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Questions tagged [ncbi]

NCBI is a National Center for Biotechnology Information, one of the most important websites used by bioinformaticians. NCBI runs a big variety of various bioinformatical web services, also provides important databases for download.

The NCBI covers a wide range of bioinformatics resources, from journal listing to gene alignments to chemical libraries databases to protein folding prediction.

NCBI's data is publicly available from the main website and from ftp repositories.

  • PubMed
    PubMed, a database of citations and abstracts for biomedical literature from MEDLINE and additional life science journals.

  • The NCBI C++ Toolkit provides a set of modules to access, modify, generate and deposit biological data. The full description can be read in its online book

  • PubChem, a chemical library database, has its own API to search and retrieve chemical compounds

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Is there a R code set to use PubMed ID or DOI to get data files for that article, please?

I am trying to get the data file names from NCBI or PubMed that are related or attached to hundreds of unique DOIs or PMIDs, in R language. For example. I have PMID: 19122651 and, I want to get the names of the three GSEs connected to it, which…
Shawn
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Why do I get BioPython HTTPError: HTTP Error 400: Bad Request when I use Esearch and Efetch

I am trying to access a list of organisms from the chordata phylum that have sequenced chromosomes from the "assembly" database in Entrez. I am trying to do this using the E-utilities in biopython. I am able to search for the organisms using esearch…
Chahna Patel
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Why doesn't rsync work when connecting to NCBI's FTP server home page?

I'm currently trying to update some code at work. I previously created a script with an up to date version of Python that logs a users path choices on NCBI's FTP webiste (ftp://ftp.ncbi.nlm.nih.gov/). The log was used to update my file system with…
grabear
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xpathApply: How to pass multiple paths or nodes?

# parse PubMed data library(XML) # xpath library(rentrez) # entrez_fetch pmids <- c("25506969","25032371","24983039","24983034","24983032","24983031","26386083", "26273372","26066373","25837167","25466451","25013473","23733758") #…
user5249203
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extract xml from xml embebed in html

im trying to get the xml presented here http://www.ncbi.nlm.nih.gov/sra/ERX086768?report=FullXml but its a bit tricky cause they dont give any suport for it. The purpose is to get the xml to php in order to go trought the xml. can someone give a…
jose bode
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getting a gene sequence from entrez using biopython

This is what I want to do. I have a list of gene names for example: [ITGB1, RELA, NFKBIA] Looking up the help in biopython and tutorial for API for entrez I came up with this: x = ['ITGB1', 'RELA', 'NFKBIA'] for item in x: handle =…
StudentOfScience
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Get XML value by attribute name

Possible Duplicates: Attribute Value Selection in SimpleXML SimpleXML: Selecting Elements Which Have A Certain Attribute Value I'm parsing an XML document and looking for a specific ID. The ID value is provided in the ArticleId element under…
a coder
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transform pmc-id -> pmid

Is it possible to transform pmc-ids (pubmed central ids) to pmids (pubmed ids) via a ncbi api? You can do it via the web form but I would like to use a program - of course I can always write a screen scraper ... thanks
cs0815
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Querying NCBI for genome version across different species using biopython

When reading an NCBI output from base_entrez_fetch, the genome version seems to be stored differently across various species. For instance, in Danio rerio, it can be found under: test = base_entrez_fetch('gene', gene_id, rettype='gb', retmode='xml',…
Julia2277
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inconsistency with ftp sites in R

I use R to access bioinformatic resources from NCBI. In recent months, my ability to do this has become less and less consistent. Today, I'm generally unable to run the following…
Ngwenyama
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wsimport import fails with NCBI/Blast

I'm trying to generate the files handling the SOAP services documented here: http://www.ncbi.nlm.nih.gov/books/NBK55699/ But wsimport fails: $ wsimport -d generated "http://www.ncbi.nlm.nih.gov/blast/netblast/blastws.cgi?WSDL" parsing…
Pierre
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Trying to download a series of archives from NCBI ftp using python ftplib but ftplib freezes at end of long file transfer

I'm trying to download the nr blastdabase form NCBIs ftp site (ftp://ftp.ncbi.nlm.nih.gov/blast/db). One of the files is quite large (16GB) and takes some time to download. At the end of downloading this file the program just hangs, it does not move…
toasted_wheat
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How can I programmatically get the PMID from the DOI of a paper that isn't in PMC (i.e., that doesn't have a PMCID)?

How can I programmatically get the PMID from the DOI of a paper that isn't in PMC (i.e., that doesn't have a PMCID)? The DOI->PMID conversion tools mentioned on https://www.ncbi.nlm.nih.gov/pmc/pmctopmid/ only works when the paper has a PMCID. DOI…
Franck Dernoncourt
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How to access xml text of child?

I have the following xml file (taken from here:
Saraha
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NCBI BLAST, nr database

I am running the command for BLAST : blastp -query /Users/shalini/Desktop/shalini/project/unmodelled_fasta/AAA18895.fasta -outfmt "7 sacc qcovs pident ppos evalue" -db=/Users/shalini/Downloads/nr…
shalini
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