From 3395fa4a5252fd3c42785b4f7ae53a0f2d5020bd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 27 Jun 2024 16:39:26 -0500
Subject: Create xapian_syntax.md

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+Global 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](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
+
+*   [performance reasons,](https://xapian.org/docs/apidoc/html/classXapian_1_1QueryParser.html#ae96a58a8de9d219ca3214a5a66e0407eacafc7c8cf7c90adac0fc07d02125aed0)
+
+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
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