Questions tagged [public-databases]

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

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NCT search in PubMed via Entrez (python)

first time I post here so, please, be patient. So I am currently working with Entrez (Biopython) in order to retrieve the number of articles for a given disease/indication. My data provide both the ...
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1answer
29 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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1answer
41 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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46 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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2answers
30 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: ...
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42 views

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

Are there any publicly available databases providing expression data for any given long non-coding RNA (lncRNA) in varying cell types of any species (preferably human inclusive)? Alternatively, are ...
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1answer
27 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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11 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 ...
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13 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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27 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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1answer
427 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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15 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 ...
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15 views

Meaning of the Flags attribute returned by Entrez.esummary(db='nuccore')

My Question Calling Entrez.esummary for the nuccore db returns records with various fields. One of these fields is Flags. I ...
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18 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 ...
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2answers
49 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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1answer
16 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, ...
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30 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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1answer
49 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:...
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20 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. I don't know how to navigate sources in bioinformatics and thus struggle to evaluate their ...
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2answers
25 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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31 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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1answer
37 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 ...
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2answers
89 views

Looking for a taxonomic dataset that links tree genera (or species) to families

I am looking for a taxonomic dataset that would allow me to links tree genera (or species) to families. In particular, I am interested in the tropical species found in the Amazon. I found a long but ...
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1answer
31 views

Proteins with one SS bond?

I would like to find proteins with exactly one SS bond. Is there a database where I can search this? I've tried advanced search on https://www.rcsb.org/, but no such option, at least I could not find ...
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1answer
121 views

Old versions of the reference genome and dbSNP

For benchmark purposes I’m trying to find an old version of the human reference genome (pre-GRCh37) and a matching version of dbSNP. Unfortunately it appears as though older versions of dbSNP aren’t ...
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1answer
29 views

Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?

I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand. I would like to download the assemblies of different E. coli genomes and group ...
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1answer
79 views

How can I get plant Genome size, total number of genes, EST, and chromosomes number

How can I get plant Genome size, total number of genes, EST and chromosome number from phytozom and plantDB?
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3answers
159 views

How do you query and explore ENCODE data?

I am looking for a modular way to query data from ENCODE. For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it? Finally, is there an ...
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1answer
34 views

How to export web NCBI tBLASTn results in table format with many queries?

Context I'm an MSc student working on writing up my thesis (back home now) from my laptop and, therefore, unfortunately don't have access to a workstation/server capable of doing the tBLASTn search ...
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1answer
100 views

Is there a way to import tables in PubMed Central to MySQL or other Relational databases?

I need to use these PMC tables from the medical journals for the purpose of integrating the data with a decision-making software. Though, I can see that one can access full-text for an article from ...
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1answer
80 views

ncbi…eutils/esearch.fcgi: How to search now in the snp database?

According to the 2017(!) textbook, it worked at that time, for instance, https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=autism At ...
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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.
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2answers
792 views

Receptor-ligand database

How can I find ligands of receptors (or vice versa)? For example, I want to find the receptors of IL-8 (CXCL8).
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1answer
60 views

How to query the Human Microbiome Project (HMP) to find all subjects with both 16s and WGS workups?

I am looking for a query to run on the HMP database that will return all subjects who have had BOTH 16s and whole genomes sequence (WGS) workups. I am currently using this query... ...
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3answers
55 views

Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?

I am not sure whether this is the best SE community for this question. I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the ...
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36 views

Gathering data on bacterial oganism growth conditions

let's say I have a list of organism names like the example below ...
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1answer
251 views

Get results of keyword search on Pfam via python script

I'm interested in all proteins that are in any way associated with Danio rerio. I decided to look them up at Pfam data base and when I just make a keyword search, I get a a nice list which looks like ...
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2answers
151 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
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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 ...
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37 views

Find the date that sequencing was performed

I've got a bunch of RNAseq datasets from ENCODE and I'm looking to identify variables contributing to variance among my samples. For example, is there any easy way to find out the precise date which ...
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1answer
30 views

What are some good sources of 3rd order gene expression data

I need good sources of gene expression data in the form of 3rd order tensors. Typically the commonly available datasets are in the form of a matrix, for instance, $sample \times gene$ or $gene \times ...
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76 views

Is there a database of protein sequences/structure along with their melting temperature?

Such databases have been constructed for example in here or here. But I can't find them anywhere online. Can someone point me to where I can find one available online? Otherwise I'll have to write to ...
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1answer
239 views

How to download SNP data from specific regions, population and positions?

I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems. To do that, I've read a lot of papers and books in order to understand the main ...
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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 ...
2
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1answer
50 views

Convert CD (cluster of differentiation) into gene symbol

I want to convert names according to the "cluster of differentiation" nomenclature into accepted gene symbols. For example, CD3 should map to "CD3a;CD3b;CD3c;CD247" and "CD45RO" should map to "PTPRC". ...
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1answer
82 views

Human SNP databases other than dbSNP

I'm working on a project to identify variants as being either germline or somatic based on nearby SNPs, and I was wondering if there were any databases of SNPs for Homo sapiens other than dbSNP? I'm ...
2
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1answer
64 views

How to add data to AnnotationHub

I recently started using the Bioconductor AnnotationHub package for accessing lots of common datasets, but I've noticed that there are a lot of newer databases that have not made it into AnnotationHub'...
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1answer
673 views

A Database for Plant Metabolome or Secondary Metabolites?

I am searching for a plant metabolome or secondary metabolite database for a college bioinformatics project. Up until now, I have found these two databases, as I am giving their links below; http://...
4
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1answer
157 views

How can I reproduce a manual NCBI search with Biopython Entrez module?

I'm trying to make a Biopython script that reproduces a manual search on the NCBI website. My manual search gives me the following URL: https://www.ncbi.nlm.nih.gov/nuccore?term=ANOS1[gene%20name]%...
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Can I upload only co-assemblies to ENA, using existing ENA samples?

Lets say I am using reads downloaded from ENA, assembling them and doing further downstream analyses. Would it be possible to then upload the results of the co-assemblies and other analyses back to ...