pubmed-parser

There are 3 repositories under pubmed-parser topic.

• pubmed_parser

  titipata / pubmed_parser

  :clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

  pythonpubmed-centralpubmed-parserparsexmlmedline-xmlarticlenlpdoipmidparser
  Language:Python 548

• Rostlab / nalaf

  NLP framework in python for entity recognition and relationship extraction

  nlpbionlprelationship-extractionnermlpythonpubmedpubmed-parserpubmed-central
  Language:Python 112

• Tian312 / PICO_Parser

  A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework

  natural-language-processingpubmed-parserpicolstm-crfpubmed-abstractspico-elementrct-abstractspico-frameworkbluebertpico-parserbertevidence-based-medicineinformation-extractiontensorflow
  Language:Python 44
• ckblib

  dermatologist / ckblib

  Tools to create a clinical knowledge graph from biomedical literature. Includes wrappers for NCBI Eutils, cTakes annotator and Neo4J

  ctakeshacktoberfestknowledge-graphneo4jpubmed-abstractspubmed-parser
  Language:Java 14

• nalomran / pubmed2doc

  Write PubMed search results with two display options (citation or listview) to PDF or Word

  bioinformaticspubmedpubmed-parserpython3biopythonfpdfdocx
  Language:Python 13

• Xiaowen-JI / Semi-automation-of-systematic-review-of-clinical-trials-in-medical-psychology-with-BERT-models

  We employed pre-trained BERT models (distillBERT, BioBert, and SciBert) for text-classifications of the titles and abstracts of clinical trials in medical psychology. The average score of AUC is 0.92. A stacked model was then built by featuring the probability predicted by distillBERT and keywords of search domains. The AUC improved to 0.96 with F1, precision, and recall increasing to 0.95, 0.94, and 0.96 respectively. Training sample size of 100 results in the most cost-effective performance.

  nlpautomationsystematic-reviewsmedicalpsychologyrctpubmed-parser
  Language:Jupyter Notebook 8

• hscells / transmute

  PubMed/Medline query transpiler

  pubmedmedlinesystematic-reviewspubmed-parsermedline-parser
  Language:Go 7

• WengLab-InformaticsResearch / PICO_Parser

  A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework

  natural-language-processinginformation-extractionpubmed-parserevidence-based-medicinenamed-entity-recognitionabstractclinical-trialspico-frameworks
  Language:Python 7

• cakmakaf / fetch_PubMed_abstracts_by_keyword

  It provides a method of how to fetch articles along with their features and text from PubMed API.

  biopythoncysticfibrosisentrezegqueryfetch-apimedline-parsepubmed-abstractspubmed-keywordspubmed-parserpubmed-records
  Language:Jupyter Notebook 4

• danielfrees / scrapemed

  ScrapeMed: Data scraping for PubMed Central.

  datadata-sciencedata-scraperembeddingsmedical-datapubmedpubmed-centralpubmed-parserpythonscrapingscraping-pythonscrapemed
  Language:Python 4

• suqingdong / pubmed_xml

  PubMed XML Parser

  pubmedpubmed-parserpubmed-xml
  Language:Python 4

• arupgsh / PubmedScripts

  Python functions to curate data from NCBI and EUROPMC API.

  python3biopythonbioinformaticspubmed-parserpubmed-records
  Language:Python 2

• PubMed2XL / PubMed2XL

  Is a Django Python web application to download PubMed data into a Microsoft Excel spreadsheet and XML files.

  djangojavascriptpubmedpubmed-abstractspubmed-articles-grabberpubmed-parserpubmed-xmlpythonexcelxlsxxlsxwriter
  Language:HTML 2

• LynxUtz / PubMed-parser

  Parse PubMed data and get it into csv or plain text

  csv-exportextensionextension-packpubmedpubmed-parserresearch-tooltxt-files
  Language:JavaScript 1

• matteotolloso / BioCograph

  A tool capable of parsing datasets of papers from pubmed, annotating entities that appear using bio-BERT, creating a network of cooccurrences on which to perform analysis with various algorithms

  biobertbioinformaticscooccurrencenetwork-analysisnetworkxpubmedpubmed-parserpython
  Language:TeX 1

• michael-pagan / BIOF-309-Project

  BIOF 309 Intro to Python Final Project

  pythonbiopythonpubmedpubmed-parserpublications
  Language:Jupyter Notebook 1

• multivacplatform / multivac-pubmed

  Update PubMed articles daily on HDFS by using Spark Cluster

  apache-sparkdataframehadoophdfspubmedpubmed-parserspark-sqlyarn
  Language:Scala 1

• natc79 / PubMed

  Download and process documents from PubMed

  pubmedpubmed-parserscraper
  Language:Jupyter Notebook 1

• samiullah / pubmed_parser

  Pubmed Parser to get author emails in csv

  lxmlpubmedpubmed-parserpython3
  Language:Python 1

• shriharipathak / ncbi

  Crawling NCBI Pubmed Data using HTML and jQuery

  ncbi-databasepubmed-parserjqueryhtmlcrawler
  Language:HTML 1

• Tian312 / MEP

  Identify PICO elements and formulate Medical Evidence Propositions from clinical trial abstracts

  knowledge-representationnatural-language-processingevidence-based-medicinepico-frameworkinformation-extractionbert-modelclinical-trialspubmedpubmed-parser
  Language:Python 1

• zakcali / pubmedapi

  get document info from pubmedapi if PMID is known

  apiarticle-apipubmedpubmed-parserphp
  Language:PHP 1

• afnan / dxipher-js

  Reference conversion library for NodeJS. Import, Export and Convert between BibTex, EndNote, XML, JSON, and more...

  endnotepubmed-parserpubmed-jsonris-jsoncitationrefrencesresearchris-parserris-jsendnote-jszotero-parserbibtex-parser
  Language:JavaScript 0

• christirichards / pubmed-link-parser

  Link parser for PubMed URLs using the Simple HTML DOM parser and Clipboard.js

  bowerclipboard-jsgrunthtml-dom-parserpubmedpubmed-link-parserpubmed-parsersimple-html-dom-parser
  Language:CSS 0
• pubmedtk

  jaytimm / pubmedtk

  An R package for accessing a variety of PubMed data, including abstracts, bibliometrics, pubtations, and full-text records, through a single, user-friendly interface.

  pubmed-centralpubmed-parser
  Language:R 0

• MattiaCazzolla / Ehealth-project

  Project from the course 'E-health methods and applications' @ Politecnico di Milano

  pubmed-parserserious-game
  Language:C# 0

• tobias76 / BioParser

  Simple PubMed XML Parser

  pubmed-parser
  Language:Python 0

• VitalikVaseyko / Dynamic-Bernoulli-Embedding

  Connecting Biological Entities From Publication Abstracts

  pubmed-parser
  Language:Python 0

• hashemi / refparser

  Python 3 library for parsing academic references in RIS or MEDLINE formats

  parserpython3medlinepubmed-parsercitationsreferencespubmedbioinformatics
  Language:Python

• Kero76 / fdd

  Data mining repository

  pubmed-parserschool-projectxml-parser
  Language:Java

• lmandres / PubMed-Publications-Search

  Script that creates automatic searches based on author names, grant numbers, or organizations.

  pubmedpubmed-parserpubmed-records
  Language:Python

• OldBonhart / EDA-NLP-PubMed-and-bioRxiv

  Rapid analysis of scientific papers from bioRxiv and PubMed

  biorxivpubmedpubmed-parsert-sneword2vecdata-visualizationdata-analysisnlpelectroactive-polymersschizophreniarasspberry-piconnectome-mappingconnectome2019-ncov-data-vis2019-ncov
  Language:Jupyter Notebook

• rsjaffe / mendeley-medline-update

  Update Mendeley keywords from medline (pubmed)

  awkmendeleypubmedpubmed-parserreference-managersqlite3
  Language:Awk

• sablokgaurav / pubmed_indexer_abstract_fetcher

  This function will prepare the abstract and the id information for all the pubmed articles that you want to read and have as a citation. I coded this using a web scraping approach and it is blazing fast and parses better than ncbi eutils

  bioinformaticscorpusgenomicslanguage-modellanguage-modelingnatural-language-processingpubmedpubmed-parser
  Language:Python

• shreyas1701 / Pubmed-PMC-Parser

  webscrapingpython3pubmed-parserpmc-articlespmc-parserpmidretrive
  Language:Python