GeneCup searches PubMed to find abstracts containing genes of interest and keywords in the custom ontologies.
+ The title and abstracts corresponding to the PMIDs are then retrieved 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. We also parse the GWAS catalog to obtain
+ genetics associations with the keywords of the custom ontology.
+
+
A list of curated addiction-related keywords can be used to search
+ addiction-related genes. We compiled the most studied 100 addiction related genes
+ 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
+ associated with these gene for efficient search of query gene to addiction gene relations.
+ We obtain 23,000 genetics associations with the addiction and psychiatric phenotypes from GWAS catalog.
+ These results are included in the search by default.
+
+
We plan to update the local PubMed archive daily and the EBI GWAS catalog quarterly.
+
+
+
+
+
+
-
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.
-
-
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 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.
-
-
+
-{%else%}
- No synonym for {{gene}} is found.
+ {%else%}
+ No synonym for {{gene}} is found.
{%endif%}
{% endblock %}
diff --git a/templates/index.html b/templates/index.html
index dc235c5..5849be9 100644
--- a/templates/index.html
+++ b/templates/index.html
@@ -2,52 +2,91 @@
{% block content %}
{{ message | safe }}
-
Relationship with Addiction Through Searches of PubMed
-
-
-
-
RatsPub is a tool to efficiently and comprehensively answer the question "What do we know about these genes and addiction?".
-
-
RatsPub answers this question by searching PubMed to find sentences containing the query terms (i.e., gene symbols) and over 300 drug addiction-related keywords that are organized into six categories. Data from NHGRI-EBI GWAS catalog are also included in the search. These gene-keyword relationships are presented as an interactive graph and a table.
-
Gene alias often include non-specific words and are thus not included in the initial search. However, a list of alias can be found by clicking on the gene symbol in the results section. These alias then can be searched with a single click.
-
-You can create an account if you need to save your results. Up to 30 gene symbols can be entered in the box below. Gene symbols can be separated by either a space or a semicolon.
- Example: Rgma Nrxn3 Chrna3.
-
-
- {%if "name" in session %}
- {{session['name']}}, your previous searches are available in the archive .
- {% else %}
- {% endif %}
-
-
-
-
-
-
-
-
-
-
-
-
+
Mining Gene Relationships from PubMed using Custom Ontologies
+
+
+
+
GeneCup is a tool to efficiently and comprehensively answer the question "What do we know about these genes and the topic I study?".
+ GeneCup answers this question by searching PubMed to find sentences containing gene symbols and a custom list of keywords.
+ These keywords are organized into a user defined ontology, which groups related keywords together for better organization of the results.
+ Human GWAS findings from NHGRI-EBI GWAS catalog are also included in the search.
+ These gene-keyword relationships are presented as an interactive graph and a table.
+
+ As an example, we present a curated ontology for drug addiction with over 300 keywords organized into seven categories.
+ A user account (free) is needed to create custom ontologies and save the search results.
+
+
+ {%if ("name" not in session) %}
+ By default, the addiction ontology is used. Custom ontologies can be created in user accounts.
+ Please choose keyword categories to be included in the search.
+
+
+
+ {% else %}
+ Welcome back, {{session['name']}}. Your previous searches
+ and custom ontologies are available from the links.
+
+
+
+ The {{ontol}} ontology is selected. Please choose categories to be included in the search.
+ Expect a longer wait time when you include Human GWAS category.
+
+
+ {% endif %}
+
+
+
+
+
+
+
+
+
+{%if "name" in session %}
+
+{% endif %}
+
{% endblock %}
diff --git a/templates/layout.html b/templates/layout.html
index 6bbfc95..00674af 100644
--- a/templates/layout.html
+++ b/templates/layout.html
@@ -10,13 +10,18 @@
- RatsPub: Relationship with Addiction Through Searches of PubMed
+ GeneCup: Mining Gene Relationships from Pubmed using Custom Ontology
+
+
{% with messages = get_flashed_messages()%}
- {% if messages %}
-
The custom ontology has four layers. The top layer is one single keyword serves as the name of the ontology. This keyword is used to select the ontology used for each search (i.e. via the dropdown menu). A new ontology will be created if the ontology does not already exist for the use. Keywords in the second layer describe the main concepts and are used to include/exclude groups of keywords for each search (via check boxes). All keywords under the same second layer are shown with the same color in the graphic output. Keywords in the third layer are shown in the results (both graphic and tabular). Keywords in the fourth layer are synonyms of those in the third layer. Results from all synonyms are grouped together and shown under the parent third layer keyword.
+
+{%if "name" in session %}
+ {{session['name']}}, your ontologies are available in the archive .
+{% else %}
+ The ontologies will be saved after login.
+{% endif %}
+
+{%if "email" in session %}
+
+{%else%}
+ Custom ontologies are available after login.
+{% endif %}
+
+
+
+
+
+
+
+
+{%if "name" in session %}
+
+ {% endif %}
+
+
+
+
+{% endblock %}
diff --git a/templates/passwd_change.html b/templates/passwd_change.html
index 43cc675..14605f9 100644
--- a/templates/passwd_change.html
+++ b/templates/passwd_change.html
@@ -22,8 +22,4 @@
-
-
-
-
{% endblock %}
\ No newline at end of file
diff --git a/templates/signin.html b/templates/signin.html
index f315d71..b4b13f3 100644
--- a/templates/signin.html
+++ b/templates/signin.html
@@ -12,7 +12,7 @@
- 