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| author | Pjotr Prins | 2022-12-05 09:34:40 -0600 |
|---|---|---|
| committer | Pjotr Prins | 2022-12-05 09:34:40 -0600 |
| commit | 3c3f988521c8de0bc2b39637eedf01cd6d70131e (patch) | |
| tree | f3bf10b76d6148b5711ec62702f7d5757d899840 | |
| parent | e808ddf723dfb7d7a2094eec4d85e96e63ee7a3a (diff) | |
| download | gn-docs-3c3f988521c8de0bc2b39637eedf01cd6d70131e.tar.gz | |
Minor edits
| -rw-r--r-- | features/index.md | 6 | ||||
| -rw-r--r-- | features/introduction.md | 1 | ||||
| -rw-r--r-- | features/search.md | 7 |
3 files changed, 6 insertions, 8 deletions
diff --git a/features/index.md b/features/index.md index 34b0be6..4247410 100644 --- a/features/index.md +++ b/features/index.md @@ -2,6 +2,6 @@ In this section we describe GN features: -=> introduction.gmi Introduction -=> search.gmi Search for genes, QTL, SNPs, etc. -=> future-work.gmi Future work +* [Introduction](introduction.md) +* [Search](search.md) for genes, QTL, SNPs, etc. +* [Future work](future-work.md) diff --git a/features/introduction.md b/features/introduction.md new file mode 100644 index 0000000..e10b99d --- /dev/null +++ b/features/introduction.md @@ -0,0 +1 @@ +# Introduction diff --git a/features/search.md b/features/search.md index dad4373..363b356 100644 --- a/features/search.md +++ b/features/search.md @@ -18,7 +18,7 @@ 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. +FIXME: 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}. @@ -35,10 +35,7 @@ and found new candidate genes included Slitrk6 and Cdk14. Slitrk6, in a Chromoso ## 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. +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 |