This page documents search queries as understood by our xapian search engine (aka "the global search").
General xapian search query syntax is documented on the xapian website: https://getting-started-with-xapian.readthedocs.io/en/latest/concepts/search/queryparser.html.
The specifics of GeneNetwork's use of xapian differs slightly in the choice of prefixes and special syntax such as the synteny search. The examples below may help to illustrate it.
Search for the term "cytochrome" in the free text.
cytochrome
Search for the term "cytochrome" and the term "P450" in the free text (only results that have both are shown):
cytochrome AND P450
Search for occurrences of the term "cytochrome" near the term "P450" in the free text:
cytochrome NEAR P450
Search for the term "cytochrome" in the free text but exclude results that have the term "P450":
cytochrome -P450
cytochrome NOT P450
Search for results pertaining to the human species:
species:human
Search for results pertaining to the BXD group:
group:BXD
or
group:bxd
The above search is case-insensitive.
Search for results pertaining to chromosome 11:
chr:11
Search for results pertaining to the BXD group and chromosome 11:
group:BXD AND chr:11
Search for results with mean between 5 and 7:
mean:5..7
Search for results with mean less than 5:
mean:..5
Search for results with mean greater than 7:
mean:7..
To do a RIF search you can use the prefixes: RIF: or rif:. Here are some searches you can try out:
rif:Brca2
rif:Brca2 mean:2.4..2.404
rif:isoneuronal mean:12.103..12.105
rif:glioma symbol:shh
rif:diabetes
To do a WIKI search you can use the prefixes: WIKI: or wiki:. Here are some example searches:
wiki:nicotine
wiki:nicotine mean:12.103..12.105
wiki:addiction species:mouse
wiki:nicotine symbol:shh
wiki:glioma species:mouse group:bxd dataset:hc_m2_0606_p
Search for results near (+/- 50 kbases) base 9930021 of chromosome 4 of the human species and syntenic locations in other species:
Hs:chr4:9930021
Search for results near (+/- 50 kbases) base 9930021 of chromosome 4 of the human species and syntenic locations in mouse alone:
Hs:chr4:9930021 species:mouse
Search for results between base 9130000 and 9980000 of chromosome 4 of the human species and syntenic locations in mouse alone:
Hs:chr4:9130000..9980000 species:mouse
Alternatively, this same query may be expressed using kilo or mega suffixes:
Hs:chr4:9130k..9980k species:mouse
Hs:chr4:9.13M..9.98M species:mouse
Due to performance reasons, pure NOT queries are not supported.
A search such as: NOT author:hager will fail.
You will need to add something to the query to prevent the error, e.g.
species:mouse NOT author:hager
