distributed databases and applications presentation
DESCRIPTION
TRANSCRIPT
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DiGIR 1
Distributed Databases and Applications
John Wieczorek
Museum of Vertebrate Zoology, UC Berkeley
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DiGIR 2
Distributed Databases – Discipline-specific
The Species Analyst (TSA) The Integrated Taxonomic Information System (ITIS) FishNet The Mammal Networked Information System (MaNIS) HerpNET The Ornithological Information System (ORNIS) …
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DiGIR 3
Distributed Databases –International
European Natural History Science Information Network (ENHSIN)
Biological Collection Access for Europe (BioCASE)
Australia Virtual Herbarium (AVH) Red Mundial de Información Sobre
Biodiversidad, Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (REMIB, CONABIO)
…
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DiGIR 4
Distributed Databases –Regional
Mountain and Plains Spatio-Temporal Database-Informatics (MaPSTeDI)
Ocean Biogeographic Information System (OBIS) Pacific Basin Information Node, National Biological
Information Infrastructure (PBIN, NBII) Species Link, Centro de Referência em Informação
Ambiental (Species Link, CRIA) A Virtual Herbarium of the Chicago Region (vPlants) Spatial Analysis of Local Vegetation Inventories Across
Scales (SALVIAS) …
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DiGIR 5
Distributed Databases –Intra-institutional
Berkeley Natural History Museums (BNHM) Association of Biological Collections, UC Davis …
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DiGIR 6
Distributed Databases –“Nodes”
LifeMapper National Biodiversity Information
Infrastructure (NBII) Global Biodiversity Information Facility
(GBIF)
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DiGIR 7
GBIF Work Programmes NODES ECAT – Electronic Catalogue of Names of
Known Organisms DIGIT – Digitisation of Natural History
Collections OCB – Outreach and Capacity Building DADI – Data Access and Database
Interoperability
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DiGIR 8
Taxonomic Database Working Group
Standards development and maintenance Access to Biological Collections Data (
ABCD) Darwin Core Version 2 (DwC2) Structure of Descriptive Data (SDD) DiGIR Others…
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DiGIR 9
DiGIRDistributed Generic Information Retrieval
John Wieczorek, Stan Blum, Dave Vieglais, P.J. Schwartz
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DiGIR 10
Information Retrieval Distributed - a protocol for retrieving
structured data from multiple, heterogeneous databases across the Internet.
Generic - a protocol independent of the data retrieved and of the software to retrieve it.
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DiGIR 11
Project Rationale Avoid multiple incongruous development
efforts Pool resources and create a support
community of experts Solve scalability problems
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DiGIR 12
Design Goals Use open protocols and standards, such as
HTTP and XML Decouple the protocol, software and
semantics Make new data provider installations as
easy as possible Develop open source software with GNU
General Public Licensing (It’s free).
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DiGIR 13
DiGIR Component Summary
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DiGIR 14
DiGIR ArchitectureProvider
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DiGIR 15
Provider Receives requests Retrieves data from
database Sends results to requestor Supplies metadata to
describe content, contacts, and capabilities
Logs requests
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DiGIR 16
DiGIR ArchitecturePortal Engine
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DiGIR 17
Portal Engine The entry point for an
application Can query a registry to
discover potential providers Can determine, based on
provider metadata, whether a provider should be queried
Can send requests to multiple providers
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DiGIR 18
Portal Engine, continued Assembles responses from
providers Returns packaged results to
the requesting application Communicates via protocol
compliant messaging only Logs activity
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DiGIR 19
Registry Provides a “yellow pages” to
advertise the existence and capabilities of a provider
Provides a means to discover potential providers of interest
May be public or private Need not be a part of the
architecture
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DiGIR 20
DiGIR ArchitectureProviderRegistry (register)
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DiGIR 21
DiGIR ArchitecturePortal EngineRegistry (discover)
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DiGIR 22
DiGIR Protocol Defines request and response message
formats for communication between provider, portal engine, and applications Metadata requests Search requests Inventory requests
Remains unfettered by the structure of the data it transfers
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DiGIR 23
DiGIR ArchitectureApplication
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DiGIR 24
DiGIR ArchitectureApplicationProtocol (request)Portal Engine
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DiGIR 25
DiGIR ArchitectureApplicationProtocol (request)Portal EngineProtocol (request)Provider
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DiGIR 26
DiGIR ArchitectureApplicationProtocol (request)Portal EngineProtocol (response)Provider
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DiGIR 27
DiGIR ArchitectureApplicationProtocol (response)Portal Engine
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DiGIR 28
Applications Must be able to assemble and send
a request document to a portal Must be able to receive and
interpret a response document from the portal
Must do something incredibly useful and interesting with the data
This is where the real fun is!
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DiGIR 29
Hot topics – Interesting problems Persistent unique identifiers Web services (converters, translators, calculators,
transformation services) Data validation (taxonomic and geographic thesauri,
ecological niche modeling, expedition analysis, outlier detection,…)
Spatial query interfaces Data quality feedback mechanisms Automated georeferencing, event gazetteers Concept libraries, schema extensions, schema libraries,
federated ontologies
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DiGIR 30
MaNIS – The Mammal Networked Information System
It’s more than just a pangolin…
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DiGIR 31
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 32
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 33
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 34
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 35
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 36
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 37
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 38
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 39
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 40
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 41
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 42
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 43
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
OnlineMS AccessDatabase
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DiGIR 44
MaNIS Network Configuration
LACMMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
OnlineMS AccessDatabase
OnlineMS AccessDatabase
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DiGIR 45
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
UAMOracle
Database
OnlineMS AccessDatabase
OnlineMS AccessDatabase
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DiGIR 46
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
OnlineMS AccessDatabase
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DiGIR 47
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 48
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 49
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MVZ-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
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DiGIR 50
MaNIS Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
MaNISDiGIRPortal
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
MaNISDiGIRPortal
MaNISDiGIRPortal
MVZ-MaNISPresentation
Layer
UMNH-MaNISPresentation
Layer
UWBM-MaNISPresentation
Layer
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
…
…
…
…
… …
… …
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DiGIR 51
“CalNet” Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
CalNetDiGIRPortal
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DiGIR 52
Event Gazetteer Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
BioGeomancerWeb
Service
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
CalNetDiGIRPortal
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DiGIR 53
NBII Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
NBIIDiGIRPortal
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DiGIR 54
GBIF Network Configuration
LACMMS AccessDatabase
OnlineMS AccessDatabase
MVZSybase
Database
LSUMZ4D-Mac
Database
OnlineMS AccessDatabase
UAMOracle
Database
OnlineMS AccessDatabase
GBIFPresentation
Layers
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
DiGIRProvider
CASSQL ServerDatabase
NBIIDiGIRPortal
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DiGIR 55
Intra-Network Configuration (BNMH)
PHMAWorking
Database
OnlineDatabase
UCBGWorking
Database
DiGIRProvider
BNHMDiGIRPortal
UCJEPSWorking
Database
OnlineDatabase
UCMPWorking
Databases (4)
OnlineDatabase
EssigWorking
Database
OnlineDatabase
OnlineDatabase
BNHMPresentation
Layer
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Other Network Configurations
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRProvider
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
WorkingDatabase
OnlineDatabase
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRPortal
WorkingDatabase
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DiGIR 57
Other Network Configurations
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRProvider
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
WorkingDatabase
OnlineDatabase
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRPortal
WorkingDatabase
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DiGIR 58
Other Network Configurations
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRProvider
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
WorkingDatabase
OnlineDatabase
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRPortal
WorkingDatabase
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DiGIR 59
Other Network Configurations
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRProvider
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
WorkingDatabase
OnlineDatabase
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRPortal
WorkingDatabase
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DiGIR 60
Other Network Configurations
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRProvider
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
WorkingDatabase
OnlineDatabase
DiGIRPortal
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRPortal
WorkingDatabase
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DiGIR 61
Other Network Configurations
WorkingDatabase
OnlineDatabase
DiGIRProvider
DiGIRPortal
WorkingDatabase
WorkingDatabase
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DiGIR 62
Project Information DiGIR is a collaborative open source
development project on SourceForge (https://sourceforge.net/projects/digir).
Software and documentation are available on the DiGIR web site (http://digir.net).
MaNIS is an international network collaboration among mammal specimen collections (http://elib.cs.berkeley.edu/manis).
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DiGIR 63
Hot topics – Interesting problems Persistent unique identifiers Web services (converters, translators, calculators,
transformation services) Data validation (taxonomic and geographic thesauri,
ecological niche modeling, expedition analysis, outlier detection,…)
Spatial query interfaces Data quality feedback mechanisms Automated georeferencing, event gazetteers Concept libraries, schema extensions, schema libraries,
federated ontologies