DOI: 10.5281/zenodo.10526492
title: Two million URL resources and contexts extracted from full text (PubMed Central) and abstracts (PubMed) of biomedical articles

description: Recently, we created a dataset containing two million biomedical online resources (URLs) and their descriptive information from two biomedical literature repositories, PubMed and PubMed Central. The dataset is helpful for biomedical researchers to find nearly any possible biomedical resources in an integrated way, thereby improving the reuse of biomedical resources and the reproducibility of biomedical research.

One of the prominent features of this dataset is that it contains not only the URL, but also the descriptive information of the resource (we call it resource context), which describes how the resource is usually used by previous research as well as the functions of the resource and the type of the resource.

In order to facilitate access to resources, we also provide a retrieval system whereby researchers can locate the resources they need. The system is now under development. In additon, we also are preparing a research paper about this. Interested researchers can contact me. My email address is zlahu@foxmail.com.

 

Data Records:






Name



Data Type



Description





pmid_or_pmcid



string



identidier of the PubMed (PM) article or PubMed Central (PMC) article





pm_or_pmc



string



‘PM’ or ‘PMC’,





url



string



url, usually starting with ‘http’





url_context



string



sentence containing the url





url_start_position



int



position of the url in the sentence





url_domain



string



web domain of the url





pub_year



int



publishing year of the article





 

Examples:






pmid_or_pmcid



pm_or_pmc



url



url_context



url_start_position



url_domain



pub_year





5177603



PMC



http://crispr.mit.edu



EZH2 gRNA (CCGCTTCTGCTGTGCCCTTATC) was designed usinghref:http://crispr.mit.edu id:intref0010(CTMRK).



59



crispr.mit.edu



2016





5438617



PMC



http://firebrowse.org



RNA sequencing data sets and clinical information of kidney PRCC patients were downloaded from the TCGA repository website (href:http://firebrowse.org/).



130



firebrowse.org



2017





5854262



PMC



http://www.southbayrestoration.org



Changes to the available prey assemblage over time, due to large-scale regional habitat restoration (href:http://www.southbayrestoration.org) or ecological shifts in the managed pond habitats, could influence tern foraging.



107



southbayrestoration.org



2018





5854262



PMC



http://www.southbayrestoration.org



Consequently, the changes we observed in relative fish abundance returned to Forster’s tern colonies over the course of our study could be a result of changes in prey selection or may be the result of changes in fish availability because of altered habitat from management associated with the South Bay Salt Pond Restoration Project (href:http://www.southbayrestoration.org).



342



southbayrestoration.org



2018





5257025



PMC



http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database



The MALDI-TOF MS spectrum of ‘Ndongobacter massiliensis’ strain Marseille-P3170is available online (href:http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database id:intref0010).



110



mediterranee-infection.com



2016