SOAP tools for identifying names and name/authors

[David Remsen]

Greeting:   I'd like to announce the release of a set of SOAP methods
that have proven useful in parsing scientific names from freetext.
Using SOAP client calls, you can use these functions locally within
your own applications.

The FindIT method accepts a URL or base-64 encoded text as input and
outputs a list of all scientific names it finds in the input text as
an XML object.   The name-recognition algorithm identifies names as
well as authorship and nomenclatural annotation.  It accepts a number
of additional input parameters.  The output includes the identified
name string, both whole, and broken into it's component parts, a
confidence score, and and nameBank identifier (if it exists).

The author abbreviation resolver methods complement the findIT
method.  It accepts author name strings and returns an array of
mapped lexical variations.  This is very useful for determining the
nomenclatural equivalence of distinct lexical forms of the same
name.  This tool has an input interface.  If you would like to
contribute to this utility I can add you to the editor list.

http://namebank.ubio.org/soap/
http://namebank.ubio.org/soap/finditSOAP.php

http://www.ubio.org/authors/index.php

That's the basic announcement.  You can stop here or continue with an
example below.

Thank you,
David Remsen
uBio Project

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Example The text below:

"The chief region of rosin production is the South Atlantic and
Eastern Gulf states of the United States. American rosin is obtained
from the turpentine of the swamp pine, Pinus australis Michx., and of
the loblolly pine, P. taeda. The main source of supply in Europe is
the landes of the departments of Gironde and Landes in France, where
the cluster pine, P. pinaster, is extensively cultivated. In the
north of Europe rosin is obtained from the Scotch fir, P. sylvestris,
and throughout European countries local supplies are obtained from
other species of pine."

passed to the findIT method will output (in part):

<?xml version="1.0" encoding="UTF-8"?>
<allNames>
         <entity>
                 <nameString>P[inus] taeda</nameString>
                 <parsedName canonical="Pinus taeda">
                         <component type="name" rank="genus">P[inus]</
component>
                         <component type="name" rank="species">taeda</
component>
                 </parsedName>
                 <score>1</score>
         </entity>
         <entity>
                 <nameString>Pinus australis Michx.</nameString>
                 <parsedName canonical="Pinus australis">
                         <component type="name" rank="genus">Pinus</
component>
                         <component type="name"
rank="species">australis</component>
                         <component type="author" id="1">Michx.</
component>
                 </parsedName>
                 <score>0.75</score>
         </entity>
</allNames>

The author abbreviation "Michx." can be input to the
namebank_search_authors method.  The search can limit to, for
example, the Brummit and Powell author abbreviations.  This returns
an author group ID for matches and a default display form for that
group.  The group ID returns all members of the group.   Example:


<?xml version="1.0" encoding="UTF-8"?>
        <authorGroup groupID="142">
                <dateRangeString>1746-1802</dateRangeString>
                <authorString>
                        <stringForm>Michaux, Andre</stringForm>
                        <stringQualifier id=1>default display form</stringQualifier>
                </authorString>
                <authorString>
                        <stringForm>Michaux</stringForm>
                        <stringQualifier id=2>Harvard University Herbarium src</
stringQualifier>
                </authorString>
                <authorString>
                        <stringForm>Michx.</stringForm>
                        <stringQualifier id=3>Brummitt and Powell src</stringQualifier>
                </authorString>
                <authorString>
                <stringForm>Andre Michaux</stringForm>
                <stringQualifier id=4>lexical variant originating in the Harvard
Univ. Herbaria database</stringQualifier>
                </authorString>
                <groupSource>Brummitt and Powell, Authors of Plant Names. Royal
Botanic Gardens, Kew, 1992</groupSource>
                <groupSource>Taxonomic Literature. Second Edition. Utrecht</
groupSource>
        </authorGroup>

_______________________________________________
David Remsen
uBio Project Manager
Marine Biological Laboratory
Woods Hole, MA 02543
508-289-7632