Questions tagged [public-databases]
Use this tag for questions about how to use, download, retrieve, check and browse public databases.
26
questions with no upvoted or accepted answers
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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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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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Map domain names from UniProt bed files to domain accessions
I want to get a bed file mapping human protein domains to the human genome. UniProt actually offers such a thing here. The problem, however, is that the file doesn't include any kind of domain ...
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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, ...
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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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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 ...
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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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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 ...
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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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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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Creating maps.fld file of protein for AutoDock GPU
I want to use AutoDock GPU, which accepts protein.maps.fld and ligand.pdbqt files.
Since I am performing high throughput virtual screening, shall I just load protein AutoDockTools and create protein....
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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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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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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 ...
- 1,784
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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 ...
- 111
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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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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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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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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 ...
- 261
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33
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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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Find the date that sequencing was performed
Background I've obtained RNAseq datasets from ENCODE and I'm looking to identify external variables contributing to sequence variance among these samples.
External variables For example, clustering ...
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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 investigation which is exploratory in nature.
Question I am seeking a ...
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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 ...
- 81
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Exporting Panther functional classification of gene list
After inputting a list of gene and running an analysis in https://www.pantherdb.org/ (such as "functional classification"), I get a result table that is limited by an X number of entries ...
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Get BioProject code of a GEO dataset
In publications the GEO code is usually shared and not the BioProject/study code.
I want to get the BioProject/Study Accession code of a GEO dataset (to later download the data from ENA).
I know that ...
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