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===== From "genes" to "phenotype": linking organism names in NCBI to their taxonomic descriptions in the biodiversity literatue =====

{{:project:make_open_data_ncbi_20150605_200323_resized_1.jpg?200 |(screenshots or sketches up here)}}
{{:project:make_open_data_ncbi_20150606_110408_resized.jpg?200 |}}


=== Issue ===

Organisms (taxa in taxonomic language) in NCBI implicitly relate to a currently accepted name in the taxonomic world, where those taxa have been established in a scientific article. However, many of those taxa have been undergoing a change in their naming history which involves often many variants, from synonyms, the original combination, to misidentifications. Synonymic lists are contained in nomenclators  (name services). They allow two essential services: to find out for any given name what the currently accepted name is, and, relevant in this context, the links to the taxonomic treatment via the bibliographic citation, or more recently a persistent idnentifier. This allows to retrieve all the content published on any of the names, and thus to have at once all the published information available. The inclusion of synonyms thus allows to expand the amount of linked data for any of the taxa in NCBI.

==== Use case ====


**Anochetus grandidieri** (Ant from Madagascar)

//NCBI Taxonomy// 

ID: [[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=269309&lvl=3&lin=f&keep=1&srchmode=1&unlock|269309]]


Other names:

synonym: Anochetus sp. BLF m2

synonym: Anochetus madecassus

synonym: Anochetus grandidieri Forel, 1891


//Taxonomy Name server//


for ants: Hymenoptera Name Server


ID [[http://hol.osu.edu/?id=187786|25263]]


alternative names or this taxon (synonyms, misspellings, misidentification) can be found by expanding the "literature" section on the page above.


=== Worflow ===

see image on top of page


=== Solution ===

A link from NCBI will find all the synonyms of the names in NCBI used for this organism (list of synonym provided by NCBI), which then will be run against nomenclatures on the biodiversity world, and then submitted to Plazi where a summary page with all the taxonomic treatments will be displayed.

{{:project:plaziwebsitemockup04_species_level_taxon_summary_page.png?200 |}} 

The data will be available as [[ 	http://treatment.plazi.org/id/31F96F41-E3E0-02BD-8898-5A4F3A20E45A|html]], [[http://plazi.cs.umb.edu/GgServer/xslt/31F96F41E3E002BD88985A4F3A20E45A|XML]] and [[http://plazi.cs.umb.edu/GgServer/rdf/31F96F41E3E002BD88985A4F3A20E45A|RDF]] (the example are here for single taxonomic treatments)


The project will be continued and hopefully tested and implemented via the NCBI link out option.

=== Follow up===

On June 26, this project has been implemented and provides the descriped linkout from NCBI: the above example [[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=269309|Anochetus grandidieri]] as well as all the 15764 [[http://tinyurl.com/nzjrjyj|Binominals]] (Scientific Latin Names) that Plazi shares with NCBI taxonomy


=== Links ===


  * [[http://www.ncbi.nlm.nih.gov/taxonomy|National Institute of Bioinformatics]] 
  * [[http://plazi.org| Plazi]]
  * [[http://plazi2.cs.umb.edu/GgServer/search?taxonomicName.isNomenclature=isNomenclature&taxonomicName.exactMatch=exactMatch&taxonomicName.taxonomicName=Anochetus+grandidieri|example]]

===== Team =====

  * [[user:donat]] Agosti, Plazi
  * Terry Catapano, Plazi 
  * Mara Hellstern
  * Philipp Kuntschik, HTW Chur  
  * Guido Sautter, Plazi
  * Elena Mastrandrea, HTW Chur


  
{{tag>status:concept needs:dev needs:design needs:data needs:expert}}