18 votes

Public database of animal specifications

You might be interested in the PanTHERIA database for several thousand mammalian species. It has up to 53 characteristics for each species (but many fields have no entry). It is available as two ...
mgkrebbs's user avatar
  • 9,054
13 votes

Public database of animal specifications

I'm not positive, but I assume you'll be hard-pressed to find a list that checks your boxes of needing both multiple metrics for multiple animals. However... Two sources that seem to prove me wrong:...
theforestecologist's user avatar
12 votes

Where can I get a file/list of the common and scientific names of species?

Maybe not a direct answer to your question, depending on what you mean with "unencoded data file", but the Global Biodiversity Information Facility (GBIF) has an API where you extract data for species ...
fileunderwater's user avatar
12 votes
Accepted

Where can I get a file/list of the common and scientific names of species?

Uniprot has a list of the controlled vocabulary for common and scientific names of species listed here. An example entry: ...
James's user avatar
  • 11.3k
11 votes
Accepted

The best free and most up to date phylogenetic tree on the internet?

Available ressources I would recommend oneZoom.org is probably the best ressource. oneZoom.org is based on openTreeOfLife.org (for phylogenetic relationships) and eol.org (Encyclopedia Of Life) (...
Remi.b's user avatar
  • 68.1k
9 votes
Accepted

What structures does our brain use for a quick indexing of all the data we store in our heads?

Brains are not computers, and do not process information like computers. The trees from CS you are talking about are ways to run linear information stores through a central processing unit. Even with ...
Bryan Krause's user avatar
  • 45.7k
8 votes

Looking for a database of plant features

-- Traits -- TRY TRY is a Plant Trait Database. More formally, it's a network of vegetation scientists headed by DIVERSITAS/IGBP, and the Max Planck Institute for Biogeochemistry, providing a ...
theforestecologist's user avatar
8 votes
Accepted

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

There is a bunch of decent protein-protein interaction databases: Biocarta, BioGrid, DIP, InnateDB, IntAct, MINT, PPID. Some of them aren't available now, but you can download datasets from the ...
Maxim Kuleshov's user avatar
8 votes
Accepted

Where are the statistics for vaccine side effects?

(World Health Organisation, 2014. p. 2) shows the adverse effect (side-effect) rates for the MMR vaccine. For instance, fever between the 7th to 12th day after vaccination occurs in 5 to 15% of ...
Jam's user avatar
  • 1,506
7 votes
Accepted

What direction is a sequence in databases written?

Directionality It is indeed the convention to represent nucleic acid sequences in the 5ʹ to 3ʹ direction. This is implied in the IUPAC/IUB document on Abbreviations and Symbols for Nucleic Acids, ...
David's user avatar
  • 25.7k
7 votes

Public database of animal specifications

Does it have to be those physical criteria that you mention, or are you just interested in datasets that include a lot of quantitative data about animals? Because if you're interested in other ...
Eff's user avatar
  • 680
7 votes

Where can I find SARS-CoV-2 genome sequences for the UK?

Oxford University's Bugbank project is designed to collect SARS-CoV-2 samples (and other microbial cultures) from UK Biobank participants for sequencing. Once completed this data will be available to ...
brazofuerte's user avatar
  • 1,582
6 votes
Accepted

How to batch convert gene names to protein IDs in Uniprot?

ID mapping This is called ID mapping. It used to be a headache as programmatic sequence comparisons were the only real way, but it is pretty trivial these days. As mentioned in the comments, by far ...
James's user avatar
  • 11.3k
6 votes

Open database of medical images

Open-access medical images: MedPix (by keyword, organic system, pathology and diagnosis A-Z) Radiopaedia (by keyword) PEIR Radiology (by keyword, organ or anatomic region) Ultrasound Cases (by ...
Jan's user avatar
  • 8,079
6 votes

How many proteins are in the Earth's proteome?

Current records According to Uniprot, there are 85,381,808 protein records, and with the UniRef90 filter (i.e removing records that can be represented by an entry with at least 90% sequence similarity)...
James's user avatar
  • 11.3k
6 votes
Accepted

How to interpret this PubChem record of L-Alanine

The PubChem format description is not that easy to find: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/asn_spec/pcsubstance.asn.html And the ASN file linked here: https://pubchemdocs.ncbi.nlm.nih....
Ashafix's user avatar
  • 695
6 votes

Where can I download a list of all plant species of the world?

This website claims to contain all the plant species we know of (and also contains some statistics on the state of their collection). Keep in mind that there are many species that have yet to be found ...
Ark Lomas's user avatar
  • 933
5 votes
Accepted

How can I make a protein interaction/protein-complex network?

This is not a trivial task depending on how well studied your network is or what information you want to gather. It sounds like an interaction dataset is what you want rather than scouring the PDB for ...
James's user avatar
  • 11.3k
5 votes

How to gather life-history traits data on bird species?

Have you tried the Ecological Data Wiki? It's an NSF-funded repository of links to ecological databases and datasets: Main page: http://ecologicaldata.org Find data tab, refined to Taxon=Birds, ...
Ian McFadden's user avatar
5 votes

Can two protein secondary structures "overlap" in the PDB?

TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment. Ambiguous secondary ...
James's user avatar
  • 11.3k
5 votes
Accepted

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

You could try the Catalogue of Life The Catalogue of Life is the most comprehensive and authoritative global index of species currently available. It consists of a single integrated species ...
theforestecologist's user avatar
5 votes

Database of cancer cells

The National Cancer Institute (NCI) has a list of doubling times for a variety of commonly used cell lines, see https://dtp.cancer.gov/discovery_development/nci-60/cell_list.htm I my experience, ...
Roland's user avatar
  • 5,705
5 votes

Database for commercially available restriction enzymes?

You are probably talking about type II endonucleases, there are a few databases available from the companies which sell these enzymes like NEB or Thermo Fisher. Additionally tools like NEBcutter, ...
Chris's user avatar
  • 51.6k
4 votes

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

A recombination map of the E. coli genome was recently published (several years after question was asked).
Maximilian Press's user avatar
4 votes

Convert gene name to uniprot ID

ID mapping This is called ID mapping. It used to be a headache as programmatic access was the only real way, but it is pretty trivial these days. As mentioned in the comments, by far the most popular ...
James's user avatar
  • 11.3k
4 votes
Accepted

Understanding common identifier codes (IDs) in biology databases

Common biology ID codes. PDB: 2BIB for example. 4 letter code for a specific structure. Uniprot: Q9NZT1 for example. A six letter combination of numbers and letters for either a TrEMBL or Swissprot ...
James's user avatar
  • 11.3k
4 votes

How can I find the mRNA sequence for a specific prokaryotic gene?

mRNA specific queries Add this to your NCBI query: AND mrna[filter] If it's not available in major databases it may not be known. However mRNA data can be ...
James's user avatar
  • 11.3k
4 votes
Accepted

Online phylogenetic tree of human lineages

Trees for haplogroups See https://www.eupedia.com/genetics/phylogenetic_trees_Y-DNA_haplogroups.shtml https://www.eupedia.com/genetics/ focus on Europe: https://www.eupedia.com/europe/...
root's user avatar
  • 206
4 votes

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

This particular ID represent RefSeq accession number. NC_ stands for a genomic molecule representing complete genomic molecule, usually reference assembly. Every sequence has a stable accession number,...
JITZ's user avatar
  • 115

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