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Options for national and ASEAN wide data sharing

Options for national and ASEAN wide data sharing. Emma Lumb emma.lumb@daff.gov.au. Where does your data come from, and why share it?. ISPM 8 – Determine of pest status in an area. General requirements for acceptable pest record:

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Options for national and ASEAN wide data sharing

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  1. Options for national and ASEAN wide data sharing Emma Lumb emma.lumb@daff.gov.au

  2. Where does your data come from, and why share it?

  3. ISPM 8 – Determine of pest status in an area • General requirements for acceptable pest record: • Current scientific name -> specimen based best so can check morphology when updating taxonomy • Life stage or state • Taxonomic group • Identification method • Date collected • Name of host • Host damage, or circumstances of collection • Abundance • Bibliographic references

  4. Pest Information Sources Grey Literature (conference proceedings; pamphlets, PRA’s, surveillance reports) Primary Literature (research papers, specialist texts) Listservers Newspapers Secondary Literature (“encyclopaedias”) Electronic sources Specimen information

  5. Consider… • Do local collections pest records always have all this information required under ISPM 8? • Is all this information always reliable?

  6. Example: Gathering information on Bactrocera tryoni Froggart. • By ISPM 8: General requirements for acceptable pest record: • Current scientific name • Life stage or state • Taxonomic group • Identification method • Date collected • Name of host • Host damage, or circumstances of collection • Abundance • Bibliographic references

  7. From collection data base #1 • Pest collected in New South Wales

  8. From collection database #2 • Pest collected in NSW, and in QLD

  9. From collection database #3 • Pest recorded on: cherry, peach, blackberry, mango, banana, tomato, apricot, and Eugenia jambosa

  10. From collection database #4 • Pest recorded on: cherry, peach, blackberry, mango, banana, tomato, apricot, and Eugenia jambosa and bush lemon, valencia orange, mulberries and mandarins

  11. From collection database #5 • Pest collected in NSW, and in QLD, and in SA and in VIC and NT • Geo-coordinates giving exact collection points help determine range of pest

  12. Searching on Bactrocera tryoni Froggart – putting it all together • National picture of: • Distribution • Abundance • Greater knowledge of host range • Knowledge of damage • Date collected • Identification methods • Authenticated records

  13. Searching on Bactrocera tryoni Froggart – putting it all together    Primary literature, master checklists    Confirm with surveillance data  Primary literature 

  14. A A B A C B B Herbarium A C The more data you have,The more robust your pest list will be! Data confidence

  15. Data sharing: general features

  16. National Phytosanitary Database Australian Plant Pest Database How can national/ regional data sharing be done? • Swap specimens and associated notes (duplicates) • OR • EXPORT local database data to master database routinely (manual process) • OR • LINK local databases together using special software and internet (distributed database system)

  17. Some examples of regional data sharing • NZ Aid Plant Protection Database (MANUAL SYSTEM) • PDD • Lao PRD, Myanmar, Cambodia and Vietnam • Version 2 - Arab Emirates - ? Distributed system? • Pacific Island Pest List Database (MANUAL SYSTEM) • PIPDL • Pacific Islands e.g. Samoa, Tonga, Marshall Islands…) • Secretariat of the Pacific Community, assisted by AusAID, NZ Aid and the EU. • Australian Plant Pest Database (DISTRIBUTED SYSTEM) • APPD • The 6 states and 2 territories in Australia • 19 plant pest collections • DAFF and Plant Health Australia • Global Biodiversity Information Facility (DISTRIBUTED SYSTEM) • GBIF • Global system • Many different databases

  18. PIPDL – Pacific Islands Pest List Database (MANUAL SYSTEM) • Many of the Pacific Islands have lots of survey data (=reports), but cannot afford to maintain pest collections (=records) • Each Island has own copy of MS Access Pest List Database • Each Island enters REPORT and RECORD information into local copy of database • Data that is a) validated by plant health specialist; or b) appears as a pest report in an internationally recognised journal, is treated as reliable evidence for the pest existing in the country. This data is marked as PUBLIC ACCESS • Data that does not meet the above requirements is still entered but marked as NON PUBLIC ACCESS, until such date as source can be validated • Each Island regularly sends a copy of their database minus NON PUBLIC ACCESS reports/ records, to head office • Head office CONSOLIDATES all copies of databases into MASTER DATABASE • Anybody with access to the web may search the master database by: • Pest list for selected host; • Host list for selected pest; • Comparative pest report (a basic PRA); • Regional pest distribution report; • Country distribution report; or • Species search (basic information)

  19. Data entry person updating local copy of PIPLD MS Access: 350 records Island 1 MS Access: 100 records Island 2 MS Access: 50 records Island 3 MS Access: 200 records Internet PIPLD Host User searching PIPLD User searching PIPLD

  20. PIPDL – Pacific Islands Pest List Database • ADVANTAGES • Easily implemented, easy to use • Easy access via internet (anyone can generate a search) • Low IT cost • DISADVANTAGES • Information for a set number of commonly occurring pests Routine updates rather than live connection, mean that data is out of data on master database instantly (high human resource cost) • Requires a number of data entry personnel and a database operator forever (ongoing cost of salaries and training) • Outputting on master database is restricted and not possible to see source of data (must go back to collection curators) • Limited detail for specimen records, and information somewhat consolidated • Requires all agencies to run/ populate the same database locally • Too simple??

  21. APPD – the Australian Plant Pest Database (DISTRIBUTED DATABASE SYSTEM) • Developed in response to the national need for a plant health information system: • Local and State governments responsible for domestic pest management; but • Federal government responsible for trade and quarantine • 20 collections of plant pests and pathogens • A vouchered specimen for all records • All collections have different systems (software, different data fields) • LINKED BY INTERNET and special, custom built software • The APPD can be searched through a single internet site • Agreed on MINIMUM DATA REQUIREMENTS for each record (ISPM 8) • Some records verified, others not, so ACCESS TO APPD IS RESTRICTED to approved, Australian plant health specialists • As is a live connection to each database, DATA IS ALWAYS UP TO DATE • Searches can be either simply on pest taxa or “Boolean based”, e.g: • Taxa+ pest host • Taxa+ pest host+geo-coordinates • Taxa+…locality…collection date • And can use “equals”; “contains” or “starts with” • Searches can be on one or multiple databases at same time • Can check taxonomy through links to master names lists • Results include: • Summary page of results • Details page (accession number, host, collector, identifier, trapping method, etc) • Mapping options

  22. Insect/ Mite/Nematode collection Herbarium DBIRD DBIRD QDPIF UQ QDPIF QDPIF DPI NSW BSES DPI NSW DAWA DPI NSW DPI NSW DAWA CALM PIR Vic CSIRO WAITE/ SARDI PIR Vic DPIWE FT

  23. NTEIC QDPIF UQIC QDPIF BSES ASCU ICDb FNIC BugBase ANIC WINC VAIC TPPD TFIC

  24. Internet Collection C: Texpress Collection B: BioLink APPD Host Collection A: MS Access Broker Distributed system querying heterogenous databases

  25. Internet Collection C: Texpress Collection B: BioLink APPD Host Collection A: MS Access Broker Distributed system – return of results from system

  26. Example 1: Trade decision support The Australian Plant Pest Database Guignardia citricarpa

  27. APPD results for Guignardia citricarpa

  28. Central Burnett Sunraysia Riverland Riverina Major citrus area Minor citrus area Overlaying records with citrus industry areas shows… • limited range disease • unlikely in commercial areas (supports Area Freedom) in a Market Access bid G. citricarpa record

  29. Present data constraints of APPD • Demonstrates “not known to occur” rather than “known not to occur” (survey data needed to prove for this) • Problem of synonomy • Incorrect (outdated/ misidentified) identifications • Seasonal occurrence of pests e.g. fruit fly in NSW • Quarantine interceptions • Not permitted in APPD but some have snuck in • Remarks: • 1. Collection curators are responsible for adhering to the data standards set up by the Steering Committee; but • APPD users should be aware that while the APPD is a useful tool for Pest Risk Analysis, it shouldn’t replace taxonomic texts nor taxonomists • APPD presently only available to plant health scientists able to scrutinise APPD data • Users acknowledge the disclaimer for every search

  30. APPD – the Australian Plant Pest Database (DISTRIBUTED DATABASE) • ADVANTAGES • Data is always up to date • No limit to data contained (over 1 million records of plant pests and pathogens) • All data is record based • Easy access via web • Secure system (password protected) • Low cost for day to day routines • Can link to GBIF later • DISADVANTAGES • Internet based (??) • Special technology (cost about 55,000 USD) [upfront cost] • Ongoing commitment by collection curators: • To provide computer/ internet for their database to the network • Add/ update data • Project officer to monitor system • Occasional outages • Occasional novel problems with the technology • Issues with data standards • Passwords

  31. General features of distributed systems • DISADVANTAGES • Need good internet connection • Upfront cost of technology • Upfront cost managing implementation phase • Need password protect for security • Advantages • If you have an internet connection and a password, you can access data (allows multiple users) • Low maintenance once system established • Information always up to date • Can participate/ gain funding and support from GBIF • Can add fancy tools: • Mapping • Links to names lists • Links to images • Downloadable formats for pest lists

  32. Global Biodiversity Information Facility(an alternative???) • ADVANTAGES • Biodiversity data • Free “wrapper” software to develop your database – but requires skilled person to install • $$ available for digitising specimen record data • International biodiversity community • DISADVANTAGES • How to consolidate national collection? • Need person for training in complex IT • Data must be publicly available (part of GBIF agreement) • Searching – requires user to have sound understanding of database systems and judgements on taxonomy in order to get most out of GBIF databases • May be a long while before partner countries can join!

  33. Priorities for establishing a system for data sharing • Agree on system (manual or distributed) • Agree on data fields (consider requirements under ISPM’s and record/ report reference) • Agree on data to share (pest based, host based, verified) and terms and conditions of sharing • Public versus non public access? • Agree on outputting: • Key fields for REPORTING and for SEARCHING (host, collector, source/ reference/ accession number) • Key tools (mapping, links to master names, sort by function, searching) • Institutional responsibility • Establish/ identify funding sources (who, where, how much, how long) • Key Drivers • Key data sources • Coordination group • Establish terms of reference for sharing data (address IP and security concerns) • Population of database • Validation of data • Monitoring of system (eg APPD) OR coordinating data updates (PIPDL) • Responsibility when technology changes/ becomes outdated

  34. BRAHMS Some of the local system available in ASEAN at present time… ? ? ? ?

  35. GROUP DISCUSSION • Discuss advantages and disadvantages of the three options presented (PIPDL, APPD, GBIF) • Consider in terms of cost and ongoing maintenance; • Ease of use; • Compliance with ISPM 8 • Data quality and quantity • Management issues (such as sharing data, intellectual property, etc) • Which system (manual or distributed) would be more practical (easy to implement) and useful for ASEAN? Why? • List the key features required for an ASEAN pest list database system and number each feature in priority. Consider: • Outputting type (what information should be given) • Searching functions (How should one be able to search) • Report back to main group on items 2 and 3 Thankyou for your attention!

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