{"id":21733,"date":"2021-05-25T07:17:51","date_gmt":"2021-05-25T14:17:51","guid":{"rendered":"https:\/\/www.novogene.com\/us-en\/?post_type=resources&#038;p=21733"},"modified":"2025-05-29T04:01:23","modified_gmt":"2025-05-29T11:01:23","slug":"free-paper-retrieval-artifact-pypubmed","status":"publish","type":"resources","link":"https:\/\/www.novogene.com\/us-en\/resources\/blog\/free-paper-retrieval-artifact-pypubmed\/","title":{"rendered":"Super easy to use free paper retrieval artifact: PyPubMed"},"content":{"rendered":"<p>\u00b7 Searching on PubMed but Internet speed is too bad?<br \/>\n\u00b7 File opening failed again! Published papers are too many to check and they cannot<br \/>\n\u00b7 I don&#8217;t want to read the abstract\/review one by one!<br \/>\n\u00b7 How to filter the impact factor, publication year, abstract? It makes me crazy when I got struggled to find a target paper!<\/p>\n<p>No need to worry anymore! With this PyPubMed gadgets, all of the problems will be solved!<\/p>\n<p>PyPubMed is a smart tool to make paper searching easier within a big database. The tool was conceived by Huan Yu, the director of Novogene Medical Department, and developed by Qingdong Su, the Senior Bioinformatics Engineer. It can help perform paper retrieval, output detailed information, and store it as an excel table quickly. With the tool, effective information will be easy to master, review and sort out.<\/p>\n<h2>Installation<\/h2>\n<p><strong>1. Install Python3 Environment<\/strong><\/p>\n<p>Enter the Python official website link:\u00a0<a href=\"https:\/\/www.python.org\/downloads\/\" rel=\"nofollow\">https:\/\/www.python.org\/downloads\/<\/a>, and click to download the installation package corresponding to your own system. Take Windows 10 system as an example.<\/p>\n<p><strong>1.1 Download and install the Windows installer (64-bit).\u00a0<\/strong><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.biostars.org\/media\/images\/ce60307c-831f-4d9a-b3d2-e4ed4dd9\" alt=\"Novogene-PyPubMed-1\" \/><\/p>\n<p><strong>1.2 During installation, check Add Python to the environment variability and complete.\u00a0<\/strong><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.biostars.org\/media\/images\/b37114f7-151d-41b6-a8a5-b7071df3\" alt=\"Novogene-PyPubMed-2\" \/><\/p>\n<p><strong>2. Install PyPubMed<\/strong><\/p>\n<p>Open the\u00a0<strong>command line<\/strong>\u00a0interface to operate: Windows system opens the command line (shortcut key is Win+R, enter cmd and press Enter), Mac system can directly enter the terminal operation interface.<\/p>\n<p>In the command line mode, execute the following command to install PyPubMed:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pip3 install PyPubmed\r\n<\/code><\/pre>\n<p><strong>Note:<\/strong>\u00a0All commands and parameters must be separated by at least one space. Non-Windows systems also need to be case sensitive;<\/p>\n<p>If the installation speed is too slow and an error is reported, you can use Alibaba Cloud mirroring to speed it up, now enter the following command:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pip3 install pypubmed -i https:\/\/mirrors.aliyun.com\/pypi\/simple\r\n<\/code><\/pre>\n<p>After installation, test whether the installation is successful, enter the following command line:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pypubmed\r\n<\/code><\/pre>\n<p>The following prompt appears, indicating that the installation is successful:<\/p>\n<ul>\n<li>Usage: pypubmed [OPTIONS] COMMAND [ARGS]&#8230;<\/li>\n<li>Toolkits for NCBI Pubmed<\/li>\n<\/ul>\n<p>View the current version:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pypubmed --version\r\n<\/code><\/pre>\n<p>Update pypubmed to the latest version:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pip3 install -U pypubmed\r\n<\/code><\/pre>\n<p><strong>3. Add API_KEY parameter<\/strong><\/p>\n<p>To increase the access frequency limit, the addition of API_KEY parameter for the first use is recommended.<\/p>\n<p>API_KEY generation method: Register NCBI account and log in, then visit the link below and click to generate your API_KEY. Link:\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/account\/settings\/#accountSettingsApiK\" rel=\"nofollow\">https:\/\/www.ncbi.nlm.nih.gov\/account\/settings\/#accountSettingsApiK<\/a><\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.biostars.org\/media\/images\/65df9339-4fc2-43e4-8569-73a95aef\" alt=\"Novogene-PyPebMed-3\" \/><\/p>\n<p>Input the command:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pypubmed -k YOUR_API_KEY search -h\r\n<\/code><\/pre>\n<p><strong>Note:<\/strong>\u00a0The -k parameter only needs to be added when it is used for the first time.<\/p>\n<h2>Function 1: Literature search function<\/h2>\n<p><strong>1. Keywords \/ PMID search<\/strong><\/p>\n<p>The commonly used method is to first use the PubMed advanced search function to get the logical fields that need to be searched and then use the pypubmed search command line to search and download the literature.<\/p>\n<p>You can enter the help command line pypubmed -h to view common commands and instructions for the first use.<\/p>\n<p>Here are a few commands to keep in mind:<\/p>\n<p>Options:<\/p>\n<ol>\n<li>-min, &#8211;min-factor FLOAT can limit the minimum impact factor of the documents to be retrieved.<\/li>\n<li>-l, &#8211;limit INTEGER, can limit the number of output documents (Important Reminder: It is recommended that each time you search, you must perform the NCBI keyword search result test according to your needs, get the best keywords and output the number of documents limit, too much output (eg tens of thousands) will cause problems such as too long running time).<\/li>\n<li>-o, &#8211;outfile TEXT, can specify the file name of the output result, the default is pubmed.xlsx.<\/li>\n<li>-c, &#8211;cache, when the translation is too slow or interrupted, the translated result can be stored in the cache file.<\/li>\n<\/ol>\n<p><strong>Query example:<\/strong>\u00a0You need to retrieve the keywords ngs and disease in the title or abstract and output the first 5 articles. Specify the output file name: ngs_disease.xlsx. We can first use PubMed advanced search function to get the field: NGS[Title\/Abstract] AND disease [Title\/Abstract], and then enter the following command:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pypubmed search \u201cNGS<span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span> AND disease<span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span>\u201d -l 5 -o ngs_disease.xlsx\r\n<\/code><\/pre>\n<p>In addition, you can also use PMID to retrieve. First use pubmed to export the txt file of the PMID after the query: pmid-NGSTitleAb-set.txt, save the path: C:\\Users\\Summer\\Desktop, and then enter the following command:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pypubmed search C: \\Users\\Summer\\Desktop\\pmid-NGSTitleAb-set.txt\r\n<\/code><\/pre>\n<p><strong>2. Advanced Search<\/strong><\/p>\n<p>If the search keyword logic field is relatively simple, you can use the pypubmed advance-search command line to search and download the literature. Enter the following command line:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pypubmed advance-search\r\n<\/code><\/pre>\n<p>For example, if you want to search the NGS literature on heart disease, follow the prompts to select:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\"><span class=\"token operator\">&gt;&gt;<\/span><span class=\"token operator\">&gt;<\/span> please choose a number of field <span class=\"token punctuation\">[<\/span>48<span class=\"token punctuation\">]<\/span>: 48\r\n\r\nyour choice is: 48-Title\/Abstract\r\n\r\n<span class=\"token operator\">&gt;&gt;<\/span><span class=\"token operator\">&gt;<\/span> please enter a search term: cardiopathy\r\n\r\nquery box now: <span class=\"token string\">\"cardiopathy\"<\/span><span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span>\r\ninput finish? <span class=\"token punctuation\">[<\/span>y\/N<span class=\"token punctuation\">]<\/span>: n\r\n\r\n<span class=\"token operator\">&gt;&gt;<\/span><span class=\"token operator\">&gt;<\/span> please choose a number of field <span class=\"token punctuation\">[<\/span>48<span class=\"token punctuation\">]<\/span>: 48\r\nyour choice is: 48-Title\/Abstract\r\n\r\n<span class=\"token operator\">&gt;&gt;<\/span><span class=\"token operator\">&gt;<\/span> please enter a search term: ngs<span class=\"token operator\">&gt;&gt;<\/span><span class=\"token operator\">&gt;<\/span> please input the logic <span class=\"token punctuation\">(<\/span>and, or, not<span class=\"token punctuation\">)<\/span> <span class=\"token punctuation\">[<\/span>and<span class=\"token punctuation\">]<\/span>: and\r\n<\/code><\/pre>\n<p>The final search fields are as follows:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">query box now: <span class=\"token punctuation\">(<\/span><span class=\"token string\">\"cardiopathy\"<\/span><span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span><span class=\"token punctuation\">)<\/span> AND <span class=\"token punctuation\">(<\/span><span class=\"token string\">\"ngs\"<\/span><span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span><span class=\"token punctuation\">)<\/span>\r\n<\/code><\/pre>\n<p>The number of retrieved documents is as follows:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">final query box: <span class=\"token punctuation\">(<\/span><span class=\"token string\">\"ngs\"<\/span><span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span><span class=\"token punctuation\">)<\/span> AND <span class=\"token punctuation\">(<\/span><span class=\"token string\">\"cardiopathy\"<\/span><span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span><span class=\"token punctuation\">)<\/span> count: 1detail: <span class=\"token string\">\"ngs\"<\/span><span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span>:14431, <span class=\"token string\">\"cardiopathy\"<\/span> <span class=\"token punctuation\">[<\/span>Title\/Abstract<span class=\"token punctuation\">]<\/span>:3534\r\n<\/code><\/pre>\n<p>If you need to download, you can continue the follow-up operation, but when the number of documents is large, this method of downloading is not recommended, and the aforementioned method is endorsed.<\/p>\n<h2>Function 2: Batch generation of document citation format<\/h2>\n<p>Enter the following command line:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pypubmed citations -h\r\n<\/code><\/pre>\n<p>Commonly used commands:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">-f, --fmt <span class=\"token punctuation\">[<\/span>ama<span class=\"token operator\">|<\/span>mla<span class=\"token operator\">|<\/span>apa<span class=\"token operator\">|<\/span>nlm<span class=\"token punctuation\">]<\/span>\r\n<\/code><\/pre>\n<p>the citation format of the final output.<\/p>\n<p>Query example: Export the reference format of 2 PMIDs: 33567694, 33546218, just enter the following command:<\/p>\n<pre class=\" language-bash\"><code class=\" language-bash\">pypubmed citations 33567694 33546218 -f apa\r\n<\/code><\/pre>\n<p>The query results are as follows:<\/p>\n<p>33567694Esposito, MV, Comegna, M., Cernera, G., Gelzo, M., Paparo, L., Berni Canani, R., &amp; Castaldo, G. (2021). NGS Gene Panel Analysis Revealed Novel Mutations in Patients with Rare Congenital Diarrheal Disorders. Diagnostics (Basel, Switzerland), 11(2), 262.33546218<br \/>\nMaggi, J., Koller, S., B\u00e4hr, L., Feil, S., Kivrak Pfiffner, F., Hanson, J., Maspoli, A., Gerth-Kahlert, C., &amp; Berger, W. (2021 ). Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases. International journal of molecular sciences, 22(4), 1508.<\/p>\n<hr \/>\n<p>PyPubMed is simple and fast to install, low in storage, convenient and efficient to use, and has won unanimous praise from users.<\/p>\n<p>Install and use it quickly, forward it and share the good things with your friends!<\/p>\n","protected":false},"featured_media":21737,"parent":0,"template":"","yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v20.8 (Yoast SEO v20.8) - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Super easy to use free paper retrieval artifact: PyPubMed - Novogene<\/title>\n<meta name=\"description\" content=\"With PyPubMed, a smart tool to make paper searching easier within a big database, effective information will be easy to master, review and sort out.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/free-paper-retrieval-artifact-pypubmed\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Super easy to use free paper retrieval artifact: PyPubMed\" \/>\n<meta property=\"og:description\" content=\"With PyPubMed, a smart tool to make paper searching easier within a big database, effective information will be easy to master, review and sort out.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/free-paper-retrieval-artifact-pypubmed\/\" \/>\n<meta property=\"og:site_name\" content=\"Novogene\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/NovogeneAmerica\/\" \/>\n<meta property=\"article:modified_time\" content=\"2025-05-29T11:01:23+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.novogene.com\/us-en\/wp-content\/uploads\/sites\/4\/2021\/06\/Novogene-pyPubmed-2.png\" \/>\n\t<meta property=\"og:image:width\" content=\"835\" \/>\n\t<meta property=\"og:image:height\" content=\"516\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@Novogene_Global\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"6 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/free-paper-retrieval-artifact-pypubmed\/\",\"url\":\"https:\/\/www.novogene.com\/us-en\/resources\/blog\/free-paper-retrieval-artifact-pypubmed\/\",\"name\":\"Super easy to use free paper retrieval artifact: PyPubMed - 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