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Questions tagged [database]

Questions pertaining to organized collections of biological data.

3
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1answer
98 views

How to interpret this PubChem record of L-Alanine

Using the PUG service from NCBI, I am retrieving 3d structure data for a molecule. Raw data here. I am trying to understand this record, specifically for the purpose of rendering in a 3D coordinate ...
1
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0answers
30 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 ...
18
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3answers
1k views

Public database of animal specifications

I'm a math teacher looking for data to help my students interested in biology complete a quantitatively flavored study of animals. (As a math person, I apologize if I'm not using discipline-...
5
votes
1answer
433 views

Where are the statistics for vaccine side effects?

My son told me that that during a discussion at school someone mentioned statistics about side effects of vaccines (I assume that the discussion was about standard vaccines in France). The numbers ...
1
vote
1answer
55 views

Open Mass Spec Database

Wondering if there is an open (freely available) database of Mass Spec Data, particularly for the Substances/Compounds listed in NCBI. Specifically, I am not sure if NCBI includes the mass ...
1
vote
1answer
28 views

Comprehensive database of cell types

Wondering if there is a comprehensive list/database of cell types, similar to this wiki list of cell types in the human body. It lists probably 100+ different types, but this is just for a human. If ...
0
votes
1answer
38 views

Where can I find hemagglutination inhibition (HI) assay data?

I am looking for hemagglutination inhibition assay data for type A influenza virus. I've checked in databases such as fludb.com, however it seems to only have genetic data. A lot of the time, ...
2
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0answers
22 views

Where to find fossil databases [closed]

Looking for sites with fossil data in the following categories. Fossil cells Fossil invertibrates Fossil fish Fossil amphibians Fossil reptiles Fossil dinosaurs Fossil birds Fossil mammals Fossil ...
1
vote
1answer
36 views

List of genes across species (or just for humans)

Wondering if there is a place that has a list/table/database of all the genes in the human genome, and/or all the known genes in all the species we've studied so far. Something that contains any of ...
1
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2answers
45 views

Tree of Life in Text Format

Wondering if there is a tree of life in Text format for open data sharing.
3
votes
2answers
106 views

Is there a publically available database of microbes that details what their wastes and food sources are

Is there a publically available database of microbes that contains what their wastes and chemical food sources are in addition to other traits. So that I could do like a sorted search for microbes ...
5
votes
2answers
109 views

List of proteins by number of amino acids / chain length

Is there any protein database online where I could obtain a list of proteins ordered by the length of their chains / number of amino acids, starting from the shortest, as well as to see their amino ...
0
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0answers
22 views

Mouse H2 allele sequences

I've been trying to find complete sequences of mouse (Mus musculus) MHC H2 locus haplotypes for quite some time now with limited success. The EBI IMGT database has a table of mouse H2 haplotypes, yet ...
1
vote
1answer
28 views

Where do I get an annotation file for yeast genome with ENSEMBL ids?

Even the annotation files hosted on the Ensembl site have systematic names (starting with Y..) instead of ENSEMBL ids (starting with EN..). I bet there would be a place where I can get an annotation ...
3
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0answers
32 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 ...
1
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0answers
16 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 ...
0
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0answers
27 views

Calculating heritability, additive variance and total variance from a simulation

I have written a program intending to test a couple of evolutionary strategies and I have calculated heritability for the population (asexual) based on the values recorded during the simulation itself....
0
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0answers
24 views

Is my heritability implementation for an asexual population wrong?

I have written a program intending to test a couple of evolutionary strategies and I have calculated heritability for the population (asexual) based on the values recorded during the simulation itself....
3
votes
2answers
239 views

What direction is a sequence in databases written?

In many databases, the DNA sequences for proteins are given as a string of a,t,g,c without specifying whether the starting is from 5' or from 3'. Also it is not specified if it is the coding or non ...
0
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0answers
19 views

Is there a authority , full scale and detailed document or database about creature taxonmy? [duplicate]

I am a fan and starter in biology. I want to know more about different creatures. Is there an official website that introduces all or a majority of creatures in the world? For example: a famous ...
4
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0answers
46 views

How much Open Access Data is there in genetics? [closed]

Type of data of interest I would like to consider Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...) Genetic - phenotype data (disease-related data, QTL, etc...) Sequence ...
2
votes
2answers
272 views

How to search NCBI in bulk for a list of accession numbers?

I have a large ( >100 ) list of accession numbers I want to look up and match to searches in NCBI (nucleotide); mainly for getting a tentative organism to match to the accession number. ex: ...
0
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0answers
19 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 ...
1
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0answers
260 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 / ...
2
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0answers
37 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, ...
2
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0answers
37 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 ...
2
votes
1answer
656 views

What is the length of gene when calculating TPM (transcripts per million)

What is the length of gene when calculating TPM (transcripts per million)? Assume I have a dataset matrix with k rows(each row is a gene) and n columns (each column is a sample), is there any way I ...
0
votes
1answer
29 views

Is there a database for immunoglobulin domain structure?

is there a database where I can find the sequences of the hypervariable domain of immunoglobulins and the sequences of the related antigens? Thank you
1
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2answers
53 views

Analyzing Messy Data Files [closed]

I was writing some code scripts to analyze some plasmodium spp. using this database. However the names assigned to the various epitopes and other items on the list is very very very disorganized. In ...
3
votes
0answers
115 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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0answers
29 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 ...
2
votes
0answers
52 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 ...
-1
votes
1answer
142 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 ...
1
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0answers
48 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 ? ...
0
votes
1answer
36 views

Retrieve the associated annotation from Uniprot

I have a dataset that I extracted using Cytoscape and STRINGAPI Hoz can I retreive the annotation of that network from uniprot as it has more than 1k proteins . and doing it manually is not possible
7
votes
1answer
220 views

Where can I find large datasets of protein-interaction networks?

Where do I find large datasets of protein interaction networks for cancer or alzheimer diseases? So far, I found String but it is does not have enough proteins for my purposes. Are there such ...
8
votes
3answers
102 views

Global database for patients with rare and important injuries or disease?

I was recently reading Christof Koch's The Quest for Consciousness, and several times he mentioned how important some patients with sad and terrible brain injuries were for the understanding of the ...
6
votes
1answer
701 views

How many proteins are in the Earth's proteome? [closed]

Humans alone have thousands of proteins. With that in mind, it seems like the total number of proteins among all species would be very large. Are there any available estimates for how many proteins ...
2
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0answers
47 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 ...
8
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1answer
70 views

Where can I find comprehensive data on animal distribution?

I'm looking for vertical distribution or tidal height of several intertidal species, specifically from the Pacific Northwest. I considered looking for published research for each species however, my ...
3
votes
1answer
483 views

Meaning of ‘NC number’ associated with a gene?‘

Genes in listings etc. often have a number of the type NC_000012.12 associated with them. How should this be interpreted?
4
votes
2answers
88 views

Looking for a database of plant features

To perform some private data science experiments I am looking for accessible information on morphological plant features (tabular information would be best). Crawling the web I found many websites ...
4
votes
1answer
488 views

Database for drug-target relation

I'm writing a thesis on bioinformatics and looking for drug-target databases. I'm implementing a open-source application for a tool called Cytoscape and so far I've used a open-source database called ...
5
votes
1answer
94 views

Database of cancer cells

I am looking for a database(or any kind of information source) of cancer cells, which has information about the speed of reproduction of these cells, how fast they grow, etc. So I could make my ...
3
votes
0answers
84 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 ...
4
votes
1answer
54 views

How to automatically obtain the “kingdom” of a species from its name?

I'm looking for a simple way (such as a database) so that a program can get the kingdom of a species, knowing its name (such as "Prunus persica"). As a matter of fact the species I'm concerned with ...
9
votes
1answer
147 views

What is the most-stable gene identifier?

I've struggled in the past with designing data(bases) around gene-identifiers that evolve over time. For example, UniProt and Ensembl change their identifiers for certain proteins/genes and the IDs ...
12
votes
2answers
1k views

Online phylogenetic tree of human lineages

I am looking for a source of information about the diversity of human lineages and their relationships. With a quick google search it is easy to find this type of tree A perfect online resource ...
2
votes
0answers
440 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 ...
3
votes
1answer
139 views

databases for plant growth temperature and altitude

Does anyone know databases which have info for plant growth temperature.It could be specific numbers or categorization as 'cold, warm,tropical and etc' ?