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

  articledoimedline-xmlnlpparseparserpmidpubmed-centralpubmed-parserpythonxml
  Language:Python 599

• 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

  bertbluebertevidence-based-medicineinformation-extractionlstm-crfnatural-language-processingpicopico-elementpico-frameworkpico-parserpubmed-abstractspubmed-parserrct-abstractstensorflow
  Language:Python 45
• 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 16

• nalomran / pubmed2doc

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

  bioinformaticsbiopythondocxfpdfpubmedpubmed-parserpython3
  Language:Python 13

• danielfrees / scrapemed

  ScrapeMed: Data scraping for PubMed Central.

  datadata-sciencedata-scraperembeddingsmedical-datapubmedpubmed-centralpubmed-parserpythonscrapingscraping-pythonscrapemed
  Language:Python 9

• 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

• PubData2XL / PubData2XL

  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 5

• 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

• 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

• AstraBert / BioMedicalPapersBot

  A Gradio bot to retrieve PubMed papers' title, doi, authors and publication date based on general search terms or on specific publication names

  academic-researchacademic-resourcesautomationpapersbiomedicalgradiopubmed-parserpythonscraping
  Language:Python 2
• puremoe

  jaytimm / puremoe

  An R package that provides streamlined access to multiple PubMed databases, including abstracts, bibliometrics, NER annotations, and full texts.

  pubmed-centralpubmed-parser
  Language:R 2

• 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 2

• kinleydhinata / PubMed-SyRev-Scraper

  A Python tool for systematic review scraping PubMed articles based on specified search queries.

  articlededuplicationdoiparserpmidpubmedpubmed-abstractspubmed-centralpubmed-parser
  Language:Python 1

• LynxUtz / PubMed-parser

  Parse PubMed data and get it into csv or plain text

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

  pubmed-parserpubmedlxmlpython3
  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

  bert-modelclinical-trialsevidence-based-medicineinformation-extractionknowledge-representationnatural-language-processingpico-frameworkpubmedpubmed-parser
  Language:Python 1

• zakcali / pubmedapi

  get document info from pubmedapi if PMID is known

  apiarticle-apiphppubmedpubmed-parser
  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

• elrf3lipes / ramon-s_portfolio

  I'm passionate about Cloud and DevOps, and for the moment I'm posting some of my work and personal projects here to showcase that. If its useful for you, feel free to integrate or contribute!

  api-integrationbiopythonclinical-trialsdata-extractiondata-parsingentrezipythonmedline-xmlpandaspubmed-parserrequestsdata-analysisdjangodockerrest-api
  0

• Kero76 / fdd

  Data mining repository

  school-projectxml-parserpubmed-parser
  Language:Java 0

• MattiaCazzolla / Ehealth-project

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

  pubmed-parserserious-game
  Language:C# 0

• ninnii55 / YAPPP

  Yet Another PubMed Python Parser

  pubmed-parserxml
  Language:Jupyter Notebook 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

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

  Rapid analysis of scientific papers from bioRxiv and PubMed

  2019-ncov2019-ncov-data-visbiorxivconnectomeconnectome-mappingdata-analysisdata-visualizationelectroactive-polymersnlppubmedpubmed-parserrasspberry-pischizophreniat-sneword2vec
  Language:Jupyter Notebook

• rsjaffe / mendeley-medline-update

  Update Mendeley keywords from medline (pubmed)

  awkmendeleypubmedpubmed-parserreference-managersqlite3
  Language:Awk

• shreyas1701 / Pubmed-PMC-Parser

  pmc-articlespmc-parserpmidpubmed-parserpython3retrivewebscraping
  Language:Python