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 ...
- 9,024
14
votes
Accepted
Where can you find the quantities of each amino acid of a particular protein or food?
There's a fantastic database available from the United States Department of Agriculture that includes almost 9,000 common foods, including their nutritional information. This database is searchable ...
- 2,368
13
votes
Accepted
Where can I find historical data on world-wide ecology parameters?
Adding some additional database sources:
-- Climate --
Prism
The PRISM Climate Group gathers climate observations from a wide range of monitoring networks, applies sophisticated quality control ...
- 29.7k
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:...
- 29.7k
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 ...
- 16.7k
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:
...
- 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) (...
- 68k
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 ...
- 44k
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 ...
- 29.7k
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 ...
- 1,025
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 ...
- 1,515
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, ...
- 24.3k
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 ...
- 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 ...
- 1,562
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 ...
- 8,049
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 ...
- 11.3k
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)...
- 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....
- 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 ...
- 925
5
votes
Where can you find the quantities of each amino acid of a particular protein or food?
Go to WolframAlpha and enter 1g potato in the input field:
Then scroll down in the results to Protein and amino acids and click the more button in the top right hand corner to get the following list ...
- 519
5
votes
Accepted
Is there a database of cell images?
There is a yearly contest on cell tracking organized by the IEEE International Symposium on Biomedical Imaging, and the associated data sets are freely available.
See for example: http://www....
- 5,675
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, ...
- 51
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 ...
- 11.3k
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 ...
- 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 ...
- 29.7k
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, ...
- 5,675
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, ...
- 51.5k
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).
- 9,112
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 ...
- 11.3k
4
votes
Are there any open plant databases (database/library/collection), containing species information and pictures?
1. DELTA identification program key. (DELTA – DEscription Language for TAxonomy).
http://delta-intkey.com/ , http://delta-intkey.com/angio/ , https://florabase.dpaw.wa.gov.au/help/keys/...
- 2,659
Only top scored, non community-wiki answers of a minimum length are eligible