506 lines
20 KiB
Plaintext
506 lines
20 KiB
Plaintext
head 1.22;
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access;
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symbols;
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locks; strict;
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comment @# @;
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1.22
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.21;
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1.21
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.20;
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1.20
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.19;
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1.19
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.18;
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1.18
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.17;
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1.17
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.16;
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1.16
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.15;
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1.15
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.14;
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1.14
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.13;
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1.13
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.12;
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1.12
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.11;
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1.11
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.10;
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1.10
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.9;
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1.9
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.8;
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1.8
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.7;
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1.7
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.6;
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1.6
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.5;
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1.5
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.4;
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1.4
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.3;
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1.3
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.2;
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1.2
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next 1.1;
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1.1
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date 2007.01.09.00.00.00; author MoinMoin; state Exp;
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branches;
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next ;
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desc
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@Initial revision
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@
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1.22
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log
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@Revision 22
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@
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text
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@*TAPIR 1.0*
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_Giovanni, R., Döring, M., de la Torre, J._
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The TDWG Access Protocol for Information Retrieval (TAPIR) is a next generation of query protocols that can be used by biodiversity information networks. It was initially proposed as a new protocol unifying DiGIR and BioCASe during the TDWG 2004 meeting. After that, many changes were incorporated to add new functionalities and to allow different levels of provider implementations. A fully functional provider software (PyWrapper) has been developed and is ready to be used.
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The TAPIR protocol consists of five operations – metadata, capabilities, ping, inventory and search – that can be invoked either through XML or simple KVP (key-value pairs) requests. Metadata response has been refactored to make use of elements from well-known namespaces like DublinCore, VCARD and the W3C Basic Geo vocabulary, and also to include additional data such as any number of related entities, multi-language support, indexing preferences, among others. Capabilities is a separate operation to retrieve technical metadata, allowing providers to have different levels of functionality. Ping can be used for provider monitoring purposes. Inventory operations now accept more than one concept. Both Inventory and Search can now make use of new filtering capabilities and can be represented by query templates.
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This session will introduce TAPIR, explaining the basic concepts behind it, like output models, query templates and the different ways of processing them. The final TAPIR 1.0 specification will be presented together with new perspectives and future directions.
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TAPIR http://ww3.bgbm.org/protocolwiki/
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PyWrapper home page: http://www.pywrapper.org/
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*Theme*: New and emerging standards, Integrating & sharing biotic information
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*Rewiewer*: Anton Güntsch
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-----------------------
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*Using TAPIR in biodiversity networks*
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_Döring, M., de la Torre, J., Giovanni, R._
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TAPIR 1.0 is ready to be used. With at least one implementation (PyWrapper) and with others coming, projects building biodiversity information networks can make use of it to set up their basic infrastructure. Existing networks, like BioCASE, or the Generation Challenge Program, already started using it for deployment.
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This session will discuss possible strategies about how to use TAPIR and will explain the different architecture components needed to build efficient networks. It will especially touch TAPIR models and their role in creating specialized networks on top of widely agreed conceptual schemas. An updated roadmap of implementations will be presented to better help people organize and target their projects.
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The presentation is being created in TapirNetworksPresentation.
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-------------------------
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*PyWrapper v2: toward a real open source community*
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_de la Torre, J., Döring, M._
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PyWrapper v2 is a major revision of the previous BioCASe Provider Software. It has been highly redeveloped to become the first TAPIR implementation. During the last year several projects had contributed to its development and extension. At the same time the project has been moved into a new development environment, outside of any institution, to promote its development by a real open source community.
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Additionally, PyWrapper has evolved into a multiprotocol middleware software. Different projects are demanding to make their data providers available through different protocols, not only TDWG related. The software has been modularized and support for BioMOBY protocol has already been implemented. Plans include providing support for LSID resolution and WFS in the middle term. The goal is to provide a single interface for providers to map their databases only once and start sharing their data in multiple different protocols.
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Finally it is also envision the development of complementary tools to bundle with PyWrapper. The first one will be the so-called QueryTool; a generic client to create web interfaces for providers databases based on AJAX technology. Hopefully the number of additionally available modules will grow as different communities contribute to the project.
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---------------------------
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Sorry, the next one is mine (Javi) and not TAPIR related , but if you have a time to look it and correct stupid things i would be very happy :)
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*Biodiversity Informatics and the GeoWeb: toward an integration of TDWG and OGC standards*
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_de la Torre, J. - Mergen, P. * - Lobo, J.M._
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_Museo Nacional de Ciencias Naturales (CSIC), C/José Gutiérrez Abascal, 2. 28006 Madrid, España_
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_* Royal Museum for Central Africa (RMCA), 13 Leuvensesteenweg, 3080 Tervuren, Belgium_
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The geospatial aspect of biodiversity is very prominent for research in ecology, biogeography, and well as for planning, conservation and management. Most use cases for biodiversity primary data involves the geospatial analysis of data using GIS tools. Therefore facilitating the access of GIS users to primary data is an important task in fulfilling many user requirements for biodiversity information networks.
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The best way to meet users demands is through the use of open standards like the ones being promoted by the Open Geospatial Consortium (OGC). OGC has been working in open standards for more than a decade now and has created several widely deployed specifications, like WMS/WFS/WCS and GML. These efforts are creating an interoperable environment where "geodata" are consumed, analyzed, integrated and published in what is starting to be called the GeoWeb.
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OGC and TDWG standards together can provide the building blocks toward a "BiogeoWeb" where biodiversity data can be visualized and analyzed together with other "geodata" sources thanks to interface and semantic interoperability. This process has already been initiated by the TDWG Spatial Data Standards subgroup and it will gain force with the creation of an agreement between OGC and TDWG. The inclusion of TDWG standards in the OGC world will also warranty further integration of our community in spatial initiatives, like GEOSS or INSPIRE, that have
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biodiversity data within their scope.
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A description on how the different existing standards can be used in biodiversity informatics, together with practical results from the setup of SYNTHESYS project services will be presented in the context of a future Biogeography Spatial Data Infrastructure, BiogeoSDI.
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_Acknowledgements: The authors wish to thank all the colleagues from SYNTHESYS, in charge with or actively collaborating to these various projects as well as also the developers of Geoserver and associated tools for their support. These activities are financed by the EU project SYNTHESYS (www.SYNTHESYS.info)_
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*Theme*: Integrating & sharing biotic information
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*Rewiewer*: John R. Wieczorek
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@
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1.21
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log
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@Revision 21
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@
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text
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@d29 2
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@
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1.20
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log
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@Revision 20
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@
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text
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@d7 1
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a7 1
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The TAPIR protocol consists of five operations – metadata, capabilities, ping, inventory and search – that can be invoked either through XML or simple KVP (key-value pairs) requests. Metadata response has been refactored to make use of elements from well-known namespaces like DublinCore, VCARD and the W3C Basic Geo vocabulary, and also to include additional data such as any number related entities, multi-language support, indexing preferences, among others. Capabilities is a separate operation to retrieve technical metadata, allowing providers to have different levels of implementation. Ping can be used for provider monitoring purposes. Inventory operations now accept more than one concept. Both Inventory and Search can now make use of new filtering capabilities and can be represented by query templates.
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d16 5
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a20 1
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----
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d29 1
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a29 1
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----
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d40 1
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a40 2
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----
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d63 1
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a63 1
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*Rewiewer* : John R. Wieczorek(tuco@@berkeley.edu)
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@
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1.19
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log
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@Revision 19
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@
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text
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@d7 2
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d11 5
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@
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1.18
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log
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@Revision 18
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@
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text
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@d35 1
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a35 1
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_de la Torre, J._
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d37 2
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a38 1
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The geospatial aspect of biodiversity is very prominent for research in ecology, biogeograpghy, evolution study and for planning, conservation and management. Most the use cases for biodiversity primary data involves the geospatial analysis with GIS tools. Therefore facilitating the access of GIS users to primary data is an important task to fulfill most of use cases for biodiversity information networks.
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d40 1
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a40 1
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The bets way to meet users demands is through the use of open standards like the ones that the Open Geospatial Consortium is creating. The OGC has been working in open standard for more than a decade now and has created several specifications, like WMS/WFS/WCS and GML, that had been widely deployed. These efforts are creating and interoperability environment where "geodata" is consumed, analyzed, integrated and published in what is starting to be called the GeoWeb.
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d42 1
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a42 2
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OGC and TDWG standards together can provide the building blocks toward a "BiogeoWeb" where georeferenced data can be visualized and analyzed together with other "geodata" sources thanks to interface and semantic interoperability. This connection has already started on the TDWG Spatial Data Standards subgroup and will increase with the creation of an agreement between OGC and TDWG.
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The inclusion of TDWG standards in the OGC world can also warranty that our community integrates well in spatial initiatives, like GEOSS or INSPIRE, that have biodiversity data in their scope.
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d44 10
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a53 1
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A description on how the different existing standards can be used in biodiversity informatics, together with practical results from the Synthesys project setting up services, will be presented on this talk. Additionally the ideas of a future Biogeography Spatial Data Infrastructure, BiogeoSDI, will be presented.
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@
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1.17
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log
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@Revision 17
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@
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text
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@d33 1
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a33 1
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*Use of OGC standards in Biodiveristy Informatics*
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a36 8
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Use of OGC standards in Biodiversity Informatics
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-Our data has a very prominent geospatial aspect
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-Open our data to GIS users using OGC
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-Using OGC standards for processing as a community -> BioGeoSDI
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-Integrating with GEOSS
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--------------
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d41 2
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a42 10
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OGC and TDWG standards together can provide the building blocks toward a "BiogeoWeb" where georeferenced data can be visualized and analyzed together with other "geodata" sources thanks to interface and semantic interoperability. This connection has already started on the TDWG geospatial subgroup
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In this presentation the results from the Synthesys project setting up OGC services for primary data and the vision on how this will be used by subsequents projects will be described together with practical results
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During the last year the Synthesys project has been working on setting up OGC services to specimen primary data for the new BioCASE portal. This way users can consume
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while the ongoing EDIT project plans to make use of it not just for visualization but for data analysis. The use of WFS, WCS, WMS, catalog service and WPS
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This tasks has proven the need towards a bigger view on a Spatial Data Infrastructure for biogeographers and biodiversity data based on OGC standards.
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d44 1
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a44 1
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This infrastructure will need the implementation of TDWG standards in OGC interfaces
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@
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1.16
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log
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@Revision 16
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@
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@d37 24
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a60 1
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The Open Geospatial Consortium is...
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@
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1.15
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log
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@Revision 15
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@
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text
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@d25 1
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a25 1
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Additionally, PyWrapper has evolved into a multiprotocol middleware software. Different projects are demanding to make their data providers available through different protocols, not only TDWG related. The software has been modularized and support for BioMOBY protocol has been already implemented. Plans include providing support for LSID resolution and WFS in the middle term. The goal is to provide a single interface for providers to map their databases only once and start sharing their data in multiple different protocols.
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@
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1.14
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@Revision 14
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@
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@d27 1
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a27 1
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Finally it is also envision the development of complementary tools to bundle with PyWrapper. The first one will be the so-called QueryTool; a generic client to create web interfaces for providers databases based on AJAX technology. Hopefully the number of additionally modules available will grow as different communities contribute to the project.
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@
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1.13
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log
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@Revision 13
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@
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text
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@d19 1
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a19 1
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*PyWrapper v2: from a project development to a real open source community*
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@
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1.12
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log
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@Revision 12
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@
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text
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@d23 1
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a23 1
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PyWrapper v2 is a major revision of the previous BioCASe Provider Software. It has been highly redeveloped to become the first TAPIR implementation. During the last year several projects had contributed to its development and extension. At the same time we had moved the project into a new development infraestructure, outside of any institution, to promote its development in a real open source community.
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d25 1
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a25 1
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Aditionally, PyWrapper has evolved into a multiprotocol middleware software. Different projects are demanding to make their data providers available through different protocols, not only TDWG related. Therefore the software has been modularized and we have implemented already support for TAPIR and BioMOBY protocols. Our plans include support for LSID resolution and WFS in the short term. The final idea is to provide a single interface for providers to map their databases once and contribute to serveral networks with different protocols.
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d27 1
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a27 1
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Finally it is also envision the development of complementary tools to bundle with PyWrapper. The first one will be a software to create web interfaces for providers databases, the QueryTool, and utilities for georeferentiation of providers datasets.
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@
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1.11
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log
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@Revision 11
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@
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text
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@d25 1
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a25 1
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Aditionally, PyWrapper has evolved into a multiprotocol middleware software. Different projects are demanding to make their data providers available through different protocols, not only TDWG related. Therefore the software has been modularized and we have implemented already support for TAPIR and BioMOBY protocols. Our plans include support for LSID resolution, SPICE and WFS in the short term. The final idea is to provide a single interface for providers to map their databases once and contribute to serveral networks with different protocols.
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@
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1.10
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log
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@Revision 10
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@
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text
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@d25 1
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a25 1
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Aditionally, PyWrapper has evolved into a multiprotocol middleware software. Different projects are demanding to make their data providers available through different protocols, not only TDWG related. Therefore the software has been modularized and we have implemented already support for TAPIR, BioMOBY and SPICE protocols. Our plans include support for LSID resolution and WFS in the short term. The final idea is to provide a single interface for providers to map their databases once and contribute to serveral networks with different protocols.
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@
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1.9
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log
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@Revision 9
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@
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@d25 1
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a25 1
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Aditionally, PyWrapper has evolved into a multiprotocol middleware software. Different projects are demanding to make their data providers available through different protocols, not only TDWG related. Therefore the software has been modularized and we have implemented already support for TAPIR, BioMOBY and SPICE. Our plans include support for LSID resolution and WFS in the short term. The final idea is to provide a single interface for providers to map their databases once and contribute to serveral networks with different protocols.
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@
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1.8
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@Revision 8
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@
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@d22 1
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@
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1.7
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@Revision 7
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@
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@d12 1
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a12 1
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_de la Torre, J., Döring, M., Giovanni, R._
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@
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1.6
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@Revision 6
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@
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@d19 11
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@
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1.5
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@Revision 5
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@
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text
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@d16 1
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a16 1
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This session will discuss possible strategies about how to use TAPIR and will explain the different architecture components needed to build networks. An updated roadmap of implementations will be presented to better help people organize and target their projects.
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@
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a3 1
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_Döring, M., Giovanni, R., de la Torre, J._
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d5 1
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a5 1
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The TDWG Access Protocol for Information Retrieval (TAPIR) is a next generation of query protocols that can be used by biodiversity information networks. It was initially proposed as a new protocol unifying DiGIR and BioCASe during the TDWG 2004 meeting. After that, many changes were incorporated to add new functionalities and to allow different levels of provider implementation. A fully functional provider software (PyWrapper) has been developed and is ready to be used.
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d7 1
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a7 1
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This session will introduce TAPIR, explain the basic concepts behind it, like output models, query templates and the different ways of processing them. The final TAPIR 1.0 specification will be presented, also showing how biodiversity networks can be designed and configured to work with TAPIR.
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d12 1
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a12 1
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_Döring, M., Giovanni, R., de la Torre, J._
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d14 1
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a14 1
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TAPIR 1.0 is ready to be used. With at least one implementation, PyWrapper, and with others coming, projects constructing biodiversity networks can make use of it to set up their infraestructure. Existing networks, like BioCASE, or the Generation Challenge Program, has already started using it for deployment.
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d16 1
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a16 1
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This session will explain different startegies on how to use TAPIR on this context and the different architecture components needed to make them possible. An updated roadmap of implementations will be presented to better help people to organize and target their projects .
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@
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a3 1
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Döring, M., Giovanni, R., de la Torre, J.
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d12 1
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Döring, M., Giovanni, R., de la Torre, J.
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de la Torre, J.
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@
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1.2
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log
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text
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TAPIR 1.0
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1.1
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text
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The TDWG Access Protocol for Information Retrieval (TAPIR) is the next generation of query protocols to be used by biodiversity information networks, unifying the existing DiGIR and BioCASe protocols. During the last year several changes were proposed...
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Topics to be covered:
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Brief introduction
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(tunning, documentation, implementation)
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Current status
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Implementations
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TAPIR network builders guide
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@
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