Queries
All anatomy pages have a number of canned queries, driven from the menu bar. Queries are tailored to the type of entity (‘query from’ in the table below). Here, for example, is the neuropil query menu:
The choice of menu bar is currently driven by a system that runs queries to find members of key classes at start up and stores a lookup for these in java, but it may be more efficient in future to use boolean tests for class membership via Brain/Elk. All queries below are live queries via Elk.
| Query From | Query returns | query text | DL query with labels | DL query with IDs |
|---|---|---|---|---|
| neuropil | classes (neurons) | neurons with some part here | neuron that overlaps some X | FBbt_00005106 that RO_0002131 some X |
| neuropil | classes (neurons) | neurons with presynaptic terminals here | neuron that has_presynaptic_terminal_in some X | FBbt_00005106 that RO_0002113 some X |
| neuropil | classes (neurons) | neurons with postsynaptic terminals here | neuron that has_postsynaptic_terminal_in some X | FBbt_00005106 that RO_0002130 some x |
| neuropil | classes (neurons) | neurons with synaptic terminals here | neuron that has_synaptic_terminal_in some X | FBbt_00005106 that RO_0002110 some X |
| neuropil | classes (tracts) | tracts/nerves innervating here | ‘neuron projection bundle’ that innervates some X | FBbt_00005099 that RO_0002134 some X |
| neuropil | classes (clones) | lineage clones with some part here | ‘neuroablast lineage clone’ that overlaps some X’ | FBbt_00007683 that RO_0002131 some X |
| tract | classes (neurons) | neurons fasciculating here | neuron that fasciculates_with some X | FBbt_00005106 that RO_0002101 some X |
| clone | classes (neurons) | components | neuron that part_of some X | FBbt_00005106 that BFO_0000050 some X |
| neuropil | individuals (neurons) | Individual neurons with some part here (clustered by shape) | (‘exemplar_of’ some ‘cluster’) and (‘neuron’ that ‘overlaps’ some X)) | |
| clusters | individuals (neurons) | ‘member_of’ some (‘has_exemplar’ value <neuron name> | ||
| All anatomy | classes (mixed) | {pre-query for expression/phenotype} | part_of some X; cell that overlaps some X * |
neuropil = ‘synaptic neuropil domain’ OR ‘synaptic neuropil subdomain’ OR ‘syanptic neuropil block’ OR ganglion. Note that use of ELK means that OR is not available, so members of this grouping are found via multiple rounds of queries with elk and then combined. This could be made much more efficient by pre-generating a union class and then asserting inferred classification under found using a DL reasoner.
tract = ‘neuron projection bundle’
clone = ‘neuroblast lineage clone’
- The expression pre-query consists of 2 separate ELK queries. 1. part_of some X 2. cell that overlaps some X. We then check for cells that are not part_of X. These get flagged with a precautionary warning in the results that the phenotype or products of expression may be localised to regions of a cell other than those that are part of the queries neuropil.
The results of expression pre-queries are piped into queries annotation in FlyBase CHADO.