Biostar

695 results • Page 2 of 14

now as (UniProt AC; MeSH ID). I'd like to have an idea of what proportion of these pairs co-occur in PubMed abstracts and titles. Diseases are not an issue because I already have the MeSH term, which I can query directly in PubMed

updated 11.4 years ago • miquelduranfrigola

this error? If not, can someone direct me towards the right package where I do multiple different pubmed search. Thank you

R pubmed

updated 6.5 years ago • Bioinformatician_in_trouble

PubTeX is a tool which lets you convert all PubMed IDs in your latex file/document to BiBTeX as well as generate the latex inline citations! Feel free to try out the example

pubmed

updated 14 months ago • by0

Hi, Please if anyone could help me, I want to download few thousands pubmed articles and organize in some format so that later on I could read it through python to identify the MeSH terms and...Hi, Please if anyone could help me, I want to download few thousands pubmed articles and organize in some format so that later on I could read it through python to identify the MeSH terms and kind

PubMed

updated 21 months ago • dreamzz.4you

I'm interested in Biomedical Literature Mining (Text mining of pubmed abstracts). I found that 'Pubmed.mineR' is one of useful packages for it. I'd be thankful if you suggest me some other good

Biomedical literature mining R Pubmed abstracts

updated 7.7 years ago • Mina Sohrabi

Hi everyone, Mine is a very very basic question. How can we make the Pubmed search results be less in number but accurate at the same time? I have read about the usage of quotes and AND/OR but that...am looking for KRAS gene related treatment options basically. Does anyone have any documentation on Pubmed search. I remember seeing it on internet once, but not able to locate it again. Thank you…

PubMed

updated 17 months ago • Bioinformatician_in_trouble

After I run my esearch in pubmed I return a list of IDs for publications. I found the following info by running einfo on pubmed" # {'Name': 'pubmed_protein_weighted...Links to protein', 'DbTo': 'protein'} # {'Name': 'pubmed_snp', 'Menu': 'SNP Links', 'Description': 'PubMed to SNP links', 'DbTo': 'snp'} # {'Name': 'pubmed_protein_refseq', 'Menu': 'Protein (RefSeq) Links', 'Description…

protein fasta Biopython Entrez

updated 13 months ago • m.brathwaite

Hi there, I am trying to fetch author names and articles' titles from pubmed. The only issue in this code is, it is giving title of articles in this form: `['R', 'o', 'u', 't', 'i', 'n', 'e', ' ', 'A', 'm', 'o', 'x', 'i', 'c', 'i', 'l', 'l', 'i', 'n', ' ', 'f', 'o', 'r', ' ', 'U', 'n', 'c', 'o', 'm', 'p', 'l', 'i', 'c', 'a', 't', 'e', ']` I mean...1}...'.format(MAX_COUNT, TERM)) Entrez.email = …

python pubmed

updated 23 months ago • dreamzz.4you

here. I want to to use RISmed package or any other package in R in order to download all the PubMed's abstracts, not a particular abstract related to a particular keyword. Is there anyone to help me in this case? Thanks

updated 4.3 years ago • saber mohammadi

I'm trying to set up a PubMed query using Entrez and MEDLINE to retrieve journals about a complicated subject. I want to retrieve the most relevant...record = Entrez.read(handle) for row in record["eGQueryResult"]: if row["DbName"]=="pubmed": print(row["Count"]) handle = Entrez.esearch(db="pubmed", term=TERM, …

Biopython Entrez Pubmed MESH medline

updated 4.9 years ago • pl640

I'm doing a project which includes data mining but for that I want to build a crawler which extract pubmed articles ids using a single term like cancer or tumor? (semantics based ) I'm currently working in python. If someone is

R python pubmed pubmedlookup

updated 6.2 years ago • aqsaawan.459

Bio2RDF (doi:10.1016/j.jbi.2008.03.004) has a SPARQL end point for PubMed, but the amount of data is so large, that a query for all properties already gets rejected because it would take too much

pubmed

updated 12.8 years ago • Egon Willighagen

I have a list of pubmed IDs and am trying to use literally any tool to access any 1) paper authors 2) date of publication and 3) MESH terms (or other...def search(query): Entrez.email = 'your.email@example.com' handle = Entrez.esearch(db='pubmed', sort='relevance', retmax='10', retmode='xml', …

MESH terms text mining pubmed esearch entrez

updated 3.9 years ago • bioguy

Dear All, Anyone can share a R command to download all abstracts of Nature in 2020 from Pubmed Thanks

pubmed abstract

updated 3.8 years ago • Shicheng Guo

Hello, I am new to text mining and am looking for a way to obtain a dump of pubmed abstracts based on a keyword input. I would like to do this in Python since I have some experience with that. I would appreciate...E D I T ------------------------------------------------- I have a list of pubmed id's and am wondering how to incorporate them into a python script which will then fetch it's corresp…

updated 7.0 years ago • ruchiksy

Hello everyone, reading this post http://www.biostars.org/p/10026/ I am asking myself if there are lists, which link gene IDs to pubmed IDs. I found some papers addressing this problem. But since text mining is just a small piece of my current project, I don...http://www.biostars.org/p/10026/ I am asking myself if there are lists, which link gene IDs to pubmed IDs. I found some papers address…

updated 11.4 years ago • Mdeng

Hi everyone, Would you please provide me a solution for pubmed searching for all Nature journals (Nature Biotech, Nature Mol Cell Biol, Nature protocols, etc.). I only know the method

pubmed

updated 2.1 years ago • biolab

I have list of terms. I want to download all the articles from pubmed for each term at a time. Is there any possible to download using any programming code

pubmed abstracts programming

updated 5.0 years ago • sreejanani31

I am interested in doing some natural language processing on the corpus of [MEDLINE/PubMed journal citations](https://www.nlm.nih.gov/bsd/licensee/medpmmenu.html). I have recently become aware of Apache Solr...with Solr, but I'm not quite sure how to translate the advice into what is necessary for MEDLINE/PubMed

NLP solr medline lucene pubmed

updated 2.6 years ago • paulparsons

Hi All, I have about 2,500 abstracts achieve from Pubmed and I want to extract all the **disease name** from these abstracts. Is there any recommended approach to do it? Thanks. Update

abstract disease id

updated 4.4 years ago • Shicheng Guo

I learned something new about PubMed today. I was recently working on a grant application and found myself helping a collaborator prepare her biosketch...collection on your [myNCBI][2] page to create a public link. An easy way to do this is to create a pubmed search result with all your papers and then hit 'Send to' -> 'My Bibliography' (while signed into myNCBI). We had a pubmed query...…

pubmed

updated 21 months ago • Obi Griffith

I'm trying to understand how to fetch recently published documents appearing in Pubmed. It's not as straightforward as you would think. Mostly I'm confused by how PDAT works. In the XML, PubDate only has month...19"[PDAT] : "2012/10/31"[PDAT] gives 21679 results There's no Day field in the Article Element of Pubmed XML for most articles. See here: qplot of PubDate/Day extracted from XML If t…

pubmed search

updated 11.5 years ago • Mr. Gunn

Hi, I have to download a large set of articles from pubmed. I first make an esearch and then for each PMID i make an efetch. The problem is that i have to discern what articles are

pubmed java

updated 10.5 years ago • d.caliano

GoPubMed is a famous third party PubMed search engine. User can filter their search result by country List item keywords MeSH Tree research To develop this

pubmed database

updated 12.0 years ago • xiaoronglv

Hi, I have to download from pubmed all articles inserted into the database within a certain date. I do it, by inserting the filter, [edat] in the esearch request

pubmed java

updated 10.5 years ago • d.caliano

provided by NCBI Taxonomy for the species or strain/isolate GeneID: unique identifier for a gene PubMed ID (PMID): unique identifier in PubMed for a citation Opening the file in Notepad++ i see over 12mil lines, 1 for each unique

genome gene

updated 3.8 years ago • eulianova89

I remember that there is a website that can help users to find a pubmed abstract based on its similarity with a paragraph of text. But I don't remember the name of such a website. Does anybody

pubmed abstract

updated 2.2 years ago • cardinal2818413

Hi, I am trying to get pubmed id with bio for all papers that an article was cited by. For example this nlmcatalog (ID: 0407712) http://www.ncbi.nlm.nih.gov...pubmed?LinkName=nlmcatalog_pubmed&from_uid=407712 Python 2.7.11+ (default, Apr 17 2016, 14:00:29) [GCC 5.3.1 20160413] on linux2...A.N.Other@example.com" >>> results = Entrez.read(Entrez.elink(dbfrom="n…

software error gene

updated 7.9 years ago • arching

How can I extract mutations/variants from Pubmed/PMC articles using terms and without need to download these articles? Any command line tool I can do that

variants

updated 4.0 years ago • dasilvauirajan

I have downloaded pubmed articles from ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/ - the files come in nxml format, and I would like to maneuver

nxml parsing pubmed

updated 6.5 years ago • Quak

Hi all, I needed to annotate variants with PubMed database. To do that I've written program in python with the use of Entrez library. It sends about 10000 question to database...File "part3_PubMedSearch.py", line 25, in getDataFromPubmed handle = Entrez.esearch("pubmed", term=search) File "/usr/lib/python2.7/dist-packages/Bio/Entrez/__init__.py", line 189, in esearch return…

pubmed

updated 7.3 years ago • agata88

When a keyword is searched in PubMed or PMC database, how can I retrieve the documents that are shown in results

information-retrieval text-mining

updated 22 months ago • davehresearch

Hello, Does anyone know of any package in R that contains a function to extract full Pubmed text? I searched in RISmed, pubmed.mineR, and easyPubMed, I believe none of them can extract full text. Any leads would

R data mining Pubmed

updated 3.4 years ago • Bioinformatician_in_trouble

If I go to PubMed and enter this query, which currently returns around 2290 results: "Retraction of Publication"[Publication Type] then...me@me.com" retmax = ncbi.esearch_count("Retraction of Publication[ptyp]", {"db" => "pubmed"}) search = ncbi.esearch("Retraction of Publication[ptyp]", {"db" => "pubmed", "retmax" => retmax}) result = ncbi.efetch(search, {"db" =&gt..…

pubmed eutils xml

updated 11.8 years ago • Neilfws

This is what I have done: esearch -db pubmed -query "lycopene cyclase" | efetch -format abstract I was struck by this error: ``` 500 Can't connect to eutils.be-md.ncbi.nlm.nih.gov...No do_post output returned from 'https://eutils.be-md.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_67454450_130.14.18.34_9001_1529992046_810451412_0MetA0_S_Mega…

edirect pubmed NCBI

updated 10 months ago • zorn21g

I have a list of 4000+ PMIDs from a meta-analysis query for which I'd like to pull abstracts from Pubmed. I can get title, description, details, nd other items using Batch Entrez http://www.ncbi.nlm.nih.gov/sites/batchentrez

pubmed meta

updated 12.8 years ago • Ryan D

I am looking at a way to visualize distribution of a set of keywords over the years in PubMed. I am sure that there must be a tool to do that. An ideal solution will be similar to Google books Ngram Viewer. Here is an

text data visualization

updated 10.5 years ago • Khader Shameer

Hi, I would like to be able to know what research topics are currently showing a lot of activity in terms of publications being deposited into pubmed. I have only been able to find existing web applications that require a specific search term as input. Are there any server...topics are currently showing a lot of activity in terms of publications being deposited into pubmed. I have only been abl…

MeSH query pubmed trend-growth

updated 2.6 years ago • craig.mckibbin

I would like to analyze some metadata about a publication and I have a perl script that parses PubMed XML formatted files. However, I do not see a way to download the "cited by" list as XML. Is there a way to do this

xml pubmed

updated 11.7 years ago • Burke

I want to count the cooccurrences of a disease pair or a disease-gene pair in all pubmed abstract to find evidence for the links. I have many such pairs and want to do an extensive search. Is there an easy way...to do that? I am thinking to download all Pubmed abstracts and do the search myself. Can anybody let me know the best way to download all Pubmed abstracts (up to a limit

text mining pubmed abstract

updated 7.9 years ago • bingshanli

Is there a tool that will download all PDFs given a query to Pubmed or PMC? Could work by pulling only articles found in PMC, but ideally would grab any article to which a link not behind

eUtils NCBI pubmed entrez

updated 17 months ago • Vincent Laufer

the use of sentiment analysis on the title and abstract fields of research articles indexed by Pubmed? I ran some more generic SA tools, but sanity checking of the results produced appeared to identify a skew towards calling

sentiment-analysis pubmed Python R

updated 10 months ago • LauferVA

Hi, everybody. I'm a beginner in R and I'm trying to retrieve some information about articles from Pubmed database.This information might include the author's name, abstract, full-text and etc... I chose the "RISmed" package...Hi, everybody. I'm a beginner in R and I'm trying to retrieve some information about articles from Pubmed database.This information might include the author's name, abstr…

updated 7.5 years ago • saber mohammadi

related to Alzheimer's disease and lipid metabolism retrieved by CoPub 5.0 are much more lower than PubMed. Could anyone tell me the reason ? Thank you very much

copub pubmed

updated 21 months ago • xi.nyi94

are ~100 SNPs associated with RA at genome wide significance. If you enter in just the SNP ID into pubmed, you can sometimes find links to other papers describing a functional effect of the variant. Individually submitting...citation list. Instead, what I am looking for is something like dbSNP Batch Query, but that hits the pubmed dbase instead of dbSNP. How might one submit a list of the form…

pubmed batch query

updated 7.7 years ago • Vincent Laufer

Hi all, I download a sra file from pubmed and transfer it to fastq, but when i open it, the file is weird.please see below: @SRR653007.1 ILLUMINA-8879DC:227:2:1:1030

ChIP-Seq

updated 5.9 years ago • mikysyc2016

I am trying to use Entrez to search and parse publication records from PubMed. The parse function used to work until recently, but a few days ago it started failing. I started getting the following...py from Bio import Entrez Entrez.email = "Your.Name.Here@example.org" handle = Entrez.efetch("pubmed", id="19304878,14630660", retmode="xml") records = Entrez.parse(handle) for record in record…

biopython pubmed entrez

updated 12 months ago • apiljic

I'm working on a project of data mining which which use pubmed articles xml files to read in python and parse its data to database, But problem is that some inline tags like `` don't read

python xml pubmed parsing html

updated 6.1 years ago • aqsaawan.459

Hi everyone, I want to execute Data Mining methods on a PubMed dataset (Medline in XML). Regarding this aim I found a paper from 2004 "Software to parse and load MEDLINE into a RDBMS...Hi everyone, I want to execute Data Mining methods on a PubMed dataset (Medline in XML). Regarding this aim I found a paper from 2004 "Software to parse and load MEDLINE into a RDBMS " and...an problem of JAXP or…

xml database pubmed

updated 10.3 years ago • bukowski.mark

make a database, however, I would like to know if there is any tool for gather the information from pubmed and previsouly published papers ? for example I would like to get all tRFs from different species and different cells

database

updated 8.0 years ago • Learner

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