From e4efbfee7b9f483374d78bd1a7ddbe971214eddc Mon Sep 17 00:00:00 2001 From: Hao Chen Date: Mon, 20 May 2019 07:57:28 -0500 Subject: documentation --- static/style.css | 3 ++- templates/about.html | 7 ++++++- templates/index.html | 2 +- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/static/style.css b/static/style.css index aa1bbd2..087c038 100644 --- a/static/style.css +++ b/static/style.css @@ -53,5 +53,6 @@ a:active { } #searchform{ - background:#F8F9F9; + background:#EBF5FB; + } diff --git a/templates/about.html b/templates/about.html index ea5e4c7..4d944e9 100644 --- a/templates/about.html +++ b/templates/about.html @@ -8,8 +8,13 @@

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. -

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. +

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 over 900 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 resulting 61,000 sentences are archived localy and can be accessed via the Addiction Genes link. We also archived 5.3 million PMIDs associatd with these gene for efficient search of query gene to addiction gene relations. + +

We also parsed the EBI GWAS catalog to obtain 23,000 genetics associations with addiction and psychiatric phenotypes. These results are included in the search by default. +

+We plan to update the local PubMed archive daily, the intermediate search results weekly and the EBI GWAS catalog quarterly. +

Source code diff --git a/templates/index.html b/templates/index.html index bbdebfa..7df2a4e 100644 --- a/templates/index.html +++ b/templates/index.html @@ -8,7 +8,7 @@ -- cgit v1.2.3

- 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?". To better answer this question, data from EBI GWAS catalog are also included in the search. + 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?". Data from EBI GWAS catalog are also included in the search to better answer this question.

The graph has many interactive elements. For example, clicking gene names 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?"