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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 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 ...
rtviii's user avatar
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5 votes
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285 views

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 ...
terdon's user avatar
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3 votes
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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, ...
Tomaž Bratanič's user avatar
2 votes
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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 ...
A.Dumas's user avatar
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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 ...
microbeprincess's user avatar
2 votes
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240 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, ...
Elisa's user avatar
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2 votes
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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 ...
Muhammad's user avatar
2 votes
0 answers
106 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. ...
TomTom's user avatar
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2 votes
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345 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 ...
kcm's user avatar
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1 vote
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75 views

Need help with binding DB API

...
Neeleshwar Pandey's user avatar
1 vote
0 answers
200 views

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....
Jatin Kashyap's user avatar
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 ...
h3ab74's user avatar
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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-...
n232's user avatar
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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 ...
kcm's user avatar
  • 1,804
1 vote
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32 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 ...
Brian Formento's user avatar
1 vote
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25 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-...
DN1's user avatar
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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 ...
Lila's user avatar
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1 vote
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157 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 ...
Oren Milman's user avatar
1 vote
0 answers
76 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 ...
Oren Milman's user avatar
1 vote
0 answers
33 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, ...
burger's user avatar
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1 vote
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52 views

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 ...
jaslibra's user avatar
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1 vote
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24 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 investigation which is exploratory in nature. Question I am seeking a ...
Obinoscopy's user avatar
1 vote
0 answers
24 views

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 ...
Imer Muhović's user avatar
0 votes
0 answers
22 views

ZINC15 database: proxy server error when trying to download catalog in any format

I am a complete beginner in the use of such databases. When navigating to the ZINC15 database website and trying to download an entire catalog with the "Download all as" option the request ...
Zea Mays's user avatar
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0 answers
8 views

Where would I get the activity profile dataset for Lantus Solostar insulin, and for other diabetes treatments such as Metformin?

I am working on a personal project for a better, more informed management of my own Diabetes Mellitus, Type 2 (aka "T2DM", or "T2D"). With some difficulty I am able to access and ...
Fritt Ro's user avatar
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16 views

Uploading manifest from CCDI to CGC project

Thank you in advance for your help! I am trying to download data from the CCDI (Children Cancer Data Initiative) and I have a manifest csv file that I downloaded from the CCDI. I'm trying to upload ...
msun5040's user avatar
0 votes
0 answers
18 views

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 ...
ricardo3889's user avatar
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0 answers
36 views

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 ...
llrs's user avatar
  • 4,713