Difference between revisions of "Update Taxon Lists"

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(Teleost Taxonomy Ontology term additions or changes)
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The following are instructions on how to update a taxon list after you have received an email from a student informing you that the taxon list for a particular publication was completed, and needs an update for taxonomy.
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If you need to create a taxon list for a publication, see  [[Creating Taxon Lists | Creating Taxon Lists instructions]].
  
====Download the taxon file from the phenoscape-fileshare====
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The following are instructions on how to update a taxon list for taxonomy and submit requests for needed taxonomic names in the VTO.
  
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====Open file in Phenex====
  
To download a copy of the taxon file, you will need to connect to the [https://phenoscape.org/wiki/Help:Contents#File_Shares Phenoscape file share].  Ask a PhenoScaper for username and password.
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Make sure that you have an internet connection before starting Phenex as the software will need to download updated ontology files if available.
  
After connecting to the file share, navigate to the Taxon List (phenote+) folder and copy the relevant file to your desktop.
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Choose the Taxon perspective by going to Window>Taxon. This will display only the Taxon panels (Taxa, Specimens, Term Info) in Phenex.
  
====Open file in Phenote+====
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====Review Taxon List====
  
Make sure that you have an internet connection before starting Phenote+ as the software will need to download updated ontology files if available.
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The Taxa and Specimens Panels are used to record information from a publication's materials list. Within the Taxa Panel, the Publication Taxon field is a free-text field listing the names of all taxa used in the publication, and the Valid Taxon field is an ontology-enabled field linked to the Vertebrate Taxonomy Ontology, and used to record the current, valid names of the taxa.  Comments or questions about a particular entry are recorded in the Taxon Comments column. The Matrix Taxon field (which you usually do not need to edit) is used to record the name of taxa used in the matrix.  Specimen information (museum vouchers) for each species is recorded in the Specimens table.
  
Start up Phenote+ (click "Update All" if the update panel appears) and check that you are using the Taxon configuration of Phenote (to check, go to Settings>Set Configuration, and confirm that ‘phenoscape_taxon’ is chosen. You may need to restart Phenote+ for the configuration to appear).
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You can sort the data by clicking on any column header.  Sort the "Taxon Comments" column to view the questions or comments that a student recorded about the taxon list.  Also sort by "Valid Taxon" to view missing entries.
  
Open the taxon file using File>Open.
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====Making updates to taxon entries====
  
====Review Taxon List====
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The names listed in the '''Publication Taxon''' column are those used in the publication, and should not require editing by curators (though edit if there is an obvious mismatch with the publication, usually because of a mistaken entry by a student).  '''Valid Taxon''' names will usually need to be updated.
  
Taxon Lists are spreadsheets with five fields used to record information from a publication's materials list (see screenshot below).  The Publication field records the name and DOI of a publication if available.  The Publication Taxon field is a free-text field used to record the name of a taxon used in the publication, and the Valid Taxon field is an ontology-enabled field linked to the Teleost Taxonomy Ontology, and  records the current, valid name of the taxon.  Comments or questions about a particular entry are recorded in the Curator Notes column, and the Specimens field is linked to a table that lists specimen information (museum vouchers).
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Not all publication taxa need to be updated with valid taxon names: only update those that were used in the matrix. To find taxa associated with matrix data, look at: 1) the '''Matrix Taxon''' column in the Taxa Panel, which will contain higher level taxon names if used by an author as a placeholder for multiple taxa; 2) the Publication Taxon column within the '''Matrix Panel''' (View > Annotation > Matrix).
  
You can sort the taxon file by "Curator Notes" to review the questions or comments that a student recorded about the taxon list.  Also sort by "Valid Taxon" to view missing entries.
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If you make any updates on a file or submit term requests for an entry, be sure to write a note in the Taxon Comments column detailing your actions.
  
====Make updates or requests====
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====Taxonomy ontology change requests====
 
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#Taxon name misspelled: Misspellings are requested as synonyms of the correctly spelled taxon name in the VTO. Choose the appropriate name from the Valid Taxon field, and add note in Taxon Comments field (e.g., Requested addition of synonym to VTO, Your Name, 7/28/2008)
The following are examples of incomplete entries that a taxon expert may encounter when reviewing a taxon list.  If you make any updates on a file or submit term requests for an entry, be sure to write a dated note in the Curator Notes column detailing your actions (and preserve any previous notes left by a student).
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#If an author has made an error in the generic assignment of a species, which does not represent a difference in taxonomic opinion or concepts, then the current valid name of that species should be chosen, and the erroneous name should be added to VTO as a synonym of the valid name.  The curator should add a comment in the Taxon Comments about the request.
 
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#Taxon name not found: If the missing taxon name is a synonym of a valid name, then the synonym will need to be added to the taxonomy ontology.  Add a note in Taxon Comments field (e.g., taxon XY is synonym of XZ: submitted VTO request on 7/28/2008 by Your Name).
#Taxon name misspelled: Choose the appropriate name from the Valid Taxon field, and add note in Curator Notes field (e.g., correctly spelled valid taxon name chosen, Your Name, 7/28/2008)
 
#Taxon name not found: If the missing taxon name is a synonym of a valid name, then the synonym will need to be added to the taxonomy ontology.  Add a note in Curator Notes field (e.g., taxon XY is synonym of XZ: submitted TTO request on 7/28/2008).  Leave the Valid Taxon field blank.
 
 
#Unnamed or unknown species:  Examples of unnamed or unknown species in a Materials list might include: Danio sp., Cyprinus sp. 1, Cyprinus sp. 2, Danio aff. dangila, Danio cf. dangila, etc... These names should be added to the taxonomy ontology with reference to the publication. In this example, for a publication by Smith 2008, the request for new species names would be:
 
#Unnamed or unknown species:  Examples of unnamed or unknown species in a Materials list might include: Danio sp., Cyprinus sp. 1, Cyprinus sp. 2, Danio aff. dangila, Danio cf. dangila, etc... These names should be added to the taxonomy ontology with reference to the publication. In this example, for a publication by Smith 2008, the request for new species names would be:
  
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*Danio cf. dangila (Smith 2008)
 
*Danio cf. dangila (Smith 2008)
  
=====Taxonomy Ontology requests for term additions or changes=====
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=====''Taxonomic Requests''=====
 
 
You need only submit one request per publication.  See [https://www.nescent.org/phenoscape/Term_Requests term request instructions] for the TTO.
 
  
[[Category:Curation]]
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You need only submit one request per publication.  See [https://www.nescent.org/phenoscape/Term_Requests term request instructions] for the VTO.
  
====Copy updated file to fileshare====
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=====''Museum Code Requests''=====
  
After you have completed your updates and made notes regarding any term requests submitted, upload your file to Phenoscape fileshare (you will overwrite the previous copy of the taxon list file).
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We use the Fish Collection Codes spreadsheet on Google Docs, along with the taxonomy term tracker, to request the addition of missing codes, or request addition of synonyms of an existing code.  See instructions [https://www.nescent.org/phenoscape/Term_Requests#Collection_Code_requests here]
  
 
====Update entry for publication on Google Docs====
 
====Update entry for publication on Google Docs====
  
Remember to make a note (dated) in the Taxon List Notes column of the shared publication spreadsheet on Google Docs (ask a PhenoScaper for access to the spreadsheet), recording that you have reviewed the taxon list and made any necessary term requests.
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Remember to make a note (dated) in the Taxon List Notes column of the shared publication spreadsheet on Google Docs (ask a Phenoscaper for access to the spreadsheet), recording that you have reviewed the taxon list and made any necessary term requests.
  
 
[[Category:Curation]]
 
[[Category:Curation]]

Latest revision as of 21:14, 26 November 2012

If you need to create a taxon list for a publication, see Creating Taxon Lists instructions.

The following are instructions on how to update a taxon list for taxonomy and submit requests for needed taxonomic names in the VTO.

Open file in Phenex

Make sure that you have an internet connection before starting Phenex as the software will need to download updated ontology files if available.

Choose the Taxon perspective by going to Window>Taxon. This will display only the Taxon panels (Taxa, Specimens, Term Info) in Phenex.

Review Taxon List

The Taxa and Specimens Panels are used to record information from a publication's materials list. Within the Taxa Panel, the Publication Taxon field is a free-text field listing the names of all taxa used in the publication, and the Valid Taxon field is an ontology-enabled field linked to the Vertebrate Taxonomy Ontology, and used to record the current, valid names of the taxa. Comments or questions about a particular entry are recorded in the Taxon Comments column. The Matrix Taxon field (which you usually do not need to edit) is used to record the name of taxa used in the matrix. Specimen information (museum vouchers) for each species is recorded in the Specimens table.

You can sort the data by clicking on any column header. Sort the "Taxon Comments" column to view the questions or comments that a student recorded about the taxon list. Also sort by "Valid Taxon" to view missing entries.

Making updates to taxon entries

The names listed in the Publication Taxon column are those used in the publication, and should not require editing by curators (though edit if there is an obvious mismatch with the publication, usually because of a mistaken entry by a student). Valid Taxon names will usually need to be updated.

Not all publication taxa need to be updated with valid taxon names: only update those that were used in the matrix. To find taxa associated with matrix data, look at: 1) the Matrix Taxon column in the Taxa Panel, which will contain higher level taxon names if used by an author as a placeholder for multiple taxa; 2) the Publication Taxon column within the Matrix Panel (View > Annotation > Matrix).

If you make any updates on a file or submit term requests for an entry, be sure to write a note in the Taxon Comments column detailing your actions.

Taxonomy ontology change requests

  1. Taxon name misspelled: Misspellings are requested as synonyms of the correctly spelled taxon name in the VTO. Choose the appropriate name from the Valid Taxon field, and add note in Taxon Comments field (e.g., Requested addition of synonym to VTO, Your Name, 7/28/2008)
  2. If an author has made an error in the generic assignment of a species, which does not represent a difference in taxonomic opinion or concepts, then the current valid name of that species should be chosen, and the erroneous name should be added to VTO as a synonym of the valid name. The curator should add a comment in the Taxon Comments about the request.
  3. Taxon name not found: If the missing taxon name is a synonym of a valid name, then the synonym will need to be added to the taxonomy ontology. Add a note in Taxon Comments field (e.g., taxon XY is synonym of XZ: submitted VTO request on 7/28/2008 by Your Name).
  4. Unnamed or unknown species: Examples of unnamed or unknown species in a Materials list might include: Danio sp., Cyprinus sp. 1, Cyprinus sp. 2, Danio aff. dangila, Danio cf. dangila, etc... These names should be added to the taxonomy ontology with reference to the publication. In this example, for a publication by Smith 2008, the request for new species names would be:
  • Danio sp. (Smith 2008)
  • Cyprinus sp. 1 (Smith 2008)
  • Cyprinus sp. 2 (Smith 2008)
  • Danio aff. dangila (Smith 2008)
  • Danio cf. dangila (Smith 2008)
Taxonomic Requests

You need only submit one request per publication. See term request instructions for the VTO.

Museum Code Requests

We use the Fish Collection Codes spreadsheet on Google Docs, along with the taxonomy term tracker, to request the addition of missing codes, or request addition of synonyms of an existing code. See instructions here

Update entry for publication on Google Docs

Remember to make a note (dated) in the Taxon List Notes column of the shared publication spreadsheet on Google Docs (ask a Phenoscaper for access to the spreadsheet), recording that you have reviewed the taxon list and made any necessary term requests.