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diff --git a/features/search.gmi b/features/search.gmi new file mode 100644 index 0000000..dad4373 --- /dev/null +++ b/features/search.gmi @@ -0,0 +1,44 @@ +# Search + +## Overview + +One of the key features of GN is the powerful search functionality. For most users it is the entry point for using the GeneNetwork web service. On the front-page a menu is offered that allows selecting species, e.g. mouse or rat, and relevant datasets grouped by family, e.g. BXD, and type, e.g. Hippocampus mRNA. +Recently we introduced the Xapian search engine that allows for fast lookups and powerful search queries. +A example search for the BRCA2 results in GN searching for the term "BRCA2" in 754 datasets and 39,765,944 traits across 10 species and found 7998 results that match the query. +The search URL looks like 'https://genenetwork.org/gsearch?type=gene&terms=BRCA2' and can be copy-pasted and shared with other users. + +More powerful queries will narrow down on field in the result table. For example to get only mouse results "species:mouse BRCA2" found 5916 results. + +Example search terms: + +``` +species:mouse BRCA2 - looks good, has Liver +species:mouse Tissue:Liver - 0 results +species:mouse tissue:Liver - 0 results +brca - only renders 2 results, why not BRCA2? +``` + +Keywords like tissue appear to be case sensitive. Should not be the case. + +GeneNetwork search functionality is used in the publication `Integrative Functional Genomics for Systems Genetics in GeneWeaver.org`. The authors present their webservice by searching for a "nociception" QTL in a region on chromosome 4 found in GN. They export the details and use it for further analysis in GeneWeaver\cite{bubier2016}. + +In the publication `Systems Genetics of Obesity` GeneNetwork search is used to find genes contributing to collagen content in adipose tissue in the BXD and find similar cis-eQTL connected with adipose tissue that exist in other studies hosted on GN\cite{brockmann2016}. + +In the paper `New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork' the authors reanalyzed an older experimental data in the GeneNetwork database. +They discovered QTLs on mouse chromosomes 3, 5, 9, 11, and 14, not found in the original study +and found new candidate genes included Slitrk6 and Cdk14. Slitrk6, in a Chromosome14 QTL for locomotion, was found to be part of a co-expression network involved in voluntary movement and associated with neuropsychiatric phenotypes. Cdk14, one of only three genes in a Chromosome5 QTL, is associated with handling induced convulsions after ethanol treatment, that is regulated by the anticonvulsant drug valproic acid\cite{PMC9024903}. + +## Future + +* Add human SNP search and synteny +* Support more sources, e.g. geneweaver + +## Methods + +GN search is built on +Xapian, an Open Source Search Engine Library, released under the GPL v2+. It's written in C++, with bindings to allow use from Python, Guile and other languages. +Xapian is actively maintained and current Xapian users include, for example, the Debian website and the notmuch E-mail indexer. +Xapian is a highly adaptable toolkit which allows developers to easily add advanced indexing and search facilities to their own applications. It has built-in support for several families of weighting models and also supports a rich set of boolean query operators\cite{Xapian}. +We build the Xapian index from SQL data and RDF data in the GN databases. + +=> topics/xapian-indexing.gmi indexing optimizations diff --git a/story-boards/.gitignore b/story-boards/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/story-boards/.gitignore @@ -0,0 +1 @@ +*.html |