Entries and Subentries
The first query retrieves all SWISS-PROT entries that include "transmembrane" in the keywords index. The ftkey index, however, has a special type, allowing it to find features of a given type within entries. Thus the second query retrieves a set of subentries within SWISS-PROT entries. Each subentry is a transmembrane feature.
Note:The second query above will retrieve many more entries than the first because most transmembrane proteins have more than one membrane spanning segment. If you requested the sequences for the entries in the second set, you would get the transmembrane segments rather than the parent entry's sequence.
Links with Sets Containing Subentries
Simple Links
It is not possible to combine sets of entries with sets of subentries using the logical operators; however, link operators may be used between sets of entries and sets of subentries. For example:
returns a set of transmembrane segment subentries found in human proteins, whereas
returns all human proteins that have transmembrane segments.
Parent Links
Sometimes it is necessary to do an explicit conversion from subentries to entries. This can be done using the operand, parent. This method looks for links from the subentries to their respective parent entries and retrieves a set containing parent entries. For example:
retrieves the parent entries (the entries to which the subentries belong) for the set of subentries from SWISS-PROT that have transmembrane sequence features. Logical operators can then be used to combine the set of parent entries with another set of entries. Furthermore, as with other SRS query language commands, it is possible to combine the link to the parent entries and the subsequent operations into the same command, see section "More Complex Links using the Parent Operand"
More Complex Links using the Parent Operand
The command:
returns all entries that have the keyword, "transmembrane", or that have "transmem" sequence features. The index search [swissprot-ftkey:transmem] results in a set of subentries whereas the index search [swissprot-key:transmembrane] returns a set of entries. These sets cannot be combined directly using a logical operator. Instead, an extra step must be added, which finds the set of parent entries to which the subentries belong. The resultant set of parent entries can then be combined with the set from the second index search using a logical operator.
This type of search may be necessary to ensure all entries with a certain property are retrieved because the annotation is often incomplete.
