From 7509e0c07c2722a2bddc4c0829f14232e19a73ae Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Mon, 13 Feb 2023 18:14:32 +0000
Subject: Document xapian search query syntax.

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+# 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
+```
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