Difference between revisions of "Flora of North America- FNA"

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'''PO-FNA webex meeting June 21st 2011'''
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[[PO-FNA webex meeting June 21st 2011]]
  
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In attendance:
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[[PO-FNA Conf Call Nov 18th, 2011]]
  
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POC members:  Laurel Cooper (OSU), Pankaj Jaiswal (OSU),  Ramona Walls (NYBG).
 
  
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Link to [https://sourceforge.net/tracker/?func=detail&aid=3376762&group_id=76834&atid=835555 SourceForge tracker]
  
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Collaborators:
 
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James Macklin (institution; Flora of North America; james.macklin@gmail.com) and Hong Cui (University of Arizona; hong1.cui@gmail.com)
 
  
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http://www.efloras.org/flora_page.aspx?flora_id=1
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Link to [http://huntbot.andrew.cmu.edu/HIBD/Departments/DB-INTRO/IntroFNA.shtml FNA online glossary], including and introduction/explanation of how the database was create.
  
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HC:
 
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Purpose of meeting: To establish collaborative relationship between them and PO/TO
 
  
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Their group is interested in text mining applications using the PO and TO, as well as other ontologies.
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[[PO-FNA mapping results]] - summary of the initial mapping efforts, plus suggestions on how to proceed.
  
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ABI proposal being prepared to annotate the Flora of North America,
 
  
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Current project @ parsing FNA is in the 3rd year, ends next year
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We now have id's for FNA terms. Still need to add new terms from the FNA list and create mapping file.
  
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New project: Taxonomic concepts: from plant family and bee(?) family, specimen descriptions
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Are we okay with using these FNA ids? They are UUID and are very long and contain dashes (e.g., 40b5fa5d-a75b-49d8-8328-b4c28d54ea66). See antheridium (PO:0025125) on dev browser for an example of how it will look.
  
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Project goal: Robustly produce the software they have developed with new applications
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''Where did this synonym go? It is still there, just doesn't show up in AmiGO.''
  
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eg. published fact eg. accepted name and synonyms. checklist
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RW is working on modifying a perl script from JE to insert FNA synonyms into the PO file. May needs some help from JE.
  
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-difficult for users to make sense of all the names etc
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-What are the plans after this?
  
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-Want to move from names to "character spaces"; parsed descriptions will describe what is held by the name
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''Once mappings are done, want to see how PO shows up in their data base. Show utility of PO for recovering descriptors from free text.''
  
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-characters and attributes, convert words back into matrices, use that to do analyses: logic-based and entropy-based ("information gain")
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''FNA is using natural language processing to map their descriptions to PO. We are starting with plant structures and later will add phenotype descriptors. We will start with leaf characters.''
  
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Assess: what is the character space held by this name?  Compare character spaces- more quantitative and interesting
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''Will use PATO as it has terms available, and add PO terms as needed. Will also help show utility of PO to systematists.''
  
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-Others (These may be longer term than the next release):
  
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* Linking ontology terms to character matrices using Morphobank.
  
  
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RW: discrete characters or continuous? JM: Want to encompass them all: Classical taxonomy has  cont. characters have been converted to discrete characters. Methods will allow for polymorphism, discrete and continuous characters.  Hardest part is defining terms and what those terms hold
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[[Category:Collaborations]]
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8:30
 
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Hong: lets discuss specifics: How and what format do the terms need to be in? To help the PO quickly evaluate and add them and give us the PO#.
 
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How can we let the software know that some term will not be there in the PO/TO?  Then they will have to figure out some other way for the SW to deal with them.
 
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HC:  List of terms from the literature (plant structures), with PO ids.  Collaborator- (Bob Morris?) and or his student Looked through the PO and many were not there. 
 
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PJ: Does the FNA assign the terms a unique ID #? Terms go into a relational table
 
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PJ: Can develop mapping file,to match our terms with theirs, conventions exist
 
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see:  link to SVN site
 
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PJ- Need to look over list and determine if they are 'valid' plant structure vs phenotype terms
 
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The FNA terms may match a PO term name, synonym, may be added as a synonym or may be considered for addition as a new term
 
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HC: We have already extracted the plant structure terms from the phenotype terms
 
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PJ: simplest first step, to examine the list/vocabulary which has been curated
 
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JM: Have a list or glossary of terms, of these, about 30% have definitions.
 
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18:30
 
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HC: During the project, we will be discovering new terms on a daily basis- is it better to save and send them as a batch or individually?
 
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PO: Either is fine, good if we have background info on the terms, taxonomic characters, literature citations etc.  Can you provide an examples of how it is used (ie: in a sentence)?
 
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PJ: Character list: Can these go into the TO? PATO may be to general, they may not want to want ot add all our specific terns- may be useful for the upper levels though.
 
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PO may consider a new ontology class- Plant Phenotype Ontology? 
 
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The PO will reference the ontology terms based to the FNA site through links, and provide examples of how it is used
 
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FNA could be added as a dbxref in the ontology and could also create a subset similar to the one for traitnet
 

Latest revision as of 16:19, 30 April 2012

PO-FNA webex meeting June 21st 2011

PO-FNA Conf Call Nov 18th, 2011


Link to SourceForge tracker


Link to FNA online glossary, including and introduction/explanation of how the database was create.


PO-FNA mapping results - summary of the initial mapping efforts, plus suggestions on how to proceed.


We now have id's for FNA terms. Still need to add new terms from the FNA list and create mapping file.

Are we okay with using these FNA ids? They are UUID and are very long and contain dashes (e.g., 40b5fa5d-a75b-49d8-8328-b4c28d54ea66). See antheridium (PO:0025125) on dev browser for an example of how it will look.

Where did this synonym go? It is still there, just doesn't show up in AmiGO.

RW is working on modifying a perl script from JE to insert FNA synonyms into the PO file. May needs some help from JE.

-What are the plans after this?

Once mappings are done, want to see how PO shows up in their data base. Show utility of PO for recovering descriptors from free text.

FNA is using natural language processing to map their descriptions to PO. We are starting with plant structures and later will add phenotype descriptors. We will start with leaf characters.

Will use PATO as it has terms available, and add PO terms as needed. Will also help show utility of PO to systematists.

-Others (These may be longer term than the next release):

  • Linking ontology terms to character matrices using Morphobank.
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