{"id":18967675,"url":"https://github.com/talschuster/biorxivretriever","last_synced_at":"2025-04-19T14:44:49.268Z","repository":{"id":57415263,"uuid":"263485188","full_name":"TalSchuster/BiorxivRetriever","owner":"TalSchuster","description":"Simple python retriever for Biorxiv articles","archived":false,"fork":false,"pushed_at":"2020-12-19T16:08:54.000Z","size":22,"stargazers_count":8,"open_issues_count":0,"forks_count":3,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-29T08:51:08.680Z","etag":null,"topics":["api","biorxiv","rxivist"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/TalSchuster.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-05-13T00:33:19.000Z","updated_at":"2025-03-15T00:19:14.000Z","dependencies_parsed_at":"2022-09-10T02:10:30.352Z","dependency_job_id":null,"html_url":"https://github.com/TalSchuster/BiorxivRetriever","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalSchuster%2FBiorxivRetriever","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalSchuster%2FBiorxivRetriever/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalSchuster%2FBiorxivRetriever/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TalSchuster%2FBiorxivRetriever/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/TalSchuster","download_url":"https://codeload.github.com/TalSchuster/BiorxivRetriever/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249213750,"owners_count":21231096,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["api","biorxiv","rxivist"],"created_at":"2024-11-08T14:44:38.348Z","updated_at":"2025-04-16T07:34:00.829Z","avatar_url":"https://github.com/TalSchuster.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"![PyPI - Python Version](https://img.shields.io/pypi/pyversions/biorxiv-retriever)\n![PyPI - Downloads](https://img.shields.io/pypi/dm/biorxiv-retriever)\n\n# BiorxivRetriever\nSimple python retriever for BioRxiv articles.\n\nWraps HTTP requests. Follow the guidelines and policies of [BioRxiv](https://www.biorxiv.org/tdm).\n\n# Purpose\nGiven a text query, search for relevant papers on BioRxiv and get their links and content.\n\n# Install\n\nInstall with pip:\n```\npip install biorxiv_retriever\n```\n\nAlternatively, clone this repo and install:\n```\ngit clone https://github.com/TalSchuster/BiorxivRetriever.git\npython setup.py install\n```\n\n# API\n```\nfrom biorxiv_retriever import BiorxivRetriever\nbr = BiorxivRetriever()\npapers = br.query('covid remdesivir')\n```\nTo get only titles and links without metadata and full text (when possible):\n```\npapers = br.query('covid remdesivir', metadata=False, full_text=False)\n```\n\nTo use [Rxivist](https://www.rxivist.org/) as the search engine (provides extra metadata but doesn't have all papers):\n```\nbr = BiorxivRetriever(search_engine='rxivist')\n```\n\n# Output\n\nExample output:\n```\n[\n{'title': 'Enisamium is a small molecule inhibitor of the influenza A virus and SARS-CoV-2 RNA polymerases',\n'biorxiv_url': 'https://www.biorxiv.org//content/10.1101/2020.04.21.053017v2',\n'posted': 'May 11, 2020.',\n'abstract': 'Abstract Influenza A virus and coronavirus strains cause a mild to severe respiratory disease that can result in death. Although vaccines exist against circulating influenza A viruses, such vaccines are ineffective against emerging pandemic influenza A viruses. Currently, no vaccine exists against coronavirus infections, including pandemic SARS-CoV-2, the causative agent of the Coronavirus Disease 2019 (COVID-19). To combat these RNA virus infections, alternative antiviral strategies are needed. A key drug target is the viral RNA polymerase, which is responsible for viral RNA synthesis. In January 2020, the World Health Organisation identified enisamium as a candidate therapeutic against SARS-CoV-2. Enisamium is an isonicotinic acid derivative that is an inhibitor of multiple influenza B and A virus strains in cell culture and clinically approved in 11 countries. Here we show using in vitro assays that enisamium and its putative metabolite, VR17-04, inhibit the activity of the influenza virus and the SARS-CoV-2 RNA polymerase. VR17-04 displays similar efficacy against the SARS-CoV-2 RNA polymerase as the nucleotide analogue remdesivir triphosphate. These results suggest that enisamium is a broad-spectrum small molecule inhibitor of RNA virus RNA synthesis, and implicate it as a possible therapeutic option for treating SARS-CoV-2 infection. Unlike remdesivir, enisamium does not require intravenous administration which may be advantageous for the development of COVID-19 treatments outside a hospital setting.',\n'full_text': '...'}\n]\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftalschuster%2Fbiorxivretriever","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftalschuster%2Fbiorxivretriever","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftalschuster%2Fbiorxivretriever/lists"}