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-rw-r--r--features/index.md6
-rw-r--r--features/introduction.md1
-rw-r--r--features/search.md7
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