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

From Plant Ontology Wiki
Jump to navigationJump to search
 
(44 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
'''PO-FNA webex meeting June 21st 2011'''
+
[[PO-FNA webex meeting June 21st 2011]]
  
−
In attendance:
+
[[PO-FNA Conf Call Nov 18th, 2011]]
  
−
POC members:  Laurel Cooper (OSU), Pankaj Jaiswal (OSU),  Ramona Walls (NYBG).
 
  
 +
Link to [https://sourceforge.net/tracker/?func=detail&aid=3376762&group_id=76834&atid=835555 SourceForge tracker]
  
−
Collaborators:
 
−
James Macklin (institution; Flora of North America; james.macklin@gmail.com) and Hong Cui (University of Arizona; hong1.cui@gmail.com)
 
  
−
http://www.efloras.org/flora_page.aspx?flora_id=1
+
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.
  
−
HC:
 
−
Their group is interested in text mining applications using the PO and TO.
 
  
−
ABI (?) proposal being papered to annotate the Flora of North America
+
[[PO-FNA mapping results]] - summary of the initial mapping efforts, plus suggestions on how to proceed.
  
−
Current project is in the 3rd year. 
 
  
−
Taxonomic concepts
+
We now have id's for FNA terms. Still need to add new terms from the FNA list and create mapping file.
  
−
Develop software New applications
+
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.
  
−
eg. published fact eg. accepted name and synonyms.  Want to move from names to character spaces
+
''Where did this synonym go? It is still there, just doesn't show up in AmiGO.''
  
−
RW: discrete characters or continuous? JM: encompass them all
+
RW is working on modifying a perl script from JE to insert FNA synonyms into the PO file. May needs some help from JE.
  
−
Hong: List of terms from the literature:
+
-What are the plans after this?
  
−
Collaborator- (Bob Muller?) Looked through the PO and many were not there.
+
''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.''
  
−
PJ: Can develop mapping file, need to look over list and determine if they are valid plant structure vs phenotype terms
+
''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.''
−
The FNA terms may match a PO term name, synonym, or may be considered for addition as a new term
 
  
−
HC: We have already extracted the plant structure terms from the phenotype terms
+
''Will use PATO as it has terms available, and add PO terms as needed. Will also help show utility of PO to systematists.''
  
−
JM: Have a list or glossary of terms, of these about 30% have definitions. 
+
-Others (These may be longer term than the next release):  
  
−
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?
+
* Linking ontology terms to character matrices using Morphobank.
−
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)?
 
  
−
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.
 
  
−
PO may consider a new ontology class- Plant Phenotype Ontology? 
+
[[Category:Collaborations]]
−
 
 
−
The PO will refernce the ontology terms based to the FNA site through links, and provide examples of how it is used
 
−
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.
Retrieved from "http://wiki.plantontology.org/index.php?title=Flora_of_North_America-_FNA&oldid=17356"