Pro-Ibiosphere D.4.2 Strategy for Improvement & Interoperability of the XML Schemas.Docx
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Project Acronym: pro-iBiosphere Project Full Title: Coordination & policy development in preparation for a European Open Biodiversity Knowledge Management System, addressing Acquisition, Curation, Synthesis, Interoperability & Dissemination Grant Agreement: 312848 Project Duration: 24 months (Sep. 2012 - Aug. 2014) D.4.2 Strategy for improvement & interoperability of the XML schemas Deliverable Status: Final File Name: pro-iBiosphere_WP4_Plazi_D4.2_VFF31_01_2014.PDF Due Date: December 2013 (M16) Submission Date: January 2014 (M17) Dissemination Level: Public Authors: Plazi, Pensoft, BGBM, NBGB, RBGK, Naturalis pro-iBiosphere FP7 Project ■ Grant Agreement #312848 Page 1 of 42 D.4.2 Strategy for improvement & interoperability of the XML schemas. Jan 31th 2014. Task Leader: Donat Agosti, Plazi 7th Framework Programme ■ Coordination and support action FP7-INFRASTRUCTURES-2012-1 ■ Subgroup programme area INFRA-2012-3.3 © Copyright 2012-2014 The pro-iBiosphere Consortium. Consisting of: FUB-BGBM Freie Universität Berlin, Germany MfN Museum für Naturkunde, Germany Naturalis Stichting Nederlands Centrum voor Biodiversiteit Naturalis, Netherlands BGM Botanic Garden, Meise, Belgium Pensoft Pensoft Publishers Ltd, Bulgaria Plazi Plazi, Switzerland RBGK Royal Botanic Gardens Kew, United Kingdom Sigma Sigma Orionis, France Disclaimer All intellectual property rights are owned by the pro-iBiosphere consortium members and are protected by the applicable laws. Except where otherwise specified, all document contents are: “© pro-iBiosphere project - All rights reserved - OpenAccess reproduction is permitted under Creative Commons (CC-BY) 4.0”. All pro-iBiosphere consortium members have agreed to full publication of this document. The commercial use of any information contained in this document may require a licence from the owner of that information. All pro-iBiosphere consortium members are committed to publish accurate and up-to-date information and take the greatest care to do so. However, the pro-iBiosphere consortium members cannot accept liability for any inaccuracies or omissions nor do they accept liability for any direct, indirect, special, consequential or other losses or damages of any kind arising out of the use of this information. pro-iBiosphere FP7 Project ■ Grant Agreement #312848 Page 2 of 42 D.4.2 Strategy for improvement & interoperability of the XML schemas. Jan 31th 2014. Task Leader: Donat Agosti, Plazi 7th Framework Programme ■ Coordination and support action FP7-INFRASTRUCTURES-2012-1 ■ Subgroup programme area INFRA-2012-3.3 REVISION CONTROL Version Author Date Status 01 Donat Agosti 15.10.2013 First draft structure 02 David Patterson 23.12.2013 Read through and revise 03 Lyubomir Penev 21-31.12.2013 Re-structuring the draft, additions, edits 04 József Geml 02.01.2014 Content on fungi pilot 05 Jordan Biserkov, Teodor 04.01.2014 Description of DwC-A Georgiev 06 Donat Agosti 07.01.2014 Content 07 Terry Catapano 07.01.2014 Content 08 Peter Hovenkamp 07.01.2014 Review 09 Donat Agosti 10.01.2014 Review of draft 10 Peter Hovenkamp 12.01.2013 Review of draft 11 Soraya Sierra, Peter 13.01.2014 Review of draft Hovenkamp 12 Thomas Hamann, Soraya 14.01.2014 Review of draft Sierra 13 Lyubomir Penev, David 16.01.2014 Editing draft, resolving Patterson, Thomas comments Hamann, Soraya Sierra 14 Donat Agosti, Robert 16-19.01.2014 Editing and resolving comments Morris, Terry Catapano 15 Andreas Müller, Soraya 24.01.2014 Review of draft Sierra, two anonymous reviewers 16 Donat Agosti, David 25-26.01.2014 Resolving comments Patterson, Lyubo Penev 17 P. Hovenkamp, Soraya 27-31.01.2014 Review and editing of final draft Sierra, Donat Agosti FF Soraya Sierra 31.01.2014 Final Draft converted to Portable Document Format (PDF) pro-iBiosphere FP7 Project ■ Grant Agreement #312848 Page 3 of 42 D.4.2 Strategy for improvement & interoperability of the XML schemas. Jan 31th 2014. Task Leader: Donat Agosti, Plazi 7th Framework Programme ■ Coordination and support action FP7-INFRASTRUCTURES-2012-1 ■ Subgroup programme area INFRA-2012-3.3 Authors: Donat Agosti (Plazi) Christine Barker (RBGK) Terry Catapano (Plazi) Hong Cui (University of Arizona) Sabrina Eckert (BGBM) Jordan Bisrekov (Pensoft) Teodor Georgiev (Pensoft) Quentin Groom (BGM) Anton Güntsch (BGBM) Gregor Hagedorn (MfN, Plazi) Thomas Hamann (Naturalis) Peter Hovenkamp (Naturalis) Patricia Kelbert (BGBM) Paul Kirk (RBGK) Don Kirkup (RBGK) Jeremy Miller (Naturalis) Robert Morris (Plazi) Anton Müller (BGBM) Sylvia Mota de Oliveira (Naturalis) Lyubomir Penev (Pensoft) Soraya Sierra (Naturalis) Tony Walduck (RBGK) Contributions from: Paul Kirk (RBGK) Christine Barker (RBGK) Vincent Roberts (Centraalbureau voor Schimmelcultures) Rich Pyle (Bishop Museum) Daniel Mietchen (Museum für Naturkunde, Berlin) Mark-up Pilot Participants: Donat Agosti (Plazi) Hong Cui (University of Arizona) Teodor Georgiev (Pensoft) Pavel Stoev (Pensoft) Lyubomir Penev (Pensoft) Jordan Biserkov (Pensoft) Quentin Groom (NBGB) Thomas Hamann (Naturalis) Peter Hovenkamp (Naturalis) Don Kirkup (RBGK) Jeremy Miller (Naturalis) Soraya Sierra (Naturalis) Sylvia Mota de Oliveira (Naturalis) Tony Walduck (RBGK) pro-iBiosphere FP7 Project ■ Grant Agreement #312848 Page 4 of 42 D.4.2 Strategy for improvement & interoperability of the XML schemas. Jan 31th 2014. Task Leader: Donat Agosti, Plazi 7th Framework Programme ■ Coordination and support action FP7-INFRASTRUCTURES-2012-1 ■ Subgroup programme area INFRA-2012-3.3 Contents Executive summary ............................................................................................................................. 6 Introduction ........................................................................................................................................ 8 What is ‘interoperability’? .............................................................................................................. 9 Data exchange among XML schemas ............................................................................................ 10 Methods and Approach .................................................................................................................... 14 Pilots .............................................................................................................................................. 14 Training ......................................................................................................................................... 15 XML schemas tested ..................................................................................................................... 15 Mark-up strategies tested ............................................................................................................. 16 Criteria to assess pilots and tasks ................................................................................................. 17 Conclusion ......................................................................................................................................... 17 Recommendations ............................................................................................................................ 21 Appendix: Pilot studies ..................................................................................................................... 22 Reports of the mark-up pilots ....................................................................................................... 22 Formicidae, Hymenoptera (Animals, Ants) ............................................................................... 22 Chenopodium (Plants) ............................................................................................................... 22 Araneae (Animals: Spiders) ....................................................................................................... 23 Basidiomycota (Fungi) ............................................................................................................... 24 Nephrolepis (Ferns) ................................................................................................................... 24 Bryophyta (Mosses) .................................................................................................................. 25 Eupolybothrus (Animals, Centipedes) ....................................................................................... 26 Loranthaceae (Mistletoes, Plants) ............................................................................................ 26 Reports of the interoperability pilots ........................................................................................... 28 Interoperability Pilot 1: Interoperability model between taxon treatments from both legacy and prospective literature from three organismic domains (fungi, plants and animals) ......... 28 Interoperability Pilot 2: Common query/response model for automated registration of higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank) ..................................................................................................................... 32 Interoperability Pilot 3: Interoperability model between PLAZI and the EDIT Platform for Cybertaxonomy based on transformations between XML-repositories and CDM-stores ....... 35 Interoperability Pilot 4: Revision of a tool (CharaParser) that generates identification keys by reusing morphological characters from published species descriptions .................................