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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

205 questions
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expected str, bytes or os.PathLike object, not InMemoryUploadedFile

I have a method to read a Newick file and return a String in Django framework which is the following: def handle_uploaded_file(f): output = " " for chunk in f.chunks(): output += chunk.decode('ascii') return output.replace("\n",…
user8577141
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How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?

I have a list of taxids that looks like this: 1204725 2162 1300163 420247 I am looking to get a file with taxonomic ids in order from the taxids above: kingdom_id phylum_id class_id order_id family_id genus_id …
aLbAc
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How do I download all the abstract datas from the pubmed data ncbi

I want to download all the pubmed data abstracts. Does anyone know how I can easily download all of the pubmed article abstracts? I got the source of the data : ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/af/12/ Is there anyway to download all these tar…
Soundarya Thiagarajan
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User Defined Function not working in dplyr pipe

I have a dataset with proteins accession numbers (DataGranulomeTidy). I have written a function (extractInfo) in r to scrape some information of those proteins from the ncbi website. The function works as expected when I run it in a short "for"…
netlak
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Downloading all full-text articles in PMC and PubMed databases

According to one of the answered questions by NCBI Help Desk , we cannot "bulk-download" PubMed Central. However, can I use "NCBI E-utilities" to download all full-text papers in PMC database using Efetch or at least find all corresponding PMCids…
s.22217330
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How to extract the first hit elements from an XML NCBI BLAST file?

Im trying to extract only the first hit from an NCBI xml BLAST file. next I would like to get only the first HSP. at the final stage I would like to get these based on best score. to make things clear here a sample of the xml file:
Schrodinger's Cat
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NCBI gene database question

I m trying to find gene_info file with genenames and chromosomal location. However, I can't seem to locate it on NCBI FTP site. Can anyone give me a pointer?
Scicare
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error with a function to retrieve data from a database

I am trying to get a FASTA file form NCBI website, I use the following function getncbiseq <- function(accession){ dbs <- c() for (i in 1:numdbs){ db <- dbs[i] choosebank(db) resquery <- try(query(".tmpquery", paste("AC=",…
nik
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How do I get gene features in FASTA nucleotide format from NCBI using Perl?

I am able to download a FASTA file manually that looks like: >lcl|CR543861.1_gene_1... ATGCTTTGGACA... >lcl|CR543861.1_gene_2... GTGCGACTAAAA... by clicking "Send to" and selecting "Gene Features", FASTA Nucleotide is the only option (which is fine…
user2509933
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Sort pubmed searches from rentrez by relevance

I'm searching PubMed using the rentrez package in R and would like to get the results sorted by relevance. Currently they are sorted by publication date. library(rentrez) query = 'regression to the mean[TITL]' entrez_search =…
agbarnett
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Biopython NCBIWWW.qblast test file -hangs on

When I try to run a test file provided by Biopython for NCBIWWW.qblast online search, it just hangs on and on and never responds. The same happens when I am trying to run any script on my own that includes NCBIWWW.qblast: it just arrives to this…
user3437828
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Downloading Protein Sequences of multiple Organisms

I am attempting to use biopython to download all of the proteins of a list of organisms sequenced by a specific institution. I have the organism names and BioProject's associated with each organism; specifically I am looking to analyze the proteins…
redvyper
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how to resolve VERY LARGE URL problem for hyperlink...with jQuery or Javascript calling any perl,php etc. script on back

I have built UI, its like a search engine for BioProcess/Disease--> Genes. e.g., User can query: "Stem Cells" or "brain tumor"and in result it will give 50 to 5000 GeneIDs (essentially those are Numbers representing a uniqe Gene at NCBI database)…
Saurin
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1 answer

convert XML data to data frame in R

I am trying to convert XML files to data frame, but it only shows few information in the column. library(XML) # LOADING TRANSFORMED XML INTO R DATA FRAME doc <- xmlParse("SRR12545290.xml") # https://www.ncbi.nlm.nih.gov/sra/?term=SRR12545290 xmldf…
shanky
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Is there any R function to extract all taxonomy name (phylum, class, order, family ...) from species taxonomic ID/ species name or genus name?

I have the taxonomic ID of species and I can get the species and genus name from NCBI (https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi). But I want phylum, class, order.. all from these data. I have tried taxize package, but…
Shaminur
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