Questions tagged [database]

Questions pertaining to organized collections of biological data.

42 questions with no upvoted or accepted answers
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How can I search through literature databases for words containing a * when the asterisk is read as syntax and not part of a query?

I'm exploring the literature on microRNA, where it is common for the less utilised strand of the miRNA duplex to be referred to as the miRNA* strand. However, I am experiencing some issue searching ...
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37 views

Is there a taxonomy of species with emergence and extinction dates?

I know the NCBI has a list of each species and their place in the evolutionary tree. But do they have the dates that these species existed? Does any such database (partial or complete) exist anywhere? ...
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37 views

How to interpret the relationships of PTMs from BioGRID's data

On BioGRID Database, PTMREL is a file that describes relationships of the PTMs (Post Translation Modification) tabulated in a PTMTAB file. I have several issues with this file. Foremost, I am not ...
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335 views

Is there a database of known riboswitches?

I'm looking for sequences and annotations of known riboswitches, but so far I haven't found a resource that actually fulfills my requirements. The best database I found so far is Rfam, which has ...
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63 views

Database of Medical Assertions

Can anyone point me toward a computationally-accessible database of medical assertions? I'm looking for something where each row in the database contains a single unit of knowledge. It could either be ...
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27 views

What websites biologists use to check what new plant or animal species have been discovered in the world?

What are the databases or websites that biologists use to check what new plants or animals have been found in the world? The service should list the location of the discovery, time of discovery, image ...
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44 views

What's the best source characterizing proteolysis cleavage sites in the phagolysosome?

I have found MEROPS and TopFIND via the survey paper Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity. These look like a good start, ...
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43 views

Do GPCRs have 7TMHs?

I've screened a non-redundant set of GPCRs acquired from UniProt. I found a handful of examples of record IDs that contain more than the 7 TMHs. For example Q89609 and P20905, both of which have been ...
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127 views

Protein/ligand affinity databases?

Is there any database that contain binding affinities reported in litterature for different proteins and ligands? I have checked uniprot already and it does not seem to included any binding affinity ...
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64 views

String-db locally downloaded

I need a ppi network of cancer and it should have 200k to 300k proteins (nodes) As the web inteface don't allow more than 2000 ...
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56 views

Open access datasets for QTL analysis?

I'm just getting started out learning how to use the QTL package in R studio, and I'm trying to find additional datasets to practice with. I've already worked through the datasets here on the Rqtl ...
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86 views

Database of time lapse stem cell differentiation

Currently I am working on a project about modelling the social behaviours of embryonic stem cells (or induced pluripotent stem cells). I need a series of time-lapse live cell images which recording ...
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711 views

Drugs with unknown mechanism of action

I want to get a list of FDA-approved drugs with unknown mechanism of action. I think that there should be a database where for each drug there is a short field "mechanism", but I haven't find one. Do ...
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74 views

Genotype-Phenotype databases?

Beyond the Stanford HIV database, what other databases out there provide a dataset linking virus/bacterial genotype to quantitative phenotype? I'm looking for high quality datasets to test machine ...
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129 views

dbSNP database table desciptions

I am trying to build a local implementation of dbSNP. I would like to know the descriptions of tables listed on ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606 and on ftp://ftp.ncbi....
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42 views

How to find a model organism's standard data about proteome size and genome size?

I want to know proteome size(the number of proteins not length) and genome size(length) of model organisms like Caenorhabditis elegans, Saccharomyces cerevisiae etc. I found www.uiprot.org and I made ...
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9 views

Cell image database for citotoxicity test

Is there any cell image database for citotoxicity tests? I know that there are several image databases available (like this, this and this one), but none of them have the images for citotoxicity tests....
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1answer
20 views

Image Dataset for Cardiac cells for Mus musculus?

I'm working on developing a transfer learning model to detect cells in a culture using microscopic images. for that i require data set of images having microscopic images of various cell types. Is ...
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13 views

Meiotic recombination hotspots

Im trying to find a proper and general file with chromosomal coordinates for meiotic recombination hotspots. I know that ucsc hgtables, has a table with recombination regions and their recombination ...
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175 views

Open database of whole slide digital pathology images

I am looking for sequential image sections (stacks) of biological structures (such as liver, kidneys etc.) that I can download and use. Most of the pathology images I have found are either one image ...
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24 views

Database of predicted protein-ligand binding/docking score

Is there a database of computationally determined "binding scores" across protein-ligand pairs in the PDB? My phrase "binding score" is deliberately generic, since any such score would be fine. In ...
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354 views

Specific activity vs turnover number of enzymes in BRENDA

From my understanding, the specific activity (A, units: umol/min/mg protein) can be derived from the turnover number (k, units: 1/seg) and the molar mass of an enzyme (MW, units: g/mol): A = k / MW / ...
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35 views

Get Network Out of proteins of interest

I have generated a list of Proteins using oncogeenes and suppressor genes of cancer. I have 5827 mapping identifier for 3916 interactions using STRINGdb R package . How do I build a network of 200k ...
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51 views

Biogrid interaction protein network

I need a ppi network for cancer or Alzheimer . I'm using BioGrid , In the search field I can specify the gene id only , I want to know how can I make an interaction network for one of the disease ? ...
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33 views

Difference between curated publications and additional publications in nextProt database?

With reference to reference papers listed in nextProt database, what is the difference between curated publications and additional publications? Anyone using nextProt, kindly explain the terms. For ...
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102 views

How to find name of the gene

Considering the kegg page, this page contains the description of the gene Edwardsiella tarda EIB202: ETAE_0074 . Now this gene has a name given in the page as : wabG. Now considering another gene 1 ...
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80 views

Download FunCat Database for Programmatic Access

I am enriching RNA-seq data for the fungus Neurospora crassa and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other ...
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58 views

Recombination frequency as a function of genomic location in E coli?

Are there any databases or papers that give recombination frequency as a function of position in the E coli genome?
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20 views

What are good databases for RNA-binding motifs?

I am asking this question because it is hard to prove non-existence (of better data): I am searching for a good RNA-binding motif database that is as up-dated as possible and covers motifs for as many ...
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12 views

Complete Hominin Fossil Database

I was wondering if there was a database or list of all hominin fossil specimens. I am doing my own personal research, and don’t need images but just names. I know of lists such as the one here, but ...
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17 views

Advice on type of database and software for research on genetic diversity of crops

for a research project I am evaluating the potential of Robusta coffee genetic resources in the tropic region of Africa. Different ex-situ genetic lines will be mapped as well as chemical, ...
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10 views

Regalecus glesne or Regalecus russelii?

I was doing research on Regalecidae, and I came across an online database. Here, on the database, there are 12 matches for Regalecus russelii. At the bottom of most of these pages, there is a related ...
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38 views

Public fermentation/cell cultivation database?

I am wondering if there are any large collections of fermentation or cell cultivation data publicly available. I am interested in all cell types used within industrial biotech and biopharma, ...
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49 views

Where can I find anthropometric data for different ethnicities?

I get that this is a sensitive topic, but please trust me, the very reason I'm asking is because I want to represent a people properly. There's a video game where peoples of different ethnic ...
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22 views

Is there any animal database or website that classifies animals as wild / domestic?

Is there any animal database or website that classifies animals wild / domestic? Or.. the site that I can get the wild / domestic information of animal list...
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15 views

Database for Macroinvertebrate Taxonomy

I compiled different data sets of invertebrate occurrences across some countries and now I want to ensure that all the taxonomic information is homogenized and correct. To this end, I am looking for a ...
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23 views

Database of colors mapped to species

I was wondering about the physics of color, and now am interested in finding out if there are any resources (databases, text files, html tables, or pdf listings) of species and their associated colors ...
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42 views

Which database has the ready made 16S rRNA Multiple Sequence Alignment File that I can download directly from?

In my case, I need the ready made 16S rRNA Multiple Sequence Alignment File for E.coli and use it to generate the phylogenetic tree file in Newick format. I've tried using the one from utexas website, ...
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20 views

Which scientific names designate eyespots?

I've found that names containing ocellata‎ and ocellatus‎ designate species that feature eyespots. Are there other words in the scientific names that designate eyespots? The problem I need to solve ...
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26 views

Size of the glycan chain in a glycosylated protein

I would like to know where I can find the (experimental/estimated) distribution of glycan sizes attached to proteins.
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907 views

Online Database for PPG (Photoplethysmography) signals (both Infrared and Red light readings)

I am looking for an online Database for PPG (Photoplethysmography) signals for SPO2 (oximetry) analysis. I have tried several sources but they only have single datasets labelled "PLETH" and not ...
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152 views

Stringdb using R Bioconductor package

I need to retreive a large dataset from String-db. I 'm newbie in R so even with the documentation , I could not get the dataset fron String How do I do to retreive a network from String 2k to 3k ...