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diff --git a/general/search/xapian_syntax.md b/general/search/xapian_syntax.md new file mode 100644 index 0000000..e849f65 --- /dev/null +++ b/general/search/xapian_syntax.md @@ -0,0 +1,100 @@ +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 |