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diff --git a/topics/xapian-search-queries.gmi b/topics/xapian-search-queries.gmi new file mode 100644 index 0000000..777ebf5 --- /dev/null +++ b/topics/xapian-search-queries.gmi @@ -0,0 +1,92 @@ +# Xapian search queries + +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. + +## Free text search + +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 +``` + +## Boolean filtering + +Search for results pertaining to the human species. +``` +species:human +``` + +Search for results pertaining to the BXD group. +``` +group:BXD +``` + +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 +``` + +## Boolean filtering using numerical ranges + +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.. +``` + +## Synteny search + +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 +``` |