project:genestobiodiversity

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project:genestobiodiversity [2015/06/06 12:29] – created donatproject:genestobiodiversity [2015/06/25 06:55] (current) – donat
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 **Anochetus grandidieri** (Ant from Madagascar) **Anochetus grandidieri** (Ant from Madagascar)
  
-NCBI Taxonomy +//NCBI Taxonomy// 
  
-ID: 269309+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]]
  
-http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=269309&lvl=3&lin=f&keep=1&srchmode=1&unlock 
  
 Other names: Other names:
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-Name server+//Taxonomy Name server// 
  
 for ants: Hymenoptera Name Server for ants: Hymenoptera Name Server
  
-ID 25263 
  
-http://hol.osu.edu/index.html?id=25263+ID [[http://hol.osu.edu/?id=187786|25263]]
  
-other names 
  
 +alternative names or this taxon (synonyms, misspellings, misidentification) can be found by expanding the "literature" section on the page above.
  
  
-Include links to your demo and/or source code.+=== Worflow ===
  
-===== Data =====+see image on top of page
  
-  * List and link your actual and ideal data sources.+ 
 +=== 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 ===== ===== Team =====
  
-  * [[user:donat]] +  * [[user:donat]] Agosti, Plazi
-  * Elena Mastrandrea, HTW Chur +
-  * Philipp Kuntschik, HTW Chur+
   * Terry Catapano, Plazi    * Terry Catapano, Plazi 
 +  * Mara Hellstern
 +  * Philipp Kuntschik, HTW Chur  
   * Guido Sautter, Plazi   * Guido Sautter, Plazi
 +  * Elena Mastrandrea, HTW Chur
  
-===== Links ===== 
  
-  * Relevant documentation ... 
-  * Blog or forum posts ... 
-  * Tools you used ... 
      
 {{tag>status:concept needs:dev needs:design needs:data needs:expert}} {{tag>status:concept needs:dev needs:design needs:data needs:expert}}
- 
  • project/genestobiodiversity.txt
  • Last modified: 2015/06/25 06:55
  • by donat