From 57dc1ef7a63f8c05e6d4369dbcd8eb0e51f40a64 Mon Sep 17 00:00:00 2001 From: Hao Chen Date: Sun, 19 May 2019 17:40:47 -0500 Subject: UI changes --- templates/about.html | 10 ++++------ templates/index.html | 32 ++++++++++++++++++++++++++------ templates/layout.html | 2 +- templates/topAddictionGene.html | 2 +- 4 files changed, 32 insertions(+), 14 deletions(-) (limited to 'templates') diff --git a/templates/about.html b/templates/about.html index 4ea4112..ea5e4c7 100644 --- a/templates/about.html +++ b/templates/about.html @@ -2,15 +2,13 @@ {% extends "layout.html" %} {% block content %} -

What does RatsPub do?

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About RatsPub ...

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RatsPub searches PubMed to find abstracts containing genes of interest and a list of curated addiction-related keywords. The abstracts corresponding to these returned PMIDs are then retrieve from a local archive of the PubMed. No limit on the date of publication is set. Each abstract is then broken down into sentences, which are then filtered by genes and keywords. +

RatsPub searches PubMed to find abstracts containing genes of interest and a list of curated addiction-related keywords. The abstracts corresponding to these returned PMIDs are then retrieve from a local archive of the PubMed. No limit on the date of publication is set. Each abstract is then broken down into sentences, which are then filtered by gene names and keywords. -

These gene-keyword relationships are presented as an interactive cytoscape graph. +

Clicking the links will bring up the corresponding sentences in a new browser window. Clicking the keywords will bring up the correponding search terms. Clicking the genes will start a new search to find sentences containing the target gene and the top 200 addiction genes. -

Clicking the links will bring up the corresponding sentences in a new browser window. Clicking the keyword nodes will bring up all the terms included. Clicking on the gene nodes will start a new search to find sentences containing that gene and the top 200 addiction genes. - -

The top 200 addiction genes were obtained by searching All human genes against addiction related keywords. The archived results for these top addiction genes can be accessed via the Addiction Genes link. +

The top 200 addiction genes were obtained by searching 29,761 human genes against addiction related keywords. To ensure comprehensive coverage, gene alias obtained from NCBI gene database were included in the search. The results were extensively curated to remove those alias that matched words that were not gene name or wrong genes. Some incorrect results remained because the same name also produced correct results. The archived results for these top addiction genes can be accessed via the Addiction Genes link.

Source code diff --git a/templates/index.html b/templates/index.html index b94853e..f5b6aea 100644 --- a/templates/index.html +++ b/templates/index.html @@ -4,16 +4,36 @@

Relationship with Addiction Through Searches of PubMed

- - This app searches PubMed to find sentences that contain the query terms (e.g., gene symbols) and keywords related to drug addiction. -
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+ RatsPub searches PubMed to find sentences that contain the query terms (i.e., gene symbols) and drug addiction-related keywords. These gene-keyword relationships are presented as an interactive graph that can efficiently answer the question "What do we know about these genes and addiction?" + +

In addition, clicking gene names in the graph will launch a new search for sentences containing the target gene and 200 addiction-related genes. These results help to answer the question "Are there genes that can link my gene of interest to addiction?" +

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+ + Up to 100 gene symbols can be searched at a time. Gene symbols can be separated by either a space or a semicolon. Gene alias will not be automatically included because the large number of false matches associated with gene synonyms retrieved from databases. +
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+ Example: Rgma Nrxn3; Chrna3 + +

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+ {% endblock %} diff --git a/templates/layout.html b/templates/layout.html index 08977c3..6a85473 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -22,7 +22,7 @@