Biostar

695 results • Page 1 of 14

Hi, I've just downloaded from pubmed all articles inserted in pubmed from 2012/01/01 to 2012/12/31 using pubmed eutils. I saved all this datas in a db, but some...No elaboration is done with that articles, so i think that there's something wrong with pubmed eutils. I checked pubmed esearch, but the problem is not there. The duplicated articles, sometimes have different entrez

pubmed

updated 10.4 years ago • d.caliano

here: https://www.biostars.org/p/190968/ I am trying to get to a list of PMIDs from a list of Pubmed titles. I have learned that people query the Pubmed Entrez system through Reutils, or other tools, that are R compilers...Markov models in medical decision making: practical guide[Title]"' esearch(query_text, db="pubmed") Unfortunately, the result is: *Warning(s): PhraseIgnored in QuotedPhras…

Pubmed R Eutils Reutils Entrez

updated 7.3 years ago • daniele.sartori01

Hi all! I would like to write a program in python which will connect to PubMed database and according to rs number or nucleotide change find all PubMed Ids. In addition I would like to have PubMed

ncbi pubmed

updated 7.7 years ago • agata88

Tagging with MetaMap seems to be very computational intensive and hard to do for the full corpus of Pubmed. Is there a way to do tagging faster with less accuracy or is there maybe a source where I can download Pubmed tagged with

pubmed text

updated 13.3 years ago • Christiank

Until LinkedIn allows us to import our publications directly from ResearchGate, Google Scholar, Pubmed,... the LinkedIn's publications' section can be populated by searching by PubMed ID or by DOI though this GreaseMonkey...script: [LinkedIn PubMed Importer v1.4][1] [1]: http://alternateallele.com/alternatealle/2015/5/4/linkedin-pubmed-importer-v14

GreaseMonkey LinkedIn PubMed DOI

updated 10 months ago • Jorge Amigo

I have many PubMedID's, e.g., PubMed ID=10698474 for breast cancer study. And I want rsID's of the variants that are referred to in those study. How to get "rs...ID" from "PubMed ID"? I visited to the following PubMed site and find the publication (PubMed=10698474), but I didn't know what to do anymore...PubMed : https://pubmed.ncbi.nlm.nih.gov

pubmed rsid

updated 2.4 years ago • jn

Hi, I am using pubmed API to return some papers. My code is this: def search(query): Entrez.email = 'z.poorbahman1@fooo.bar' handle = Entrez.esearch...db='pubmed', usehistory = 'y', sort='relevance', retmax=str(_num), retmode='xml', …

Assembly

updated 4.6 years ago • z.poorbahman1

What is the best way to download PDFs from PubMed programmatically. For example, given a PubMed URL: http://www.ncbi.nlm.nih.gov/pubmed/9016068 Whats the best way to

pubmed

updated 11.9 years ago • sebrowns

Hi all, I have set of genes ( ASCL1, AEBP1, MLF1) i want to search PUBMED for literature in glioma. Means i want to get Pubmed Ids for these genes in glioma. To acheive this i tried biopython script...as follows from Bio Import Entrez Entrez.email = "my email" data = Entrez.esearch(db="pubmed",term = "ASCL1 and glioma", "AEBP1 and glioma") res=Entrez.read(data) PMID = res["IdList"] print PMID …

biopython

updated 10.7 years ago • Nitin

I know I can use elink to get the related GSE ID and GSM ID given a Pubmed ID. However, I found some papers have put their data on SRA but not on GEO, which I can't find the related data from a Pubmed...ID. Does anyone have ideas about how to get SRA informations routinely given a Pubmed ID (For example, this Pubmed ID: 23664764

pubmed sra geo

updated 10.7 years ago • Hanfei Sun

hi all, i have several paper abstracts and not the PubMed IDs. I wanted to know if there is a way to try to get the PubMed ID for that abstract, even if i had a list of probable IDs, then

pubmed

updated 3.4 years ago • win

of curiosity (I have no plans to actually do this), but I wonder how the various groups who analyse Pubmed abstracts for co-citation or gene-interaction (or anything else) actually access the data ? Do they run a lot of batch...pubmed searches and parse the results, do they access the pubmed database via some kind of web-service API, or is there a way of

pubmed text

updated 12.8 years ago • Lyco

Alex Trebek and Sasha Grey) and it'll draw the shortest path between them. Anything like this for Pubmed? Or could be adapted for Pubmed searches? Another thought would be something like a Wordle on author names to see which

text pubmed network

updated 13.2 years ago • Ryan D

I have a table of several thousands of pubmed ids, and I wonder if there is a smart way to infer the publication date for each of them. My first thought was to search...I have a table of several thousands of pubmed ids, and I wonder if there is a smart way to infer the publication date for each of them. My first thought was to search for...a table somewhere with a column of the pubmed id toge…

pmid year pubmed

updated 7.2 years ago • Giovanni M Dall'Olio

Hi, For pubmed search, I know there's a filter called free full text [sb] that allows you to get only free full text articles. But my question

pubmed

updated 10.5 years ago • d.caliano

I am trying to load pubmed locally. I downloaded all of the pubmed XML files provided by NCBI to create a local copy of pubmed. I searched if anyone...I am trying to load pubmed locally. I downloaded all of the pubmed XML files provided by NCBI to create a local copy of pubmed. I searched if anyone has done this before and I found a good paper "Tools for loading MEDLINE into a local relational da…

mysql data

updated 12.7 years ago • Smandape

Is there a way to retrieve an article's citation index via Pubmed or Pubmed's eutils or any other way in Pubmed/Entrez? Or a way to filter the search results based on citation index in...pubmed

Pubmed Citation TextMining

updated 9.9 years ago • vigprasud

Hi，guys I want to convert PubMed xml to other format, For example: endnote enw file RIS format BibTex Format Are there Projects in github that convert...PubMed xml file to other format? I would appreciate if could help me. thanks PS PubMed xml: http://eutils.ncbi.nlm.nih.gov/entrez...eutils/efetch.fcgi?db=pubmed&id=22805184&rettype=xml Endnote enw: %0 Journal Artic…

pubmed

updated 6.4 years ago • xiaoronglv

We've downloaded the [annual baseline PubMed data][1] and are in the process of installing [BaseX][2] to serve the XML files but I was wondering how the NIH do it - what type

pubmed database xml

updated 4.4 years ago • theoharis

I want to use a LinkOut tag as a select in PubMed e.g. Chemistry > BindingDB but this does not seem to be indexed in advanced search. Suggestions please? (yes I know I...I want to use a LinkOut tag as a select in PubMed e.g. Chemistry > BindingDB but this does not seem to be indexed in advanced search. Suggestions please? (yes I know I can...try NCBI help desk but a) I might get m…

PubMed

updated 2.3 years ago • cdsouthan

Dear all, I am looking for a library in Python to download abstracts from PubMed. I am looking preferentially for a library that allows to download abstracts, metadata, if it is cited from other papers...and so on. I have downloaded from PubMed in the past using a library in R, however my pipeline is in Python (after downloading and cleaning I will use a machine

python pubmed

updated 19 months ago • salvatore.raieli2

I am using Bio::DB::EUtilities to query the Pubmed DB with given PMIDs (Pubmed Id). use Bio::DB::EUtilities; use strict; use warnings; my @ids = (23298400); my $factory = Bio::DB::EUtilities...email => 'mymail@foo.bar', -db => 'pubmed', -retmode => 'xml', -id =&g…

perl bioperl xml pubmed eutils

updated 10.5 years ago • Matthias

I have a list of articles (couple hundreds) that I would like to download the full text from PubMed central in PDF. Unfortunately, even though all of them can be found at PubMed central, I can only download less than 10

ncbi pubmed

updated 19 months ago • pacman

Is there a way to query pubmed articles that includes the type of data included? For instance, suppose I wanted to locate all pubmed articles where...data and genotype data (of some kind) are both provided. some of this can be done using the pubmed advanced search page, here: https://pubmed.ncbi.nlm.nih.gov/advanced/. But, I dont see a way to filter by data availability...to anther ncbi site, …

search data pubmed query

updated 6 months ago • LauferVA

I am trying to automate routine pubmed searches for daily use. My goal is for the program to output the publications present on pubmed for that day e.g. to get...date +"%Y/%m/%d")[EDAT] query="\"$i[jour] AND $date\"" echo "$query" esearch -db pubmed -query "$query" | efetch -format abstract > ./$(date +"%Y-%m-%d")/"$i".txt done When I run the script, all I get are em…

bash pubmed

updated 4.1 years ago • nattzy94

I am trying to mine data or related paper from pubmed using R using library such as "RISmed" ,"rentrez" i will post the code so far what I have done library(RISmed) library(rentrez...to use that returned ID in the later code which is this fetch.pubmed <- entrez_fetch(db = "pubmed", id = your.ids, rettype = "xml", parsed = T) So can anyone help…

updated 7.3 years ago • krushnach80

I am currently writing a programme using Biopython and part of it involves searching Pubmed using an entry specified by the user. This returns all the records that match this entry. I then want to search just these...Entrez.email = "A.N.Other@example.com" def pbmd_search(): #searches pubmed database, using Biopython documentation handle = Entrez.egquery(term="brainbo…

Biopython pubmed

updated 7.4 years ago • flisstee

Is there any easy way to extract all the references using a batch Pubmed ID numbers

ncbi pubmed

updated 11.0 years ago • bioinfo

null; String WebEnv = ""; String query_key = ""; // STEP #1: search in PubMed for "cat" // try { eUtils.eUtilsServiceSoapClient serv = new eUtils.eUtilsServiceSoapClient(); // call NCBI ESearch utility...URL encoded eUtils.eSearchRequest req = new eUtils.eSearchRequest(); req.db = "pubmed"; …

pubmed webservice c

updated 11.9 years ago • sergiomanuelrodriguesdacosta

Hi, Is any tool/method to convert article title to pubmed ID? Anyone know? Thank you

pubmed

updated 10 months ago • BIOTIN

Is it possible to get the entire bibliography of a single paper through pubmed using eutils?. If not what are the alternatives? Thanks

pubmed reference eutils

updated 8.7 years ago • seqseek

I have a collection of several hundreds of Pubmed Abstracts. What I want to do is to extract all the gene names reported there. What's the best way to go about it programmatically...Later I'd simply create a hash with pubmed ID as keys and gene names as its members

pubmed

updated 10.1 years ago • gundalav

I m using this "PubMed-w2v.bin" from this tutorial [link][1] the last updates is on 2013 so is there any updated version available for the same...PubMed-w2v.bin ][2] [1]: https://jef.works/blog/2018/02/06/fun-with-word2vec/ [2]: http://evexdb.org/pmresources/vec-space-models

updated 5.8 years ago • krushnach80

I want to get all the results that are shown to a keyword search in European Pubmed Central. I want the resulting full-text articles to be downloaded into my database. Can I use REST API of European Pubmed

text-mining rest pubmed api

updated 21 months ago • davehresearch

Hi, For a given query, how can I retrieve a list of all the PMCIDs, from Pubmed Central, (using Java/Perl) that are returned. Thanks

pubmed text

updated 12.1 years ago • Yogesh Pandit

Hi, I am trying to extract PubMed records via Bio Python library based one some gene names (e.g. all pmids which contains these gene names in their Abstracts...similar gene Symbols (e.g. P53 for TP53) or Synonyms of them or not. And also, can I trust to PubMed filtering with this approach or I should get all of the abstracts and manually search/filter them. handle = Entrez.esearch...db=…

python biopython pubmed gene

updated 5.7 years ago • willson

I want to make a complex query / a lot of queries to pubmed api. My problem is I have a lot of gene symbols (~ 20.000) and some term as input (for example, inflammation). I want to search...through all pubmed titles and abstracts and get list of most popular genes that occure with the term. So my naive algorithm is to make 20000

pubmed

updated 10.0 years ago • fedotovp

host-pathogen pairs mentioned I asked about here I was thinking about using organism co-mentions in Pubmed articles. I can easily make a script that retrieves all of the PMIDS that result from a search for every organism name...more 'elegant' way of doing this. Does anyone know of an NLP tool for searching organism mentions in Pubmed ... or perhaps a database which annotates these? Thanks

updated 12.2 years ago • Will

So I'm using this "RISmed" library to do some query of my gene or protein of interest and the output comes with pubmed ID basically, but most of the times it consist of non-specific hits as well which are not my interest.As I can only see the pubmed ID so i have to manually put those returned ID and search them in NCBI to see if the paper is of my interest or not. So my question...this "RISmed"…

updated 7.4 years ago • krushnach80

Hi, I have a bunch of Pubmed IDs, and I need to generate citations for them. I know I can retrieve a specific Pubmed record's XML using annotate::pubmed...script to transform a set of IDs into a dataframe: https://www.r-bloggers.com/r-function-to-retrieve-pubmed-citations-from-pmid-number/ However, the script seems a little complex, and neither solution offers an easy way to generate

pubmed

updated 6.9 years ago • ericfournier3

I know how to search for a pubmed identifier in citeulike. Since yesterday I have tried to do the opposite that is to get all pubmed identifiers of collection

updated 12.0 years ago • Andra Waagmeester

392668221993529345 \tweet 392668221993529345 http://www.ncbi.nlm.nih.gov/pubmedcommons/ > **PubMed Commons** is a system that enables researchers to share their opinions about scientific publications. Researchers...can comment on any publication indexed by PubMed, and read the comments of others. PubMed Commons is a forum for open and constructive criticism and discussion of scientific.…

ncbi pubmed

updated 14 months ago • Pierre Lindenbaum

Hi, I'm using Pubmed Eutilities for Java to download a large set of articles. I First make a Esearch to download 1000 pubmed ids, then for each

pubmed java

updated 10.5 years ago • d.caliano

Hi guys Is it possible to buy / license a local copy of the entire pubmed / medline with full-text? Best, Kasper

text Pubmed mining Medline Full Data

updated 3.1 years ago • Stemcellmonkey

Hi, Any one help me out in downloading pdf full free articles from pubmed or from pmc database (both pmids and pmc ids are in bulk) Thank you

pubmed pmc api

updated 7.7 years ago • anithanagaraj93

I have [the URL for a file download][1] that lists the IDs of abstracts found in Pubmed. Here is the URL: Part of the URL is a HistoryID: NCID_1_1822965_130.14.18.97_5555_1553809026_4183211640_0MetA0_S_HStore...I have [the URL for a file download][1] that lists the IDs of abstracts found in Pubmed. Here is the URL: Part of the URL is a HistoryID: NCID_1_1822965_130.14.18.97_5555_1553809026_41…

pubmed etools eutils e-utilities entrez

updated 5.1 years ago • TerryH

10 abstracts for 10 specific mouse genes (for a total of 100 abstracts). I was thinking of searching Pubmed for it, so I put in my first gene (FOS) in the search bar. But there was no option (that I could find) for mentioning the species...either for 'Humans' or 'All organisms'. Since this is a pretty basic feature, I was hoping that Pubmed would allow it inherently. But it wasn't even mentione…

pubmed search

updated 7.0 years ago • c_u

I'm a doctor expert in fertility and especially in endometriosis. I saw good examples on how text mining on pubmed database and genes understanding could help. This disease remains very difficult to understand and the average delay...expert in fertility and especially in endometriosis. I saw good examples on how text mining on pubmed database and genes understanding could help. This disease rem…

text-mining fertility pubmed

updated 11 months ago • jeromebouaziz

Are there any lookup tables between PubMed IDs and Web of Science IDs? While I have both databases locally, matching through ISSN and title appears messy due to...PubMed, but not Web of Science, having migrated from print ISSN numbers to web-content ISSN numbers (and matching all entries

web of science pubmed

updated 7.2 years ago • unksci

DNA sequences extracted from biomedical articles. http://www.ncbi.nlm.nih.gov/pubmed/21325301 - Figure text extraction in biomedical literature. http://www.ncbi.nlm.nih.gov/pubmed/21249186 - LINNAEUS...pubmed/18614584 - BioLit: integrating biological literature with databases. http://www.ncbi.nlm.nih.gov/pubmed/18515836...the literature: a method for automatically tracking research results. ht…

pubmed papers full-text

updated 21 months ago • Casey Bergman

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