Questions tagged [data-retrieval]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1
vote
0answers
7 views

Drug classification database information

Is there any database that give information about the drug class. Right now I have all the MeSH id of the drugs from different publications. So right now I'm looking one by one drug looking at the ...
1
vote
3answers
55 views

How can I obtain FTP links to studies in ENA?

How can I programmatically obtain ftp links to RNA seq fastq files in ENA? Here's an example of a link that I would be interested in obtaining: ...
0
votes
0answers
19 views

Could not parse String db protein interaction network PSI-MI XML file with GenerateDS Python parser

I want to get a list of all evidence types for interactions String db finds based on a list of gene names in order to filter in only those pieces of evidence I have confidence in. I downloaded a ...
0
votes
0answers
14 views

Retrieve FASTA sequences using sequence ids in cdbfasta

I'm using cdbfasta command to retrieve sequences using ids, all works well but I find some sequences repeated in my output and the command does not retrieve all the sequences I want.
0
votes
1answer
39 views

Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?

Are there databases that contain information about gene or protein expression before and after targeted therapy or chemotherapy? I am curious about different cancer cell lines or cancer types. Any ...
0
votes
1answer
208 views

Raw Data frame manipulation in python

Using python 3 I need to process qPCR sequencing raw data outputs by searching for the first occurrence of a user defined string and then making a new data frame using all lines after that string. I ...
1
vote
1answer
38 views

NCBI retrieve genome assembly with splicing or “modifications”

I am trying to fetch genome assemblies that include splicing information. E.g. Here, is a genome assembly of a yeast, where genes show variants like this: ...
1
vote
1answer
42 views

Retrieving Metabolic networks from WIT Database

How can I get the dataset for all the 43 metabolic networks for this paper: https://www.nature.com/articles/35036627 It looks like the WIT database does not exist anymore.
0
votes
0answers
38 views

P21 mutant Colon Cancer cell lines (RNA SEQ)

I need to obtain RNA sequence datasets for my project. The datasets should include P21 mutation, knockout and wild type in any Colon Cancer cell lines, Preferably in the same study. I'm not sure if ...
1
vote
1answer
114 views

List of human transcription factors

I'm looking for a list of human transcription factor (TF) genes. Where can I find a TF database or how can I retrieve this list from other databases?
1
vote
0answers
23 views

Where can I find hemagglutination inhibition (HI) assay data?

I am looking for hemagglutination inhibition assay data for type A influenza virus. Could someone please give me a link to a database with this information? Thanks.
0
votes
2answers
159 views

GDC data portal cancer subtype

I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (https://portal.gdc.cancer.gov/repository) to classify breast cancer subtypes (luminal ...
3
votes
1answer
41 views

Where to download baseline/average gene expression level of all human coding genes?

I am looking for the most appropriate dataset for downloading baseline gene expression level across all human coding genes during development. I am aware that EMBL Expression Atlas is one of the ...
2
votes
2answers
63 views

Blueprint replicates

On Encode, it's pretty easy to find out replicate information about the experiments, however I am having some difficulty finding this information on BLUEPRINT DDC, at http://dcc.blueprint-epigenome.eu ...
1
vote
0answers
18 views

Viral Load and Antiretroviral Therapy Dataset

My project is on Mathematical Modeling of the relationship between viral load and antiretroviral therapy. Its purely an academic one which is exploratory in nature. Intend using the different ...
5
votes
1answer
88 views

CRISPR Sequence Finder and Database Download

I am searching for tools to pull CRISPR Spacers from Bacterial Genomes. I am aware of the CRISPRDB and the corresponding identification tool on the web server. Are there other tools for finding ...
3
votes
2answers
86 views

NCBI - edirect suite to download all genome sequences associated with a query - troubleshooting

Not sure if this is allowed but I cannot think of a better place to ask. I am attempting to download all genomic sequences from refseq associated with the query Peptostreptococcaceae. I have been been ...
3
votes
1answer
51 views

Automating sequence download from Wormbase

I'm working on the C. elegans model organism, for which there exists an online biological information database: Wormbase. I'm able to manually search for a transcript (say "K06C4.12") and this gets ...
4
votes
2answers
381 views

Retrieve abstract/summary for NCBI bookshelf via Entrez

I want to retrieve abstracts/summaries for NCBI bookshelf entries, eg: "NBK1440" Docs say the dbname is "books" and efetch guide says a rettype of "docsum" works for all databases. However when I ...
0
votes
2answers
150 views

How to access organism IDS, taxon nodes from UniProt?

I try to find organism IDs used by UniProt (e.g. 9606 for "Homo sapiens") and information about the 'taxonomic kingdom' this organism belongs to. The only source on UniProt I could find is this file ...
1
vote
2answers
311 views

How to interconvert InChI and InChIKey?

I would like to retrieve IDs from several databases using InChI as an input, e.g. ...
3
votes
1answer
257 views

How to retrieve InChI key for KEGG compound?

I would like to retrieve the InChI representation for a given KEGG compound but I fail to find a direct solution for this (preferably doing it via bioservices). One could do it via ChEBI like this: ...
9
votes
1answer
191 views

How to retrieve logical expressions (KO based) for reactions from KEGG?

The completeness of a module can easily be checked by looking at the Definition entry associated with the module. For example, in module M00010, it is given as: <...