Episode #125 of the Stack Overflow podcast is here. We talk Tilde Club and mechanical keyboards. Listen now
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Well you are assuming one sequenced genome/proteome per NCBI tax id. That is no longer true. So if you click on the proteome filter it decreases by half. Which gets you into the 60,000 range. Now not all of these are "different" conceptual proteins, many are artifacts from the way GenBank/EMBL/DDBJ interact with the TrEMBL section of UniProtKB i.e. they are ...


18

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 plain text files, each with one line per species (plus header line) and fields separated by tabs. The files and data descriptions are available at http://esapubs....


13

Uniprot has a list of the controlled vocabulary for common and scientific names of species listed here. An example entry: ACAER E 111511: N=Acanthodactylus erythrurus C=Spanish fringe-toed lizard S=Lacerta erythrura In the example the N is the scientific binomial name (Canthodactylus erythrurus), C is the common name (...


13

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: Thayer Watkins's webpage (San José State Univ.) found here, which includes: Blood pressure, height of head above heart, weight, avg heart rate, longevity, ...


12

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 measures, and develops spatial climate datasets to reveal short- and long-term climate patterns. WorldClim WorldClim is a set of global climate layers (climate ...


12

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 and available from the USDA Agricultural Research Service. Here is a link for the online searchable database. Within the database you are able to search for a ...


12

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 names. Their database includes common names (aka vernacular names) when they have that, and often common names from different languages. Using this API, you ...


10

For species occurance data the Global Biodiversity Information Facility (http://www.gbif.org/) database should be an obvious choice. It contains both historical records from museums etc and information from more recent surveys and inventories. Note that the occurrence data can both come from standardized inventories and observational records from specialists ...


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For climate related data you can start from Realclimate pages on data repository. For ecological data I always found less global data, but a good starting point may be the Ecological Society of America Data Registry page. An overview of repositories can be found the the Simmons University Open Access Directory.


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Databases There are too many databases to list here, but Wikipedia has a decent list of the genome databases. For example, there are databases dedicated to genes of individual species, like Wormbase, SGDB and countless others. Alternatively, as others mention a great place to kick off your search is the NCBI. Finding your nucleotide sequence in databases ...


9

CCCEEE etc. are the secondary structural elements. In this case, the C refers to non-strand and non-helix regions i.e loop regions rather than a coiled region. The C or E usually refers to whether the residue is coiled (C) or part of a strand (E). H would be used to denote a helix, however, in the question, it appears that there are no helices. These letters ...


9

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) (mainly for the pictures I think). If you do not fancy to much the display and links of oneZoom/org, then I would just recommend openTreeOfLife.org. There is also ...


8

NCBI is a good option. http://www.ncbi.nlm.nih.gov If you're looking for a gene sequence, you can search for the gene name in the nucleotide database. For example, here is the annotated human insulin gene; http://www.ncbi.nlm.nih.gov/nuccore/J00265.1


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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 Expression2Kinases download page because they are integrated into X2K pipeline as part of Genes2Networks analysis. If you need more proteins, you can submit your list ...


8

(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 vaccine recipients and rashes occur in 2-5% of vaccines, etc. Page 6 summarises the results in a table. As you point out, the adverse effects are variable in ...


7

You can find biochemical pathways on KEGG pathway for example. KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks for: 1. Metabolism Global/overview Carbohydrate Energy Lipid Nucleotide Amino acid Other amino Glycan Cofactor/vitamin ...


7

-- 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 global archive of curated plant traits. BioTraits This is an online resource for empirical data on how biological traits respond to environmental drivers such as ...


7

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 quantitative data, then you may be interested in the dataset included here. This is a dataset that consists of various life-history variables of many species. Some of ...


6

There does not appear to be a current standard, but Veg-X is a standard that has been developed to facilitate exchange of plot-based vegetation data, and may provide the closest to what you are looking for. Veg-X is described in Wiser et al 2011 and the project home page is http://wiki.tdwg.org/Vegetation/ From the abstract: The exchange standard for ...


6

So if you're reading the flowchart, understanding the notation of the arrows is important: We have rectangles around the gene products There's a circle, denoted by DNA, noting that the proteins are expressing the product that follows through interaction with DNA The solid line with an arrowhead means there's some sort of interaction The solid line with the ...


6

This is to a large extent a question of how reliable the data in the database needs to be. Reliability (and spatial scale) will differ between datasets and between species groups within datasets, and it is difficult to give a general recommendation. I doubt that you will find a single database with good coverage over all taxonomic groups, even if it is in ...


6

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 the most popular and easy method is to use Uniprot's list uploader for mapping. The corresponding publication can be found here. Example Programmatic access ...


6

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), there are 42,424,511. However, these databases are moving targets and will change over time. We will sequence more species, find novel splice isoforms, and ...


6

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, Polynucleotides and their Constituents, although not stated explicitly — presumably because this was written in 1974, before the large nucleic acid databases ...


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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.gov/data-specification I am correct in saying that the numbers in the 'element' array are corresponding to Atomic Numbers? Yes, 1 is hydrogen, 6 is carbon, ...


5

Large online floras have the advantage of not only having details and often photographs and illustrations, but also being (more or less) definitive, that is, botanists will refer to them. See my answer here for links to examples, and also for some of the problems with using floras (e.g. not easily downloadable).


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I recognize this was asked like 7 months ago, but in case you're still looking for a good resource: I used a CD of heart sounds that is called something like "Harvey Heart Sounds," which I got with the purchase of my stethoscope. If you can find a copy of this, I found it an excellent tool when training to recognize the differences. These are good heart ...


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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 structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be useful ...


5

I know that 1000 Genomes has sequenced Mother-Father-Child genomes from populations around the world (I think at least some of these samples were obtained from HapMap) and their data is publicly available by following the links in their website.


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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, Ecological level=Species: https://ecologicaldata.org/search?f[0]=taxonomy_vocabulary_2%253Aname%3ABirds&f[1]=taxonomy_vocabulary_6%253Aname%3ASpecies The '...


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