From fe2d644507548dcbaaf8d675d2e5c96795101d70 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 3 Dec 2023 09:39:57 -0600 Subject: Move xapian files --- topics/xapian/xapian-search-queries.gmi | 114 ++++++++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) create mode 100644 topics/xapian/xapian-search-queries.gmi (limited to 'topics/xapian/xapian-search-queries.gmi') diff --git a/topics/xapian/xapian-search-queries.gmi b/topics/xapian/xapian-search-queries.gmi new file mode 100644 index 0000000..74966f7 --- /dev/null +++ b/topics/xapian/xapian-search-queries.gmi @@ -0,0 +1,114 @@ +# 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 +``` + +## Gotchas + +### Pure `NOT` queries are not supported + +Due to +=> https://xapian.org/docs/apidoc/html/classXapian_1_1QueryParser.html#ae96a58a8de9d219ca3214a5a66e0407eacafc7c8cf7c90adac0fc07d02125aed0 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 +``` -- cgit v1.2.3