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diff --git a/topics/features/genenetwork/search.gmi b/topics/features/genenetwork/search.gmi deleted file mode 100644 index dad4373..0000000 --- a/topics/features/genenetwork/search.gmi +++ /dev/null @@ -1,44 +0,0 @@ -# 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 |