10 ms·

Encyclopedia of Life

104 points by matthberg 3y ago

oever 3y ago
With Subtree of Life you can find relationships between species: https://sol.vandenoever.info/ https://sol.vandenoever.info/
- emernic 3y ago
  The info on that site is... not even close to correct. Choanozoa as the sister group of all other life including bacteria and archaea? All eukaryotes broken into Opisthokonta, Chloroplastida, and Amoebozoa? Maybe the stuff on metazoans is more accurate, but in the big picture of the genetic diversity of life on earth they're barely a footnote.
  - oever 3y ago
    The tree only shows species that are selected and their closest common ancestors. The relationships are obtained from opentreeoflife.org.
  - oever 3y ago
    Here's an example: two bird species selected via uid share as most recent_common ancestor Passeriformes. https://sol.vandenoever.info/?uids=695336,1093902 https://sol.vandenoever.info/?uids=695336,1093902 When another bird species is added, one more closest common ancestor pops up: https://sol.vandenoever.info/?uids=695336,1065606,1093902 https://sol.vandenoever.info/?uids=695336,1065606,1093902 https://en.wikipedia.org/wiki/Most_recent_common_ancestor https://en.wikipedia.org/wiki/Most_recent_common_ancestor
- samuell 3y ago
  FWIW, TimeTree is based on phylogenic trees sourced from the the literature: https://timetree.org https://timetree.org ... and publishes references to the literature backing a relationship. This is important since the tree you get can vary even depending on the gene you study, which can raise some questions about how to interpret these trees.
- willpearse 3y ago
  If you like Subtree of Life, you're going to love 'Onezoom' (https://www.onezoom.org/ https://www.onezoom.org/) which is a very attractive 'Google Maps of life' sort of site, and TimeTree (http://www.timetree.org/ http://www.timetree.org/) which is similar but the visualisation is much more traditional (not fractals) in comparison with the first.
krylon 3y ago
Wildly OT, but: The domain name is a bit funny, when I read "eol" my brain jumps to "end of life". ;-)
- zabzonk 3y ago
  for a computer guy, "end of line", surely?
  - npsomaratna 3y ago
    CRLF
    - comboy 3y ago
      LF
      - zabzonk 3y ago
        CR (pre OS X)
        hoosieree 3y ago
        Or the rare LRCF.
  - tshaddox 3y ago
    As a software developer I definitely run into “end-of-life” a lot more than “end of line.”
    - zabzonk 3y ago
      well, if you have a full-sized keyboard, you will see the (goto) end (of line) key peering up at you all the time. but i must admit, i hardly ever use it.
      - 3y ago
xipho 3y ago
See also https://opentreeoflife.github.io/ https://opentreeoflife.github.io/, https://opentreeoflife.org https://opentreeoflife.org. And some shameless plugs- One of the EOL lead devs is now a member of our group https://speciesfilegroup.org/ https://speciesfilegroup.org/. We have two open-source projects that seek to contribute in this field, TaxonWorks, https://taxonworks.org https://taxonworks.org, a web-workbench that lets you gather the data behind these types of pages and TaxonPages, an effort to make it possible, ultimately, for anyone to produce Species/Taxon pages - https://github.com/SpeciesFileGroup/taxonpages/ https://github.com/SpeciesFileGroup/taxonpages/. We expect to have 50k+ TaxonPages (akin to species pages) available this year as we transition some legacy data forward.
dalf 3y ago
wikidata [1] [2] has "few" species with links to many other databases like * plazi.org list taxonomic treatment (~ species description) found in journals, papers using OCR when needed. * gbif.org list specimens (and other things) using normalized datasets provided by various institutions (including Plazi). one process among many others : some algorithms run by GBIF find potential matches between species and specimens, with some human curation, we can link between a specimen and the related papers. [1] https://www.wikidata.org/wiki/Q309337 https://www.wikidata.org/wiki/Q309337 [2] https://www.wikidata.org/wiki/Q106254624 https://www.wikidata.org/wiki/Q106254624
qingcharles 3y ago
It turns out that humans have a "litters per year" of approximately 0.3.

104 points by matthberg 3y ago

With Subtree of Life you can find relationships between species: https://sol.vandenoever.info/ https://sol.vandenoever.info/

emernic 3y ago
The info on that site is... not even close to correct. Choanozoa as the sister group of all other life including bacteria and archaea? All eukaryotes broken into Opisthokonta, Chloroplastida, and Amoebozoa? Maybe the stuff on metazoans is more accurate, but in the big picture of the genetic diversity of life on earth they're barely a footnote.
- oever 3y ago
  The tree only shows species that are selected and their closest common ancestors. The relationships are obtained from opentreeoflife.org.
- oever 3y ago
  Here's an example: two bird species selected via uid share as most recent_common ancestor Passeriformes. https://sol.vandenoever.info/?uids=695336,1093902 https://sol.vandenoever.info/?uids=695336,1093902 When another bird species is added, one more closest common ancestor pops up: https://sol.vandenoever.info/?uids=695336,1065606,1093902 https://sol.vandenoever.info/?uids=695336,1065606,1093902 https://en.wikipedia.org/wiki/Most_recent_common_ancestor https://en.wikipedia.org/wiki/Most_recent_common_ancestor
samuell 3y ago
FWIW, TimeTree is based on phylogenic trees sourced from the the literature: https://timetree.org https://timetree.org ... and publishes references to the literature backing a relationship. This is important since the tree you get can vary even depending on the gene you study, which can raise some questions about how to interpret these trees.
willpearse 3y ago
If you like Subtree of Life, you're going to love 'Onezoom' (https://www.onezoom.org/ https://www.onezoom.org/) which is a very attractive 'Google Maps of life' sort of site, and TimeTree (http://www.timetree.org/ http://www.timetree.org/) which is similar but the visualisation is much more traditional (not fractals) in comparison with the first.

krylon 3y ago

Wildly OT, but: The domain name is a bit funny, when I read "eol" my brain jumps to "end of life". ;-)

zabzonk 3y ago
for a computer guy, "end of line", surely?
- npsomaratna 3y ago
  CRLF
  - comboy 3y ago
    LF
    - zabzonk 3y ago
      CR (pre OS X)
      - hoosieree 3y ago
        Or the rare LRCF.
- tshaddox 3y ago
  As a software developer I definitely run into “end-of-life” a lot more than “end of line.”
  - zabzonk 3y ago
    well, if you have a full-sized keyboard, you will see the (goto) end (of line) key peering up at you all the time. but i must admit, i hardly ever use it.
    - 3y ago

xipho 3y ago

See also https://opentreeoflife.github.io/ https://opentreeoflife.github.io/, https://opentreeoflife.org https://opentreeoflife.org. And some shameless plugs- One of the EOL lead devs is now a member of our group https://speciesfilegroup.org/ https://speciesfilegroup.org/. We have two open-source projects that seek to contribute in this field, TaxonWorks, https://taxonworks.org https://taxonworks.org, a web-workbench that lets you gather the data behind these types of pages and TaxonPages, an effort to make it possible, ultimately, for anyone to produce Species/Taxon pages - https://github.com/SpeciesFileGroup/taxonpages/ https://github.com/SpeciesFileGroup/taxonpages/. We expect to have 50k+ TaxonPages (akin to species pages) available this year as we transition some legacy data forward.

dalf 3y ago

wikidata [1] [2] has "few" species with links to many other databases like * plazi.org list taxonomic treatment (~ species description) found in journals, papers using OCR when needed. * gbif.org list specimens (and other things) using normalized datasets provided by various institutions (including Plazi). one process among many others : some algorithms run by GBIF find potential matches between species and specimens, with some human curation, we can link between a specimen and the related papers. [1] https://www.wikidata.org/wiki/Q309337 https://www.wikidata.org/wiki/Q309337 [2] https://www.wikidata.org/wiki/Q106254624 https://www.wikidata.org/wiki/Q106254624

qingcharles 3y ago

It turns out that humans have a "litters per year" of approximately 0.3.