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linkIt man page Tools - LinkIT - Help


LinkIt
written by: Patrick Leary (pleary@ubio.org)
Filesize: 9290
Last modified: April 18, 2009, 11:04 pm

LinkIt is a tool that locates scientific names in web pages and (soon) PDF documents and adds links to taxonomic authority lists if the name is present in the list. It uses advanced lexical processing tools to identify names within the document text. These names are compared to the NameBank lexicon, a registry of over 4 million organism name strings. NameBank identifiers are mapped to the unique identifers of taxonomic authority databases. During the execution, LinkIt also logs all instances of mapped names to their sources using a SOAP-based logging call to NameBank. Thus, if someone uses linkIt to map the names in, for example, their publication list, and some of the names originated with Index Fungorum or FishBase, then each instance is logged in the daily log for these providers. The intention is to link use of LinkIt to the taxonomic authorities that enable it to function, increasing the linkage and relevance of the expert and user communities. (See figure below).

LinkIt uses a modified version of the full uBio name recognition algorithm FindIt that limits returned names only to forms already indexed in NameBank. Unlike FindIt, this version currently does not match author names making homonym discrimination problematic. The full FindIt algorithm is able to locate suspected scientific names and can distinguish authorship. The predominance of canonical names in recorded publications is the primary reason we haven't implemented this degree of disambiguation.

Arguments:

url: The only mandatory argument is a document URI.

map: The map argument defaults to 'all' which will return a link to any authority list that links to the identified name. Names not present in authority lists but indexed in NameBank are linked to a standard NameBank record form where a classificationSearch may provide additional taxonomic contexts from other indexed catalogs. LinkIt can be set to map to specific authority lists such as ITIS or the Species 2000 site. Current accepted values for map are ("itis" | "sp2000" | "fungi" = Index Fungorum | "alg" = Algaebase | "fish" = FishBase, "ncbi"=NCBI Taxonomy, "nz"=Nomenclator Zoologicus ). Others will be added.

no_logo: This argument takes a 1 or 0 (default=0) and toggles the presence|absence of the small uBio icon to indicate where a name link has been added to the page.

redirect: A redirect=1 will hyperlink the entire name instead of creating an annotation with the link. If map=all link_type will be disabled since more than one URL may be represented.

classify: A classify=1 will parse the name content of the page within the context of the ITIS classification for all names present within ITIS within a new division.

synonyms: Setting this parameter to one of the following languages (eng | fre | spa | ger | jpn | por | rus) will display a vernacular name with the scientific name in the selected language (if available).



Examples:

Links fish photos to FishBase
http://ubio.org/tools/linkit.php?map=fish&url=http://www.reef.org/webres/gallery/haw/page01.htm

Links names to Species 2000
http://ubio.org/tools/linkit.php?map=sp2000&url=http://www.rmh.uwyo.edu/research/FloristicInventoryRMFloraproject.htm

Links to ITIS with no logo and name hyperlinked
http://ubio.org/tools/linkit.php?map=itis&no_logo=1&link_type=1&url=http://www.reef.org/webres/gallery/haw/page01.htm

Add LinkIt to your Browser toolbar. (Thank you Rod Page)

In FireFox, Ctrl-Click on the bookmark bar and choose New Bookmark.

javascript:void(location.href='http://ubio.org/tools/linkit.php?map%5B%5D=all&link_type=2&url=' + location.href)


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