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Taxonomic Name Resolution Service http://evoio.org/wiki/Phylotastic/TNRS by Gaurav Vaidya (http://ggvaidya.com /) Monday, 28 January, 13

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Page 1: Phylotastic TNRS, January 28, 2013

Taxonomic Name Resolution Service

http://evoio.org/wiki/Phylotastic/TNRSby Gaurav Vaidya (http://ggvaidya.com/)

Monday, 28 January, 13

http://evoio.org/wiki/Phylotastic/TNRS
http://evoio.org/wiki/Phylotastic/TNRS
http://ggvaidya.com
http://ggvaidya.com
Page 2: Phylotastic TNRS, January 28, 2013

Panthera tigris

Monday, 28 January, 13

Page 3: Phylotastic TNRS, January 28, 2013

Panthera tigris

http://en.wikipedia.org/wiki/Panthera_tigris

Monday, 28 January, 13

http://en.wikipedia.org/wiki/Panthera_tigris
http://en.wikipedia.org/wiki/Panthera_tigris
Page 4: Phylotastic TNRS, January 28, 2013

Panthera tigris

http://eol.org/pages/328674/overview

Monday, 28 January, 13

http://en.wikipedia.org/wiki/Panthera_tigris
http://en.wikipedia.org/wiki/Panthera_tigris
Page 5: Phylotastic TNRS, January 28, 2013

Panthera tigris

http://www.ncbi.nlm.nih.gov/nuccore?term=Panthera%20tigris

Monday, 28 January, 13

http://www.ncbi.nlm.nih.gov/nuccore?term=Panthera%20tigris
http://www.ncbi.nlm.nih.gov/nuccore?term=Panthera%20tigris
Page 6: Phylotastic TNRS, January 28, 2013

Panthera tigris

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9694&lvl=3&lin=f&keep=1&srchmode=1&unlock

Monday, 28 January, 13

http://www.ncbi.nlm.nih.gov/nuccore?term=Panthera%20tigris
http://www.ncbi.nlm.nih.gov/nuccore?term=Panthera%20tigris
Page 7: Phylotastic TNRS, January 28, 2013

Panthera tigris

http://data.gbif.org/occurrences/searchWithMap.htm?c[0].s=20&c[0].p=0&c[0].o=5219416

Monday, 28 January, 13

http://data.gbif.org/occurrences/searchWithMap.htm?c%5B0%5D.s=20&c%5B0%5D.p=0&c%5B0%5D.o=5219416
http://data.gbif.org/occurrences/searchWithMap.htm?c%5B0%5D.s=20&c%5B0%5D.p=0&c%5B0%5D.o=5219416
Page 8: Phylotastic TNRS, January 28, 2013

Panthera tigris

http://www.mappinglife.org/Panthera_tigris

Monday, 28 January, 13

http://www.mappinglife.org/Panthera_tigris
http://www.mappinglife.org/Panthera_tigris
Page 9: Phylotastic TNRS, January 28, 2013

Problems

Monday, 28 January, 13

Page 10: Phylotastic TNRS, January 28, 2013

Synonymy

http://species.wikimedia.org/wiki/Panthera_tigris

Monday, 28 January, 13

http://species.wikimedia.org/wiki/Panthera_tigris
http://species.wikimedia.org/wiki/Panthera_tigris
Page 11: Phylotastic TNRS, January 28, 2013

Synonymyhttp://data.gbif.org/occurrences/searchWithMap.htm?c[0].s=20&c[0].p=0&c[0].o=4969819

Monday, 28 January, 13

http://data.gbif.org/occurrences/searchWithMap.htm?c%5B0%5D.s=20&c%5B0%5D.p=0&c%5B0%5D.o=4969819
http://data.gbif.org/occurrences/searchWithMap.htm?c%5B0%5D.s=20&c%5B0%5D.p=0&c%5B0%5D.o=4969819
Page 12: Phylotastic TNRS, January 28, 2013

FormattingPanthera tigrisP. tigrisPanthera tigris (Linnaeus, 1758)Panthera tigris Linnaeus, 1758Panthera tigris L.Panthera tigris Linn.Panthera_tigrisPtigris_gi_440919618felidae/panthera/panthera_tigris

Monday, 28 January, 13

Page 13: Phylotastic TNRS, January 28, 2013

MisspellingsPantera tigrisP. tigrsPanthera tigris (Linneaus, 1758)Panthera tigris Linnaeus, 1858Panthera tigris l.Panthera tigris linn.Panthera_tigriscoiPt_gi_440919618felidae/panthera/panthera_tigris

Monday, 28 January, 13

Page 14: Phylotastic TNRS, January 28, 2013

Homonymshttp://en.wikipedia.org/wiki/Crucibulum

Monday, 28 January, 13

http://en.wikipedia.org/wiki/Crucibulum
http://en.wikipedia.org/wiki/Crucibulum
Page 15: Phylotastic TNRS, January 28, 2013

Homonymshttp://en.wikipedia.org/wiki/Crucibulum_(gastropod)

Monday, 28 January, 13

http://en.wikipedia.org/wiki/Crucibulum_(gastropod
http://en.wikipedia.org/wiki/Crucibulum_(gastropod
Page 16: Phylotastic TNRS, January 28, 2013

Changes in circumscription

http://www.inaturalist.org/taxon_changes/31

Monday, 28 January, 13

http://www.inaturalist.org/taxon_changes/31
http://www.inaturalist.org/taxon_changes/31
Page 17: Phylotastic TNRS, January 28, 2013

Changes in circumscription

http://www.inaturalist.org/taxon_changes/31

Monday, 28 January, 13

http://www.inaturalist.org/taxon_changes/31
http://www.inaturalist.org/taxon_changes/31
Page 18: Phylotastic TNRS, January 28, 2013

Changes in circumscription

http://www.inaturalist.org/taxon_changes/31

Monday, 28 January, 13

http://www.inaturalist.org/taxon_changes/31
http://www.inaturalist.org/taxon_changes/31
Page 19: Phylotastic TNRS, January 28, 2013

Changes in circumscription

http://www.inaturalist.org/taxon_changes/31

Monday, 28 January, 13

http://www.inaturalist.org/taxon_changes/31
http://www.inaturalist.org/taxon_changes/31
Page 20: Phylotastic TNRS, January 28, 2013

Differences in opinionhttp://www.inaturalist.org/taxon_changes/31

Monday, 28 January, 13

http://www.inaturalist.org/taxon_changes/31
http://www.inaturalist.org/taxon_changes/31
Page 21: Phylotastic TNRS, January 28, 2013

iPlant TNRS

For more information: http://www.biomedcentral.com/1471-2105/14/16

http://tnrs.iplantcollaborative.org/TNRSapp.html

Monday, 28 January, 13

http://www.biomedcentral.com/1471-2105/14/16
http://www.biomedcentral.com/1471-2105/14/16
http://tnrs.iplantcollaborative.org/TNRSapp.html
http://tnrs.iplantcollaborative.org/TNRSapp.html
Page 22: Phylotastic TNRS, January 28, 2013

Taxosaurus

Monday, 28 January, 13

Page 23: Phylotastic TNRS, January 28, 2013

Taxosaurus

http://api.phylotastic.org/tnrs

Monday, 28 January, 13

http://api.phylotastic.org/tnrs
http://api.phylotastic.org/tnrs
Page 24: Phylotastic TNRS, January 28, 2013

What works?

An API for matching names.

Names => URLs

Software which matches names against:

Mammal Species of the World, 3rd ed

NCBI Taxonomy

iPlant TNRS

Monday, 28 January, 13

Page 25: Phylotastic TNRS, January 28, 2013

What’s next?More databases:

ITIS (all life)

IRMNG (all life)

WoRMS (marine species)

More features:

Fuzzy matching.

Provenance.

More reliable.

Monday, 28 January, 13

Page 26: Phylotastic TNRS, January 28, 2013

But ...

Monday, 28 January, 13

Page 27: Phylotastic TNRS, January 28, 2013

Matching names against names

Bininda-Emonds et al (2007)Nature 446: 507-512 http://dx.doi.org/10.1038/nature05634

Monday, 28 January, 13

http://dx.doi.org/10.1038/nature05634
http://dx.doi.org/10.1038/nature05634
Page 28: Phylotastic TNRS, January 28, 2013

Matching names against names

Bininda-Emonds et al (2007)Nature 446: 507-512 http://dx.doi.org/10.1038/nature05634

Logo from http://www.bucknell.edu/msw3/Monday, 28 January, 13

http://dx.doi.org/10.1038/nature05634
http://dx.doi.org/10.1038/nature05634
http://www.bucknell.edu/msw3/
http://www.bucknell.edu/msw3/
Page 29: Phylotastic TNRS, January 28, 2013

Matching names against names

Monday, 28 January, 13


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