The PLAZI Markup System Donat Agosti Terry Catapano

The PLAZI Markup System Donat Agosti Terry Catapano Robert “Bob“ Morris Guido Sautter Universität Karlsruhe (TH) Research University – founded 1825 / 21

Guido Sautter The PLAZI Markup System Universität Karlsruhe (TH) 2 The PLAZI Markup System Document markup, external referencing Golden. GATE Document Editor Taxon LSIDs, Geo. Data New Taxon Names Links, Materials Citations Marked-Up Documents XML & PDF storage, treatment server PLAZI Server External Data Sources Taxonomic data sources & web services Queries Treatments, Detail Data, PDF Document Handles PLAZI Search Portal Search portal, TAPIR provider, RSS feed

Guido Sautter Universität Karlsruhe (TH) The PLAZI Markup System 3 The PLAZI Server • Golden. GATE Search & Retrieval Server (SRS) – Extracts individual treatments from XML documents – Stores and indexes treatments – Based on independend, pluggable Indexers Taxonomic names Materials citations Document meta data Full text • DSpace – Stores PDF and XML documents – Issues Handles for documents Web Service SRS FT MD MC Index Data File System TN Document Management Data – Serves treatments or indexed details Indexers XML Documents • • Postgre. SQL

Guido Sautter The PLAZI Markup System Universität Karlsruhe (TH) 4 The PLAZI Markup System Document markup, external referencing Golden. GATE Document Editor Taxon LSIDs, Geo. Data New Taxon Names Links, Materials Citations Marked-Up Documents XML & PDF storage, treatment server PLAZI Server External Data Sources Taxonomic data sources & web services Queries Treatments, Detail Data, PDF Document Handles PLAZI Search Portal Search portal, TAPIR provider, RSS feed

Guido Sautter Universität Karlsruhe (TH) The PLAZI Markup System The PLAZI Search Portal • Series of Java Servlets running in Apache Tomcat • Front-end for SRS Web Service • Linker plug-ins create hyperlinks to other web sites • HTML based search portal for humans – – Search treatments & index data Links submitting new search queries Links to external data sources (e. g. HNS, Google. Maps) Links to PDF document & XML versions of treatments • XML document access in various XML schemas • TAPIR provider – Taxonomic names – Materials citations • RSS feed for new treatments 5

Guido Sautter Universität Karlsruhe (TH) The PLAZI Markup System The PLAZI Search Portal Probolomyrmex tani 6

Guido Sautter The PLAZI Markup System Universität Karlsruhe (TH) 7 The PLAZI Markup System Document markup, external referencing Golden. GATE Document Editor Taxon LSIDs, Geo. Data New Taxon Names Links, Materials Citations Marked-Up Documents XML & PDF storage, treatment server PLAZI Server External Data Sources Taxonomic data sources & web services Queries Treatments, Detail Data, PDF Document Handles PLAZI Search Portal Search portal, TAPIR provider, RSS feed

Guido Sautter Universität Karlsruhe (TH) The PLAZI Markup System The Golden. GATE Editor • Java-based editor for semi-automated document markup • Extensible through plug-in mechanism • Independent of specific XML schema • Element-level XML editing (XML syntax is generated) • Flexible display for clear view on all detail levels • Existing plug-ins provide broad spectrum of functionality: – NLP-based markup generation • Regular expressions, gazetteers, GATE JAPE • Homegrown and third-party NLP components • Import of data from external sources (e. g. LSIDs) – Specialized document views for correcting NLP results – Markup transformation & filtering – IO components for different data formats & storage locations (e. g. for uploading XML documents to PLAZI server) 8

Guido Sautter Universität Karlsruhe (TH) The PLAZI Markup System The Golden. GATE Editor 9

Guido Sautter The PLAZI Markup System Universität Karlsruhe (TH) 10 The PLAZI Markup System Document markup, external referencing Golden. GATE Document Editor Taxon LSIDs, Geo. Data New Taxon Names Links, Materials Citations Marked-Up Documents XML & PDF storage, treatment server PLAZI Server External Data Sources Taxonomic data sources & web services Queries Treatments, Detail Data, PDF Document Handles PLAZI Search Portal Search portal, TAPIR provider, RSS feed

Guido Sautter Universität Karlsruhe (TH) The PLAZI Markup System The External Data Sources • Hymenoptera Name Server (HNS) – Retrieve LSIDs for taxon names – Enter new taxon names in HNS database • Further LSID sources: Zoo. Bank, Index Fungorum • GBIF pulls materials citations via TAPIR • EOL pulls treatments via TAPIR (to start soon) 11

Guido Sautter Universität Karlsruhe (TH) The PLAZI Markup System Outlook • Tighter integration of Golden. GATE editor with server – Load plug-ins from server Easier update distribution – Upload documents directly after OCR – Host documents at server throughout markup Users can share markup work (experts do LSIDs, etc) Treatments available in search portal soon as marked up – Auto-distribute documents to different storage locations – Run automated markup generation on server side – Get corrections from community via online feedback forms • Other extensions of Golden. GATE editor – Simplified, more flexible plug-in architecture – Extensible user interface 12

Thank you! Questions? Donat Agosti Terry Catapano Robert “Bob“ Morris Guido Sautter agosti@amnh. org catapanoth@gmail. com ram@cs. umb. edu sautter@ipd. uka. de PLAZI homepage http: //plazi. org PLAZI search portal http: //plazi. org: 8080/Gg. SRS Golden. GATE homepage http: //idaho. ipd. uka. de/Golden. GATE Universität Karlsruhe (TH) Research University – founded 1825 / 21

Guido Sautter Universität Karlsruhe (TH) The PLAZI Markup System The Golden. GATE Editor V 3 Plug-in GUI extensions (hideable) Simplified, more flexible architecture Document navigator finding stuff more quickly Pre-OCR page images for correcting OCR errors 14