The GoldenGATE Editor Homepage

The GoldenGATE Document Editor

Download the demo version of the GoldenGATE editor here (version date 2011.11.21.12.15, archive last modified 2011.11.21.12.15).

The demo version of the GoldenGATE editor includes all the resources needed to convert OCRed biosystematics documents into XML content marked up in the TaxonX XML schema. The description will guide you in marking up any of the test documents:

New Species of Ants from the Island of Mauritius (pdf available here)
A New Genus and Species of Formicidae from Mauritius (pdf available here)
New Species of Ants from China and Mauritius (pdf available here)
Two New Species of Metapone from Madagascar (pdf available here)
An Aberrant New Genus of Myrmicine Ant from Madagascar (pdf available here)
Endemic families of Madagascar. VII. A synoptic revision of Leptolaena (abridged) (pdf available here)

Description

The intention of the GoldenGATE editor is to build a bridge between NLP components and XML markup of natural language text according to arbitrary XML schemas. It allows the deployment of NLP components to marking up the bodies of literature they were designed for. In this way, it enables transforming the texts into XML content according to an XML schema that was designed to gain maximum benefit from the knowledge provided in them.

The GoldenGATE editor picks up the ideas of plug-in processing resources and pipelined processing implemented in the GATE framework (http://www.gate.co.uk), which has been widely used in many areas of NLP research. At the same time, it provides a full XML editor including assistance for manipulation of both text and markup, thus allowing users to improve data quality by manual intervention.

In order to achieve maximum flexibility and extensibility, the GoldenGATE editor provides plug-and-play interfaces on many levels: Individual automated components for markup creation and manipulation, entire groups of functionalities, components accessing documents in arbitrary storage locations, and arbitrary document data formats.

Publications

Sautter, G., K. Böhm, and D. Agosti. 2006. A combining approach to find all taxon names (FAT) in legacy biosisystematics literature. Biodiversity Informatics 3, 41-53. (http://jbi.nhm.ku.edu/index.php/jbi/article/view/34/16)
Sautter, G., D. Agosti, K. Böhm. 2007. Semi-Automated XML Markup of Biosystematics Legacy Literature with the GoldenGATE Editor. In Proceedings of PSB 2007, Wailea, HI, USA, 2007 (http://psb.stanford.edu/psb-online/proceedings/psb07/sautter.pdf)
Sautter, G., K. Böhm, F.Padberg, and W. Tichy. 2007. Empirical Evaluation of Semi-Automated XML Annotation of Text Documents with the GoldenGATE Editor. In Proceedings of ECDL 2007, Budapest, Hungary, 2007 (http://idaho.ipd.uka.de/GoldenGATE/ecdl2007.pdf)
Sautter, G., D. Agosti, K. Böhm, C. Klingenberg. 2009. Creating Digital Resources from Legacy Documents - an Experience Report from the Biosystematics Domain. In Proceedings of ESWC, Heraklion, Greece, 2009 (pdf)
Sautter, G., K. Böhm, C. Kühne, T. Mathäß. 2010. ProcessTron: Efficient Semi-Automated Markup Generation for Scientific Documents. In Proceedings of JCDL, Gold Coast, Australia, 2010 (pdf)
Sautter, G., K. Böhm. 2011. High-Throughput Crowdsourcing Mechanisms for Complex Tasks. In Proceedings of SocInfo, Singapore, 2011 (Best Paper Award) (pdf)
Sautter, G., K. Böhm. 2012. Improved Bibliographic Reference Parsing Based on Repeated Patterns. In Proceedings of TPDL 2012, Pafos, Cyprus, 2012 (pdf)
TaxonX wiki (http://wiki.cs.umb.edu/twiki/bin/view/Ants/WebHome)

Markup Examples

Marked-Up taxonomic treatment on ant species Probolomyrmex tani, extracted from Fisher, B. L. 2007. A new species of Probolomyrmex from Madagascar. In: Advances in ant systematics (Hymenoptera: Formicidae): Homage to E.O. Wilson - 50 years of contributions, pp. 146-152: 148-150
Marked-Up taxonomic treatment on ant species Monomorium dentatum, extracted from Sharaf, M. R. 2007. Monomorium dentatum sp. n., a new ant species from Egypt (Hymenoptera: Formicidae) related to the fossulatum group. Zoology in the Middle East (41), pp. 93-98: 94-97

Contact Information

Christiana Klingenberg (Designer of the markup process and manual), State Museum of Natural History Karlsruhe, Karlsruhe, Germany
Donat Agosti (Specialist for taxonomic literature), American Museum of Natural History, New York, USA
Terry Catapano (Designer of TaxonX XML schema), Columbia University, New York, USA
Guido Sautter (Developer of the GoldenGATE Document Markup System), Universität Karlsruhe (TH), Karlsruhe, Germany

The package natively includes:

Resources for automated and semi-automated markup:

Management and application of gazetteer lists for automated markup creation
Management and application of regular expressions for automated markup
Integration of third-party NLP applications
Management and application of markup transformation rules
Management and application of JAPE grammars
Management and application of bundeling automated processing steps into pipelines, making them accessible as one
Management and application of markup modification scripts, including a scripting console
Batch processing lists of input files with some automated processor
Management and application of AnnotationDiffer style markup quality assessment
Management and application of markup quality assessment scripts

Components for viewing documents in specialized ways:

View and edit a document as an XML tree
View and edit annotations in a list using customly predefined or ad hoc XPath filtering
View and edit a part of a document using a sliding window

Components for loading and storing documents:

Document IO using file system
Document IO using URLs
Document upload to the Search & Retrieval Server backing the search portal

Components providing support for a variety of document formats:

TXT document format
Custom SGML document formats, both HTML and XML
ARFF document format (http://www.cs.waikato.ac.nz/~ml/weka/arff.html)

Documentation:

Read the online help for the GoldenGATE editor here.

Read the JavaDoc of the GoldenGATE editor and its backing components (not for the actual implementations of the plugin interfaces, though)

StringUtils (utilities for hanlding Strings and CSV data) download
HtmlXmlUtils (utilities for handling XML, including XPath, based on a flexible, error correcting parser) download
Gamta (basically a slightly reduced implementation of LMNL, but XML compatible and editable in exchange, requires StringUtils and HtmlXmlUtils on the classpath) download
EasyIO (utilities for IO (file system, web, JDBC), especially for configuration data, plus eMail, requires mail.jar, StringUtils and HtmlXmlUtils on the classpath) download
GoldenGATE (the core of the GoldenGATE editor, platform for all plug-ins, requires StringUtils, HtmlXmlUtils, Gamta and EasyIO on the classpath) download

Update Sources:

URLs where the GoldenGATE editor can fetch updates from. These URLs are not meant to access manually through a browser, but to be listed in the UpdateHosts.cnfg file in your GoldenGATE root folder. The GoldenGATE editor automatically downloads and installs updates from the URLs listed in this file.

http://idaho.ipd.uka.de/GoldenGATE/Udates
http://plazi.cs.umb.edu/GgServer/Updates
http://plazi2.cs.umb.edu/GgServer/Updates
http://plazi.org:8080/GgSRS/GgUpdates