BioGeomancer

Training Set from Manis MaNISLocTypes1-500.txt.

The MaNIS file can be transformed into a format for B2K learning using the shell script conditionManis.sh. This script is dependent on two other programs. The first, TitleTagManisTraining_ex05_stream.pl transforms xml to title format. The second program onelineperfile.pl converts each line of the input file to a file in the output directory. Each module is documented internally. The final collection of files is available here as a zipped tar file biogeo.tar.gz.

Locality Examples from New Mexico, USA. Documentation on the files is available at NMexicoLocations.txt

• UNMHerbNMLocforGeoref_20040903.csv
• WNMU_BirdLocalities_20051012.csv
• WNMU_FishLocalities_20051012.csv
• WNMU_HerbLocalities_20051012.csv
• WNMU_HerpLocalities_20051012.csv
• WNMU_MammalLocalities_20051012.csv
  

Transformation Program to get file into D2K format Java code

D2K Itinerary for NB D2K website

Locality Types (Category names) for Locations Frame

Hand coded parses of training set (Eugene)

• Eugene's signature files and folders: Signature Directory
• Eugene's XML data output, mostly correct location classification of MaNIS500 records. These records should be verifyed by hand which should be easier than marking up the locality types from scratch.
• Hand Validated Records should go here.
  

Herbis

Data Files

• Raw OCR output in an excel spreadsheet: log-200501Labels.xls
• Raw OCR output in an a directory structure: herbis-text.tar.gz
• Raw OCR output in an a directory structure with XML semantic files (Good only): herbis-text-good.tar.gz

Demo,
Source Code
Example: How to get Herbis NLP result in JAVA
Source Code of GoldenGate_Herbis
Souce Code of NLP Parsing

Webvibe

• Swish-ex - XML enabled swish-e full-text indexing
• BIBE Java Client Application: This application allows you to search several databases of species descriptions of plants and insects.
• System Administration Documentation

Openkey

• Conversion of Image of Species for use in descriptions Software to assist in converting large collections of image information into an XML format that can be used in OpenKey for Species Descriptions
• Load images from Image XML files to selection lists: Software to make character and state images available as selection choices on the BIBE interface.
• Filemap - Interactive flowchart of indexing of XML to databases and HTML pages.
• Convert Openkey XML species descriptions to HTML: OpenKey XML species pages follow an format that is easily converted to HTML.
• Convert species descriptions written in XML to HTML.
• Taxon Entry Form: an Excel spreadsheet.
• Processing a list into XML: Perl script that can process a list of character groups, characters, and states with definitions. Our script creates xml files out of each individual state, character, and character group.
• extract values of characters from description files and save them as selection list
• extract state definitions

TeleNature

• PDA Programs: These are programs to run on PDAs to gather information on biodiversity.
  (examples of PDAs: Palm and Handspring devices)
• Phone Connection A document explaining how to use a cell phone as a modem for a laptop.
• Instant Messaging And Picture Transfer A document explaining both the instant messaging used in the TeleNature project as well as the automated picture transfer system and HTML gallery page generation.
• TeleNature Field Guide Tools Download software required to download Floras and Faunas to your PC and support TeleNature search on your computer.