Questions tagged [public-databases]

Use this tag for questions about how to use, download, retrieve, check and browse public databases.

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What data set was used Gene Expression Data of Postmortem Tissues?

I want to run the experiments "Sample Application to Genotype-Tissue Expression (GTEx) Project Gene Expression Data of Postmortem Tissues" mentioned in "Enter the Matrix: Factorization ...
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1 vote
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GSEA. Subsetting Gene Ontology, Biological Processes, by gene set families of interest

I have run GSEA - on Gene Ontology , Biological Processes (GO and BP hereafter) - on some Mouse bulk RNA-seq data, and am currently in the process of going through the results. To do this, I have used ...
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2 votes
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Active sites of the query protein does not align with the top hit using HHpred

I am having difficulties with an alignment on HHpred and was wondering if anyone had any answer to the following: I am trying to align my protein (PDB 2VU9, a Botulinum Neurotoxin Type a) with one of ...
0 votes
0 answers
5 views

SwissVar 2016 release

I am trying to find the October 2016 release of the SwissVar Database (which was discontinued since 2020). I already tried the Uniprot FTP site but was only able to find the 2021 release. Any ideas ...
0 votes
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DAVID returning invalid KEGG pathways in gene enrichment analysis

I'm using the latest version of DAVID Knowledgebase (v2021q4, Available at https://david-d.ncifcrf.gov) for enrichment of a set of genes that I have. Using the ...
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2 votes
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63 views

What is the difference between flat and stereo stitch id?

For my thesis, I'm working on side effect prediction in a machine learning framework and I am working on data available on SIDER (http://sideeffects.embl.de/download/). If you open the README file, ...
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3 votes
2 answers
130 views

What happened to sra ftp server?

My whole (professional) life I am downloading sequences from SRA and ENA databases. Long time ago, I used prefetch from sra-tools, but later I switched to simply using wget from ftp servers of the two ...
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3 votes
0 answers
21 views

OMIM diseases to UMLS mapping

Is there any public available mapping between Online Mendelian Inheritance in Man (OMIM) diseases and Unified Medical Language System (UMLS) concepts? OMIM has mapping for genes to entrez or ensembl, ...
3 votes
2 answers
88 views

How to get the number of complete phage genomes available on ncbi?

I am looking to establish the total number of complete phage genomes available on NCBI. I am not looking for any specific type, but want to understand the total diversity available. How can I perform ...
0 votes
0 answers
40 views

What is the meaning of multiple "cases" in GDC data files

I thought I had a good handle on the data model of GDC, but a recent query on the TARGET dataset revealed something I had not seen before. TL;DR- what does it mean when multiple "cases" are ...
2 votes
0 answers
39 views

Mapping ICD9 codes in UKBB data to PheCodes using PheWAS package

I am working on the UKBB data and trying to specify cases and controls by converting ICD9 codes to PheCodes. I have input data (icdt) where the first column (f.eid) is patient IDs and the remaining ...
-1 votes
1 answer
136 views

How to get a FASTA format file with the DNA sequences of all annotated genes?

I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published here in NCBI. When I click on "Send to">"Gene Features">"FASTA format" I ...
2 votes
1 answer
91 views

dbSNP GRch37 Download

I am still new to this. I am trying to download the GRch37 dbSNP data from the NCBI dbSNP Browser using the "Send to:" button. But whenever I select "Send to:" > "File"...
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1 vote
1 answer
54 views

Where to find publicly available Sanger chromatography data?

I am looking for any public available databases where I can download Sanger chromatography data ideally in Ab1 or SCF file format. I need extremely large amounts of this, since I want to use it for ...
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0 votes
1 answer
21 views

Where can I find a basic example for testing association between a phenotype and each of the variants of a chromosome?

I am a statistics student trying to find data suitable for a particular method. From what I have read so far, it is of interest to determine if variants within a chromosome are associated with a ...
2 votes
1 answer
692 views

How to download data from SRA in Linux systems via the command line?

My workflow for downloading data from SRA has been the following: Access SRA Run Selector. Enter the accession number for the project of interest. Download "Accession List" for the "...
3 votes
2 answers
41 views

Retrieval of metadata of a batch of 3953 sequence data from GISAID database

I need to retrieve COVID-19 metadata (such as date of collection of sequence data, location, etc.) for a batch of 3953 GISAID accessions from the GISAID database. I am not very comfortable with GISAID....
1 vote
1 answer
38 views

How to specify the list of contigs in AGP gap file used for ENA submissions

I am battling the submission of scaffolded assembly to EBI, somehow I can not get AGP gap file right. background The only option seems to be using the Webin-CLI submission interface. For the ...
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2 votes
0 answers
68 views

PubMed Central Open Access archives are corrupted

I'm trying to download PubMed Central Open Access articles from ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk. However, I am not able to decompress the archives without errors. ...
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1 vote
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13 views

Ccle miRna data units

Does anybody know what units the mirna expression data on ccle is in? I saw the pipeline in the original paper but it doesn't mention units. Original paper: https://www.nature.com/articles/s41586-019-...
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1 vote
1 answer
42 views

Question about public availability of human SNP dataset with country of origin

Is there a publicly available data set for humans SNPs, preferably together with the country of origin? If so, could someone please point me towards it. I've looked through other questions on the site ...
1 vote
1 answer
67 views

How to identify genes from a genome assembly of C. Elegans?

I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...
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1 vote
1 answer
40 views

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases ...
2 votes
1 answer
81 views

What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?

(I am not a Bioinformatics expert, please forgive and educate me if I've used any wrong terms or assumptions here) I bought a "Whole Genome Sequence" kit, which gave me the following VCF ...
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6 votes
1 answer
83 views

How to search for high coverage SRA entries

The Question I want to find high coverage SRA entries, e.g., above 100x. I guess the best way is to use https://www.ncbi.nlm.nih.gov/sra with an appropriate search term. I don't mind if the search ...
0 votes
1 answer
651 views

OpenAPI-Generator Python Client Instructions Examples

Trying to learn a little bit of Python and Biopython I ended up figuring out what a Rest API is when the RCSB PDB repository released its new Rest API. I tried to retrieve info from the PDB repository ...
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1 vote
1 answer
64 views

What datasets are available out there for prediction based on DNA sequences? [closed]

I am looking for publicly available data for a genomics deep learning project. My goal is to compare different architectures to predict biological insights from DNA sequences. I have heard about ...
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1 vote
0 answers
9 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 ...
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0 votes
4 answers
116 views

Where can I find Single Cell Data with Location "Coordinates"?

Does single cell data typically have the following meta-data: the "coordinates" (e.g. on a tissue, adjacent tissues) saying where each cell in the sample was located relative to other cells? ...
1 vote
0 answers
28 views

Fastq dataset after clustering

I'm doing a project for DNA archival storage systems Is there an open-source dataset used as ground truth for clustering? E.g A file containing the ground truth strand sequences, which have been ...
2 votes
0 answers
186 views

Convert MeSH term to drugbank ID

I have set of annotated term of drugs extracted from PubTator those drugs are annotated in form of MeSH terms. I would like to map them into drugbank ID. I do search the the MeSH term i find the ...
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2 votes
2 answers
127 views

Where can I find the genotype frequencies for the SNP's that are tested at 23andMe, Ancestry and FTDNA/MyHeritage?

I want to add the frequencies of the genotypes to a baseline of raw DNA data I've got from the DNA testing companies 23andMe, Ancestry and MyHeritage (tested at all). All in build 37 human genome. ...
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1 vote
1 answer
65 views

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG ...
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0 votes
1 answer
78 views

europmc and tidypmc R library for extracting or making metadata from publication

I'm trying to use this europmc r libray where I have a list of pmids to look for. I tried with pubtator but its bit complicated.In Europmc i can all the annotated terms etc. ...
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2 votes
4 answers
330 views

How can I obtain FTP links to studies in ENA given a BioProject ID?

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: ...
4 votes
0 answers
57 views

Where can I find lncRNA expression data for different cell types?

Are there any publicly available databases singularly providing expression data for any given long non-coding RNA (lncRNA) for varying cell types any species preferably including humans? ...
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0 votes
1 answer
37 views

Determine if an organism is microbic or unicellular

I am doing some metagenomic analysis of samples which can only contain microbes due to the experimental setup. For this, it would be useful to be able to distinguish whether a specific organism is a ...
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1 vote
0 answers
21 views

How do protein-protein interaction databases work?

I am a student and just trying to gain a base level understanding of PPI databases and how to interpret their data. For example, when inputing multiple genes into String, does it only give protein-...
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1 vote
0 answers
29 views

miRNA dataset for prediction experiments

I am from the field of Computer Science and I want to perform some experiments related to miRNA and mRNA prediction.I have been searching for datasets in this area and found one called mirWalk ...
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1 vote
1 answer
4k views

local BLAST error: BLAST Database error: Error: Not a valid version 4 database

I want to use a local blastn command to BLAST a multifasta file ~700 sequences using following command: ...
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1 vote
0 answers
50 views

How to (efficiently) search nuccore to retrieve only annotated sequences?

I wish to efficiently search nuccore to retrieve only annotated sequences. By "annotated" I mean that the nuccore entry contains annotation information. An equivalent definition (if I understand ...
1 vote
0 answers
40 views

Is there a built-in parser for the textual feature table that Entrez.efetch returns?

Entrez.efetch helpfully gives me the feature table of a nuccore entry. If I understand correctly, efetch can only return the ...
3 votes
2 answers
487 views

Downloading all COI sequences from BOLD fails

I have metabarcoding sequence data (COI) from bulk animal samples (including arthropoda, nematoda, annelida, mollusca) and I want to BLAST all of these sequences. I used following command to do this: <...
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1 vote
1 answer
155 views

Available phenotype data from GTEx

I am using gene expression data from the The Genotype-Tissue Expression (GTEx) project, available here: http://gtexportal.org. I would also like to use phenotype data for each sample (especially age, ...
5 votes
0 answers
236 views

What exactly does each of InterPro, PANTHER, Pfam bring to the table individually in classifying a protein?

I would be very grateful if somebody could sketch out the methods Pfam and PANTHER use to assign a family to a given protein and how they are different. My (cursory) understanding is that InterpProp ...
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2 votes
1 answer
824 views

How to download RNAseq gene expression data from GTEx

I would like to download RNAseq gene expression data from GTEx from the liver only. What is the best way to do this? I have tried a few things. I downloaded several files from the GTEx website (https:...
5 votes
1 answer
36 views

Are there any "canonical" sources of C. elegans connectome?

I found that there are a couple of projects that allow the user to simulate the neural system of C elegans, for example OpenWorm one update being here. I don't know how to navigate sources in ...
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1 vote
2 answers
43 views

Appropriate value to replace outliers in clinical studies

I am working on clinical study where I am focusing on binary classification problem. There are few variables which has outliers. I am trying to know which would be the right value to replace ...
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1 vote
0 answers
32 views

Human Cell Atlas - cell annotations

Human Cell Atlas Preview Datasets have been available for a while now (there was some discussion about that earlier). However, although the raw data is available, cell labels are not (for example, ...
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1 vote
1 answer
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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 ...
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