn:noexp], result is for particular taxa. when it’s Escherischia coli [orgn:exp] it gives every data contains Escherischia coli. Result may not be specific to Escherischia coli and sequence may contain pieces from different species.

Student 3 90

When I search Escherichia Coli [Orgn:exp], I found 69873180 results in protein database. When I search Escherichia Coli [Orgn:noexp], I found 56811657 results in protein database. Changing part is expand or no expand which means, if we search expand we find all the searches and sequences includes E.coli and its subunit but if we search no expand we will only find results related with E.coli directly.

Student 4 90

The responses will be the Escherichia coli’s all proteins. Therefore, we can get nucleotide sequences, accession numbers etc. If we write Escherichia coli[orgn:exp] the results will be with subtrees. But if we write [orgn:noexp] there will be no subtrees, no expand, it will be smaller search space.

Student 5 90

When we enter the query as E.coli[orgn:exp], we saw the results of the all E.coli’s subtrees. But when we search as E.coli[orgn:noexp], we can reach the results about E.coli’s protein database not included subtrees.

Student 6 90

In the entrez with expand, it shows 69873180 results. With no expand, 56811657 results. Result numbers are changed. Because expand shows that all taxas about E. coli. But searching with noexpand shows just a particular taxas proteins.

Student 7 100

When I write Escherichia coli[orgn:exp], I see all of the entries that map into taxonomy at or below this taxon. Exp is related with the subtree links in taxonomy browser.. When I write Escherichia coli[orgn:noexp], I see entries that map directly to this taxon. Noexp is related with the direct links in taxonomy browser.

Student 8 50

escherichia coli[organism:exp] . 69873180 is the result of this search. If we change the query to escherichia coli[organism:noexp] then we got the number of 56811657. So the number decreeased. by searching with exp gives us everything that belongs to this taxa. That s why the number of exp search is higher than noexp.

Student 9 80

All protein sequences for all of the strains of Escherichia coli. All protein sequences for only Escherichia coli without its stains.

Student 10 99

İf we look the query Escherichia coli [orgn: exp] ,we find all protein in any strain of E.coli that contain subtrees(indirect link). However if we look Escherichia coli[orgn: noexp] , we find only E.coli protein without subtrees(direct link).

Student 11 99

The response to ““Escherichia coli [orgn:exp]”” is 69873180. In this query ““exp”” means, expand to subtrees, thus we get results including all of the substrains of E. coli.

If the query is ““Escherichia coli [orgn:noexp]”” the results do not include substrains of E.coli. Therefore, the result will be less than the other; 56811657 answers are resulted.

Student 12 99

If we write E.coli [orgn:noexp] we achieve only the protein results about this particular branch, it does not include all subspecies of E.coli. But, if we write E.coli[orgn:exp] we find more results because it includes protein results about all the subspecies of E.coli.

Student 13 90

Escherichia coli [orgn:exp] gives 69873180 results in protein database (It would give the same answer if I search without exp). If we search Escherichia coli [orgn:noexp] it gives 56811657 results in protein database. When wi say noexp it means that in the results don’t include expensional results.

Student 14 100

For the query Escherichia coli[orgn:exp] results include all the subtree links, meaning all the entries that map into the taxonomy at or below this taxon. 69873180 results.

For the query Escherichia coli[orgn:noexp] results include only direct links meaning only the entries that map directly to this taxon. 56811657 results.