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| -rw-r--r-- | templates/about.html | 36 | ||||
| -rw-r--r-- | templates/layout.html | 15 |
2 files changed, 28 insertions, 23 deletions
diff --git a/templates/about.html b/templates/about.html index bdf52f7..3cdefc5 100644 --- a/templates/about.html +++ b/templates/about.html @@ -7,25 +7,25 @@ <h3> About GeneCup </h3> <hr> - <p>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 - <a href="https://dataguide.nlm.nih.gov/edirect/archive.html">local archive of the PubMed</a>. - 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 + <p>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 + <a href="https://dataguide.nlm.nih.gov/edirect/archive.html">local archive of the PubMed</a>. + 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. - <p>A list of curated <a href="/ontology">addiction-related keywords</a> 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 <a href="/allTopGenes">Addiction Genes</a> 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. + <p>A list of curated <a href="/ontology">addiction-related keywords</a> 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 <a href="/allTopGenes">Addiction Genes</a> 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. - + <p> We plan to update the local PubMed archive daily and the EBI GWAS catalog quarterly. </div> @@ -37,9 +37,7 @@ Cite: Gunturkun MH, Flashner E, Wang T, Mulligan MK, Williams RW, Prins P, Chen H. <a href="https://academic.oup.com/g3journal/article/12/5/jkac059/6548160" target=_new>GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships.</a> G3 (Bethesda). 2022 May 6;12(5):jkac059. doi: 10.1093/g3journal/jkac059. PMID: 35285473; PMCID: PMC9073678. -<p> <a href="https://github.com/chen42/ratspub"> Source code </a> +<p> <a href="https://git.genenetwork.org/genecup/">Source code </a> {% endblock %} - - diff --git a/templates/layout.html b/templates/layout.html index 20dbcbe..814e5b6 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -4,7 +4,7 @@ <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta http-equiv="X-UA-Compatible" content="ie=edge"> - + <!-- Bootstrap CSS --> <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"> <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-wfSDF2E50Y2D1uUdj0O3uMBJnjuUD4Ih7YwaYd1iqfktj0Uod8GCExl3Og8ifwB6" crossorigin="anonymous"></script> @@ -20,7 +20,7 @@ <div class="col-1"> <a href="/"><div class='img'><img src="/static/white_logo.png" class="img-fluid", style="width:60%"></div></a> </div> - + <a class="navbar-brand" href="/">GeneCup</a> <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> @@ -95,10 +95,17 @@ {% block content %}{% endblock %} </div> +</ hr> +<div id="footer" align="right"> + <a href="https://git.genenetwork.org/genecup/">Source code</a> + | + Cite <a href="https://academic.oup.com/g3journal/article/12/5/jkac059/6548160">GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships. doi:10.1093/g3journal/jkac059. PMID: 35285473; PMCID: PMC9073678.</a> + | + Powered by Tensorflow on <a href="https://genenetwork.org/">GeneNetwork.org</a> +</div> + <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script> </body> - - |