PO-FNA Conf Call Nov 18th, 2011

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POC-FNA meeting, Webex Conference Call; Date: Monday Nov 14th, 2011 10am (PST)

Planned In attendance: Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Ramona Walls (NYBG)


Collaborators: Hong Cui, James Macklin


Back to: Main Flora_of_North_America-_FNA page

PO-FNA mapping

*Received the initial file from HC (FNA Term glossary (PO071811) (HC 7-18-11).csv)- renamed for clarity from "PO071811" From HC (by email)- "Attached please find the set of terms with definitions. This set was extracted from FNA glossary (see below). This CSV file has three columns: term, definition, and limitation. The limitation indicates where the structure is found. Definitions were given by botanists."

Note that the initial file we received had three columns: "term, category, limitation", but no definitions.

From JM (by email): The FNA glossary was produced by Bob Kiger at the Hunt Institute in Pittsburg. It is available in printed form and on-line. The glossary was a first attempt at standardization for the project but was quickly built on but never officially updated. I think Hong says that there are now 70% more terms than the original and we are not even done yet! The on-line version is here: http://huntbot.andrew.cmu.edu/HIBD/Departments/DB-INTRO/IntroFNA.shtml so you can cite it.

*Initial mapping was done using the program "OBOL" with assistance from CM. see: link

Mungall, C. J. (2004). Obol: Integrating Language and Meaning in Bio-Ontologies. Comparative and Functional Genomics, 5, 509-520.

Straight entity-matching to PO, with no TO

The set of matches was appended on as additional columns.

Each match is a quad of:

1. PO ID 2. PO Label 3. Match Label (stemmed) 4. Match synonym scope

In general, if there were multiple matches, only the best one was shown. (Sometimes it is hard to disambiguate).

Eg. aerial root >STRUCTURE > match(PO:0000042; shoot-borne root, syn: aerial root,narrow) match(PO:0009005; root, syn: aerial root, narrow)

note: this may reveal some synonyms that need to be revised in the PO, The syn for PO:0009005 seems odd.

*Manual editing of the mapping file by RW to Release #16: See detailed notes in the excel file: "FNA_Term_glossary(HC 7-18-11)_to_PO_release16.xlsx"

Mapping results

See the Summary of the initial mapping efforts on this page: PO-FNA mapping results

PO follow-up tasks

  • add 364 synonyms to existing terms
  • fix several errors that were discovered while doing the mappings
  • add 143 unique new terms, plus their synonyms

-FNA provides definitions, so this will be relatively easy -A few of these are already on our list of terms to add, some from other users (e.g. phyloclade).

  • create an official mapping file

Open questions

need unique IDs for FNA terms

in order to deal with duplicates (multiple concepts with same name)

Examples:

FNA:columella has two meanings. One maps to gynophore, the other maps to fruit columella

FNA:ligule has 4 different meanings (3 structures and 1 character)

plus many others

FNA terms that map to >1 PO term

Examples:

FNA:apex matches to PO:bract apex, leaf apex, petal apex, petiole distal end, phyllome apex, reproductive shoot apex, sepal apex, shoot apex, tepal apex, vegetative shoot apex, bract apex, leaf apex, petal apex, petiole distal end, phyllome apex, reproductive shoot apex, sepal apex, shoot apex, tepal apex, vegetative shoot apex

FNA:blade matches to PO:lamina and PO:leaf lamina

When possible, we should make general term (e.g., organ apex, lamina) and only map FNA term to the general term. FNA can use reasoner to find all of the subtypes. If it is not possible to create one general term (e.g., tendril), we will need to map to each term separately.

Should have a separate line for each unique concept (each line is one FNA id and one PO id).

For future text mining, HC will try to include the parent structure (e.g., leaf base, rather than just base), so it is more clear what to map to.

FNA terms that map to obsolete PO terms

  • 8 terms, inlcudes duplicate plural forms, 5 unique.

pyrene: obsolete. The hard inner portion of a drupe, consisting of osseous endocarp and included seed.

coccus, cocci, mericarp: obsolete. One of the segments of a dehisced schizocarp; usually one-seeded and itself indehiscent.

microphyll: obsolete (What about megaphyll? Currently mapped to vascular leaf. Microphyll could map there too.)

also:

multiple fruit: mapped to obsolete PO:0020086 multiple fruit, but now maps as synonym to PO:fruit


  • 3 have been replaced by GO terms:

papilla, papipillae: map to obsolete PO:0020053. Could map to plant cell papilla (GO:0090395) or could be character term (papillate).

wall: maps to obsolete pollen wall PO:0020059 now GO:0043667 (also maps to 6 other PO terms)

FNA terms that are too general for PO

101 character terms: areole 1, beak 1, diffuse root, blotch, scallop, etc.

12 terms that are too vague, but hard to define as characters: commissure, isthmus, lamella, lamellae, membrane, suture, tubercle, indument, indumentum, indumenta, vestiture, vesture

Phenotype/character terms form FNA

  • begin work on phenotype/character terms, inlcuding the 101 from this list plus all of the FNA character terms
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