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165 public repositories
matching this topic...
BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences
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Feb 26, 2020
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Jupyter Notebook
BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).
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Dec 2, 2020
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Python
NLP framework in python for entity recognition and relationship extraction
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Dec 18, 2020
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Python
Runs a pubmed query, returns results and allows user to explore high-level structure of returned documents
A high performance bibliographic information service
A framework for keeping biomedical text mining result up-to-date
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Jul 11, 2020
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Python
I, Librarian - open-source version of a PDF managing SaaS.
ReCiter: an enterprise open source author disambiguation system for academic institutions
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Dec 29, 2020
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Java
Retrieve and process PubTator annotations
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Oct 15, 2020
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Python
R Interface to Europe PMC RESTful Web Service
Sample code and explanations for doing basic text mining tasks in R
Code used to extract and analyse gender data from PubMed and arXiv in 2018 PLOS Biol paper
Get literature information via PubMed ID, such as the author, title, journal_name, pub_date and so on.
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Sep 11, 2016
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Python
Fetches PubMed article IDs (PMIDs) from email inbox, then crawls PubMed, Google Scholar and Sci-Hub for respective PDF files.
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Oct 23, 2018
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Python
Subclassification of disease states based on the intersection of literature and expression
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Jan 15, 2019
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Python
A Python package to download full article PDFs from OA publications
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Jul 18, 2019
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Python
Write PubMed search results with two display options (citation or listview) to PDF or Word
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Oct 18, 2020
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Python
EasyPubMed is an extension to make new PubMed easy to use
A web tool that helps biomedical researchers understand how their work is being used by others, by analyzing the content in papers that cite them
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Oct 19, 2018
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HTML
Scientific Paper Management Tool
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Dec 26, 2020
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Kotlin
Parse PubMed XML into a data frame in R
Batch scripts curating BioRxiv and PubMed articles by using Altmetric score.
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May 9, 2020
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Python
webpage crawling tools for pubmed, google scholar and rss
Trends in scientific publishing delays
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Mar 20, 2017
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Jupyter Notebook
Search Workbench is a tool for visually appraising, editing and comparing PubMed searches
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Apr 24, 2020
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JavaScript
index and query scripts for free reference bioinformatics datasets
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Jul 5, 2020
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Python
Monitor biomedical trends visually across ALL of PubMed + bioRxiv
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Oct 23, 2018
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Python
Query analysis pipeline framework
Analyzing diversity of ISCB keynote speakers & fellows compared to the field of bioinformatics
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Nov 23, 2020
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Jupyter Notebook
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Use "Open Access Journals" category in Wikipedia, to lookup journals. Available via DBpedia.org: