=Paper=
{{Paper
|id=None
|storemode=property
|title=Mapping of glossary terms from the Flora of North America to the Plant Ontology
enhances both resources
|pdfUrl=https://ceur-ws.org/Vol-897/poster_6.pdf
|volume=Vol-897
|dblpUrl=https://dblp.org/rec/conf/icbo/WallsCMMCSJ12
}}
==Mapping of glossary terms from the Flora of North America to the Plant Ontology
enhances both resources==
https://ceur-ws.org/Vol-897/poster_6.pdf
Mapping of glossary terms from the Flora of North America to the
Plant Ontology enhances both resources
Ramona Walls1,* Hong Cui2, James A. Macklin3, Chris Mungall4, Laurel Cooper5,
Dennis Stevenson1 and Pankaj Jaiswal5
1
New
York
Botanical
Garden,
Bronx,
New
York,
USA
2School
of
Information
Resources
and
Library
Science,
University
of
Arizona,
Tucson,
Arizona,
85719
USA
3Research
Branch,
Agriculture
and
Agri-‐Food
Canada,
Ottawa,
Ontario,
Canada
4Lawrence
Berkeley
National
Lab,
Berkeley,
California,
USA
5Department
of
Botany
and
Plant
Pathology,
Oregon
State
University,
Corvallis,
OR,
USA
where the FNA has multiple terms with the same name but
1 INTRODUCTION separate meanings that should map to separate PO terms. A
Traditional taxonomic literature can provide a wealth of curator mapped the remaining FNA glossary terms to PO
data, but access to that data is limited by its free-text format. terms, based on the FNA and PO definitions.
Taxonomic treatments such as the Flora of North America A total of 193 FNA terms mapped to existing PO pri-
(FNA Editorial Committee 1993) consist of terse descrip- mary term names and 126 mapped to existing synonyms.
tions of the characters used to identify taxa, such as: 333 FNA terms had the same meaning as existing PO terms
“…Leaves usually alternate or opposite, sometimes in and have been added as synonyms to the PO, citing the FNA
basal rosettes, rarely in whorls; rarely stipulate, usually glossary as the source. 143 unique new terms will be added
petiolate, sometimes sessile…” to the PO, corresponding to 180 FNA glossary terms. 118
Converting taxonomic descriptions to computer-readable FNA terms could not be mapped to PO terms, either because
format makes them available for automatic retrieval and they were too vague (12 terms, e.g., FNA:lamella, which
large-scale analyses. Ontologies such as the Plant Ontology could apply to many different tissue types), because they are
(PO) play a central role in automatic annotation, by provid- subcellular components and belong in the Gene Ontology (5
ing semantic meaning for the words in a description. We terms, e.g., FNA:flagella), or because they are better mod-
used automated and manual methods to map terms from the eled as qualities (93 terms, e.g., FNA:puncta is better treated
Categorical Glossary for the Flora of North America Project as the quality punctate).
(http://128.2.21.109/fmi/xsl/FNA/home.xsl) to the PO. The PO is fairly extensive in its coverage of plant ana-
tomical entities, as many of missing terms are specialized
2 METHODS structures found only in a few taxa. The PO benefits from
this mapping through increased coverage of plant terminol-
Terms from the pre-existing categories of “structure”,
ogy. Text mining tools such as CharaParser (Cui 2012) that
“feature”, or “nominative” were extracted from the FNA
are being developed to mine taxonomic descriptions can
glossary, roughly corresponding to the PO class plant ana-
now use the PO more effectively for automated text annota-
tomical entity. An automated mapping to PO release 16 was
tion and in return mine more candidate terms from the lit-
done using Obol software (Mungall 2004). We manually
erature to further enrich PO. The mapping of FNA IDs to
checked the automated mapping, and removed any matches
PO IDs is available at http://tinyurl.com/FNAPOmapping.
that were incorrect. Remaining glossary terms were either
manually mapped to existing PO terms, classified as inap-
ACKNOWLEDGEMENTS
propriate for the PO, or marked to be added to the PO.
NSF-IOS: 0822201 to the Plant Ontology Project, and the
3 RESULTS AND DISCUSSION Flora of North America Association.
839 terms were extracted from the FNA glossary, com-
REFERENCES
pared to 1080 terms in the plant anatomical entity branch of
Cui, H. 2012. CharaParser for fine-grained semantic annotation of organism
the PO. Using text matching, Obol mapped 264 FNA terms morphological descriptions. J. of Am. Soc. of Information Science and
to 313 existing PO terms or synonyms, including 49 FNA Technology. 63(4) doi:10.1002/asi.22618
terms that matched more than one PO term or synonym. FNA Editorial Committee, eds. 1993. Flora of North America North of
Mexico. 16+ vols. New York and Oxford.
Most duplicate matches arose because the PO has many Mungall, Christopher J. 2004. “Obol: Integrating Language and Meaning in
synonyms in Spanish that are identical to the English term Bio-‐‑ontologies.” Comparative and Functional Genomics 5 (6-‐‑7) (Au-
name. Only 30 Obol matches had to be removed, in cases gust 1): 509–520. doi:10.1002/cfg.435
1