Biology Stack Exchange
Biology Stack Exchange

Questions tagged [database]

Questions pertaining to organized collections of biological data.

178 questions
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Where can I find historical data on world-wide ecology parameters?

I hope this is the right StackExchange forum for such a question. I'm looking for large data sets on world-wide ecology parameters, such as annual temperatures by latitude, annual rainfall, CO₂ and O₂ concentration in the atmosphere and in the…
Tobia
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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-appropriate vocabulary in my request here.) I'd like to…
Jared
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Can two protein secondary structures "overlap" in the PDB?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: HELIX 4 4 MET A 255 ILE A 265 1 11 SHEET 2…
Douglas S. Stones
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Where can I get a file/list of the common and scientific names of species?

I am searching for an un-encoded data file with common and scientific names for example of a few hundred species or tens of thousands, where I can search the common and scientific labels of organisms.
bandybabboon
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Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein coding genes in the human genome. Is this something to do with splice isoforms, like…
James
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Are there any open plant databases (database/library/collection), containing species information and pictures?

I would like to download a plant database containing photos and species details. Do you know if there are any openly available online?
Eszter
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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 would... Contain a lot of lineages going to the most…
Remi.b
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The best free and most up to date phylogenetic tree on the internet?

I found phylogenetic tree in wikipedia is lacks of accuracy. It actually confusing with versions. Some terms was not scientifically accurate with dna analysis anymore So are there anyone know where is the most updated datasource on the internet?
Thaina
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How can I find the mRNA sequence for a specific prokaryotic gene?

What I want to find out is the start of the transcription for a specific gene, how long the UTR is before the actual coding sequence starts. I've looked at various databases like NCBI Gene, Refseq or a specialized one like PRODORIC. But none of them…
user19833
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Database of Geographic Range of Species

Is there a database of organisms which would contain their queriable geographic location? I would need to perform a rather simple query, such as Animals of , where Location is some well defined geographic area such as Czech Republic or…
Jan Drábek
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Is there a standard format for plant community composition data?

FIA has a nice database of forest Inventory data, this would be great except that it does not seem capable of handling data from non-tree species (e.g., grasslands, wetlands). Is there a standard database or flat-file format for collecting plant…
David LeBauer
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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 go stale after a while (years). HGNC seems…
roadnottaken
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Where can you find the quantities of each amino acid of a particular protein or food?

Taking a potato as an example. If I wanted to know how much µg or % of each of it's amino acids there are in 1 gram of pure potato protein, where can I find this information? Is there a freely accessible database online with these statistics? Or,…
Happy
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How to search for organisms by criteria such as growth substrate and overflow metabolites?

I'm looking for a database or a systematic way to search for organisms which meet certain criteria. My criteria descending importance are: growth substrate chemolithoautotrophy (on which substrate) overflow…
ib84
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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 working of the brain. It made me wonder how brain…
Mario Krenn
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