560 lines
24 KiB
Plaintext
560 lines
24 KiB
Plaintext
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head 1.15;
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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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1.15
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date 2007.07.07.18.17.42; author JavierTorre; 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 2007.01.31.22.35.58; author RenatoDeGiovanni; 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 2006.11.16.00.01.17; author DaveVieglais; 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 2006.11.16.00.00.13; author JavierTorre; 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 2006.11.15.23.50.19; author AimeeStewart; 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 2006.11.15.23.49.04; author JavierTorre; 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 2006.11.15.23.36.46; author DaveVieglais; 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 2006.11.15.21.15.00; author DaveVieglais; 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 2006.11.15.15.26.47; author PatriciaMergen; 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 2006.11.15.09.09.18; author PatriciaMergen; 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 2006.11.15.03.36.39; author TimSutton; 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 2006.11.15.02.20.08; author TimSutton; 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 2006.11.15.01.55.20; author JavierTorre; 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 2006.11.14.21.21.03; author TimSutton; 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 2006.11.09.22.27.54; author AimeeStewart; state Exp;
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branches;
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next ;
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desc
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@none
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@
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1.15
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log
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@
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text
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@%META:TOPICINFO{author="JavierTorre" date="1183832262" format="1.1" version="1.15"}%
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%META:TOPICPARENT{name="GeoAppInter"}%
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---++ BioGeoSDI TIP Proposal - November 2006
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*Title:* TDWG Interoperability Testbed Pilot Project
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---++++*Objective:*
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We envisage en environment where the many different TDWG initiatives can interoperate to provide a rich set of tools for biodiversity knowlege exploration, analysis and discovery - a Biological Geospatial Data Infrastructure. This proposal is a first step towards creating such an interoperability environment. We aim to test and demonstration of the use of biodiversity informatics and geospatial standards, mainly TDWG and OGC(1), by creating and implementing a very simple use case that integrates various *existing* tools and standards within the TDWG universe.
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---++++*Responsible:*
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The newly formed SubStandards task group. The SubStandards task group is a new task group that is being created under the TDWG Geospatial Subgroup. The group is still not an official TDWG task group but will likely be in the near future. The convener of this task group will be Javier de la Torre.
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---++++*Outcomes:*
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The main result of the meeting will be a demonstration of the interoperability and usability of the different standards involved in the experiment. To do so a create a workflow of chained services will be designed and demonstrated in a web application which integrates *existing* projects, technologies, and standards. We place a strong emphasis on the use of 'existing' facilities since we want to produce a rapid prototype and limit _de neaveau_ development to strictly the minimum needed to achieve interoperability between the components listed below, and the provision of a simple web interface that will allow the user to 'test drive' our test bed.
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Three major components- taxonomic object services (TOS), the Spatial Data Library (SDL) and to a lesser extent, high performance OM web services (HP-OMS) of such a work flow are beyond the scope of development within a workshop such as this, and so development tasks for these are submitted as separate proposals or obtained elsewhere (SEEK-Taxon, SPICE for TOS). However, the development of both SDL and HP-OMS are driven primarily by their respective use cases, which are to a certain extent, expected to be defined at this developer workshop. Hence it is important that the SDL and HP-OMS are available as prototypes for the workshop.
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Tagging of these data sources and services with LSIDs will be an important component of the envisaged work flow, and will be critical to the operation of the SDL and to enable tracing of the data through the work flow.
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The workflow will include:
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* Use of taxonomic Name/Concept resolution service with LSIDs.
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* Primary data harvesting using WFS(2), TAPIR, and/or DiGIR
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* Visualization of primary data with other Geospatial sources using WMS.
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* Discovery of environmental layers using catalog services CSW (4).
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* Use of the [[http://openmodeller.sf.net][openModeller]] Web Service to accomplish a model experiment
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* Presentation of the results in a web application using WMS and other OGC standards
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* Assignment of LSIDs to analysis outputs
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All the source code of the workshop will be available as Open Source on the biogeosdi.org trac system and the working prototype will be accessible to the general public.
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---++++*Tentative list of participants:*
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* Main.TimSutton (openModeller Web Service)
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* Aimee Stewart (SDL Catalog, Environmental Data Management)
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* Dave Vieglais (Taxonomic Concept Service, Mapping and Web UI, LSIDs)
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* Javier de la Torre (Mapping interfaces with WMS/WFS, Catalog service, TAPIR)
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* Dave Neufeld (Data retrieval using WFS)
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* Peter Brewer (SPICE protocol, taxonomic services from Species 2000)
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* Patricia Mergen (RMCA, Reporting on web applications combining OGC and TDWG standards)
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---++++*Dates and Location:*
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The proposed dates for the workshop are 2nd to 6th of April 2007. The first day will be for coordination and planning and 4 days for coding in groups.
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The proposed place for the workshop is CRIA (to be confirmed) in Campinas, Brazil.
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---++++Funding Requirements
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Travel and accommodation for 7 participants. The figure below takes into account that 1 participant will not require any travel and accommodation cover if the even takes place at the location proposed above.
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*Total amount requested:* US$ 13,000
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---++++Acronyms:
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* OGC: Open Geospatial Consortium
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* WFS: Web Feature Service
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* WMS: Web Map Service
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* CSW: Web Catalog Service
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* HP-OMS: High Performance Open Modeller Services
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* SDL: Spatial Data Library
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---+++ Attachments
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I mocked up this diagram which we could possibly use..(TS)
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* [[%ATTACHURL%/BioGeoSDITIPDiagram.graffle][BioGeoSDITIPDiagram.graffle]]: BioGeoSDITIPDiagram.graffle
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* BioGeoSDITIPDiagram.png: <br />
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<img src="%ATTACHURLPATH%/BioGeoSDITIPDiagram.png" alt="BioGeoSDITIPDiagram.png" width='551' height='543' />
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* [[%ATTACHURL%/Substandard_TIP.pdf][Substandard_TIP.pdf]]: DRAFT version of TIP by DaveV
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%META:FILEATTACHMENT{name="BioGeoSDITIPDiagram.graffle" attr="" autoattached="1" comment="" date="1163561596" path="BioGeoSDITIPDiagram.graffle" size="35426" user="Main.TimSutton" version="1"}%
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%META:FILEATTACHMENT{name="Substandard_TIP.pdf" attr="" autoattached="1" comment="DRAFT version of TIP by DaveV" date="1163625300" path="Substandard_TIP.pdf" size="98343" user="Main.DaveVieglais" version="1"}%
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%META:FILEATTACHMENT{name="BioGeoSDITIPDiagram.png" attr="" autoattached="1" comment="" date="1163561688" path="BioGeoSDITIPDiagram.png" size="54775" user="Main.TimSutton" version="1"}%
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@
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1.14
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text
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@d1 1
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a1 1
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%META:TOPICINFO{author="RenatoDeGiovanni" date="1170282958" format="1.1" version="1.14"}%
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a61 82
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-----
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-----
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-----
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---+FROM HERE THE TEXT IS JUST ARCHIVE!!! PLEASE ONLY CONSIDER VALID AS A PROPOSAL UNTIL HERE. IF YOU WANT TO ADD SOMETHING FROM BELOW COPY IT INTO THE TEST ABOVE
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Please take from the old stuff and place it on the fresh at the top...
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---+++ Who is going to do it?
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The newly formed SubStandards Geospatial subgroup task group on application-interoperablity is interested in submitting a proposal for the TDWG Infrastructure Project.
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The newly formed SubStandards task group. The SubStandards task group is a new task group that is being created under the TDWG Geospatial Subgroup. The group is still not an official TDWG task group but will likely be in the near future.
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The SubStandards task group is formed of people involved in different projects related to biodiversity informatics and biogeography, like OpenModeller, SYNTHESYS, SEEK and GBIF MAPA.
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The main organizers of the meeting will be:
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* Javier de la Torre
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* Tim Sutton
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---+++ What issue/problem is going to be addressed?
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The use of georeference biodiversity data has been identified as major need in many end-user and stakeholders surveys. For the last years different projects have been working on different data models and communication standards to enable the sharing and analysis of this data together with other geospatial data. In this process several TDWG standards had been created and are being used.
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At the same time, the Geospatial community, through the Open Geospatial Consortium, has been working on a set of open standards to enable the interoperability of geospatial services using the Internet.
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...(I am stucked here)
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TDWG and other communities have created a set of standards
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We would like to create a workflow of interconnected projects which use existing TDWG and other well-accepted standards and technologies, such as OGC, DiGIR, TAPIR, GBIF Portal, SEEK TOS, TCS, DataTester, openModeler, TDWG Ontologies ... From this project we expect to determine where the weaknesses and holes in the existing Bioinformatics Infrastructure, fix the simple ones and extend standards where it is appropriate. By
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We expect this project to be a prototype for a more extensive, complex project with many of the same objectives, but extending existing and creating new component projects. The more complex project could also incorporate a research component.
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---+++ What is going to be produced?
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The main result of the meeting will be a demonstration of the interoperability and usability of the different standards involved in the experiment. To do so a create a workflow of chained services will be designed and demonstrated in a web application which integrates existing projects, technologies, and standards. The initial objective of the workflow will be to create distribution ranges of a species. Data exploration can occur at every step of the process, allowing data visualization and display of metadata for datasets, individual data components, and data providers.
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The workflow begins with a query on a simple species name. The Name/Concept Resolution service will return a list of LSIDs/namestrings and information on how they relate to the original query term. The researcher selects the LSIDs/namestrings to be used in the analysis. This list is then sent to the Data Harvester which returns a set of occurrences for the list. Each occurence includes the latitude, longitude and a globally unique identifier. The interface allows map visualization and metadata queries of some or all of the returned data. ___In addition there are options to let the researcher use DataTester and Biogeomancer to explore and perhaps improve the data quality of the returned data.___
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Depending on the availability of
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The occurrence data can then be sent to openModeller to perform a fundamental ecological niche analysis. When the researcher submits this request, the job is assigned a unique id/link which is sent to the researcher when the job is complete. Clicking a link in the email takes him to a page that lets him download the model via WCS, and download the original occurence points via WFS, or visualise the model in an interactive web mapping application with the original occurrence points overlaid.
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---++++ List of candidate standards/technologies/projects to be used on the workflow
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---+++ Where is the work going to be done?
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The vision of the group is to have a live demonstration that will be completed with succesive workshops or projects. We will have a bottom-up strategy where simple use cases and interoperability cases will be demonstrated towards a complex infraestructure where the different standards can be used.
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Preparatory discussions would occur via the wiki and the listserv to map out what standards/technologies would be represented and the implementation status of them to be easily integrated. A trac system with a subversion repository has been created to start bringing some code prior to the workshop and as project management system.
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The main part of the work will be done in a series of workshop or code fest. The workshops will last 5 days. The first one there will be preparatory and coordination discussions and the other 4 days will be spent programming or adapting the requiered software to fullfil the workflow.
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The first workshop is planned to be the 12th to 16th March in Campinhas, Brazil.
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Aditionally we look forward to collaborate with other similar initaties coming from the Geospatial side, as GEOSS and their interoperability test beds.
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---++++ List of participants and expertise for the first workshop:
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* Tim Sutton (Open Modeller Web Service)
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* Aimee Stewart (SEEK taxonomic service, GUI)
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* Dave Vieglais (
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* Javier de la Torre (Mapping interfaces with WMS/WFS, Catalog service, TAPIR)
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---+++ How much will it cost?
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We need a (subset of?) the active contributers - possibly developers who would meet for a workshop. Any thoughts?
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Cost of initial workshop.
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Cost of mid-project workshop to work out emerging difficulties?
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---+++ Holes in this document
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* List of candidate standards/technologies/projects to be used at each stage of the workflow (I think we should just point to the minimal workflow use case and then flesh out the technologies list there TS)
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* List of areas we expect to tweak to fit or advance
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* List of workshop attendees and portions of the workflow they will contribute to
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* Concrete goals of the workshop
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* Timetable for intermediate steps
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* Clear vision of the final product
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* Spellcheck !
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@
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%META:TOPICINFO{author="DaveVieglais" date="1163635277" format="1.1" version="1.13"}%
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d44 1
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The proposed dates for the workshop will be the 12th to 16th March 2007. The first day will be for coordination and planning and 4 days for coding in groups.
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@
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%META:TOPICINFO{author="JavierTorre" date="1163635213" format="1.1" version="1.12"}%
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d25 1
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a25 1
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* Discovery of environmental layers using catalog services CSW (4) *If feasible.*
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@
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%META:TOPICINFO{author="AimeeStewart" date="1163634619" format="1.1" version="1.11"}%
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d16 1
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a16 1
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Three major components- taxonomic object services (TOS), the SDL and to a lesser extent, high performance OM web services (HP-OMS) of such a work flow are beyond the scope of development within a workshop such as this, and so development tasks for these are submitted as separate proposals or obtained elsewhere (SEEK-Taxon, SPICE for TOS). However, the development of both SDL and HP-OMS are driven primarily by their respective use cases, which are to a certain extent, expected to be defined at this developer workshop. Hence it is important that the SDL and HP-OMS are available as prototypes for the workshop.
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d25 1
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* (Discovery of environmental layers using catalog services CSW (4)) *Not decided if feasible.*
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@
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%META:TOPICINFO{author="JavierTorre" date="1163634544" format="1.1" version="1.10"}%
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d35 2
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a36 2
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* Aimee Stewart (SEEK taxonomic service, GUI)
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* Dave Vieglais (Mapping and Web UI, LSIDs)
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%META:FILEATTACHMENT{name="Substandard_TIP.pdf" attr="" autoattached="1" comment="DRAFT version of TIP by DaveV" date="1163625300" path="Substandard_TIP.pdf" size="98343" user="Main.DaveVieglais" version="1"}%
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%META:TOPICINFO{author="DaveVieglais" date="1163633806" format="1.1" version="1.9"}%
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Travel and accommodation for 6 participants. The figure below takes into account that 1 participant will not require any travel and accommodation cover if the even takes place at the location proposed above.
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*Total amount requested:* US$ 10,000
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d54 7
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a60 5
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---++++References:
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1 OGC: Open Geospatial Consortium
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1 WFS: Web Feature Service
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1 WMS: Web Map Service
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1 CSW: Web Catalog Service
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d68 1
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%META:TOPICINFO{author="DaveVieglais" date="1163625300" format="1.1" version="1.8"}%
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d16 4
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d23 1
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a23 1
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* Primary data harvesting using WFS(2) or TAPIR
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d28 1
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d154 1
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%META:FILEATTACHMENT{name="Substandard_TIP.pdf" attachment="Substandard_TIP.pdf" attr="" comment="DRAFT version of TIP by DaveV" date="1163625300" path="Substandard_TIP.pdf" size="98343" stream="Substandard_TIP.pdf" user="Main.DaveVieglais" version="1"}%
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@
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1.7
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@d1 1
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a1 1
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%META:TOPICINFO{author="PatriciaMergen" date="1163604407" format="1.1" version="1.7"}%
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d145 2
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d149 1
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@
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1.6
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%META:TOPICINFO{author="PatriciaMergen" date="1163581758" format="1.1" version="1.6"}%
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d35 2
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a36 2
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* Patricia Mergen (SYNTHESYS Itineary services, web application combining OGC and TDWG standards)
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* Bart Meganck (SYNTHESYS Itineary services, web application combining OGC and TDWG standards)
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a144 1
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@
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1.5
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@
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@d1 1
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a1 1
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%META:TOPICINFO{author="TimSutton" date="1163561799" format="1.1" version="1.5"}%
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d35 2
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d85 1
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a85 1
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TDWG and other communities had created a set of standards
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a145 1
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@
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a1 1
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%META:TOPICINFO{author="TimSutton" date="1163557208" format="1.1" version="1.4"}%
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d22 1
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a22 1
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* Use of the Open Modeller Web Service to accomplish a model experiment
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d134 13
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@
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1.3
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@d1 1
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a1 1
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%META:TOPICINFO{author="JavierTorre" date="1163555720" format="1.1" version="1.3"}%
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a2 1
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d7 2
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a8 2
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*Objective:*
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We envisage en environment where the many different TDWG initiatives can interoperate to provide a rich set of tools for biodiversity knowlege exploration, analysis and discovery - a Biological Geospatial Data Infrastructure. This proposal is a first step towards creating such an interoperability environment. We aim to test and demonstration of the use of biodiversity informatics and geospatial standards, mainly TDWG and OGC(1), by creating and implementing a very simple use case that integrates various existing tools and standards within the TDWG universe.
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d10 1
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a10 1
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*Responsible:*
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d13 3
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a15 2
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*Outcomes:*
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The main result of the meeting will be a demonstration of the interoperability and usability of the different standards involved in the experiment. To do so a create a workflow of chained services will be designed and demonstrated in a web application which integrates existing projects, technologies, and standards.
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d18 10
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a27 6
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* Use of taxonomic Name/Concept resolution service with LSIDs.
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* Primary data harvesting using WFS(2) or TAPIR
|
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* Visualization of primary data with other Geospatial sources using WMS.
|
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* (Discovery of environmental layers using catalos services CSW (4)) Not decided if feasible.
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* Use of the Open Modeller Web Service to accomplish a model experiment
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* Presentation of the results in a web application using WMS and other OGC standards
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d29 6
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a34 1
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All the source code of the code fest will be available as Open Source on the biogeosdi.org trac system and the working prototype will be accessible.
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d36 1
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a36 1
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*Tentative list of participants:*
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d38 1
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a38 6
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* Tim Sutton (Open Modeller Web Service)
|
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* Aimee Stewart (SEEK taxonomic service, GUI)
|
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* Dave Vieglais (Mapping and Web UI, LSIDs)
|
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* Javier de la Torre (Mapping interfaces with WMS/WFS, Catalog service, TAPIR)
|
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* Dave Neufeld (Data retrieval using WFS)
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* Peter Brewer (SPICE protocol, taxonomic services from Species 2000)
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d40 1
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a40 1
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*Dates and Location:*
|
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d42 1
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a42 1
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The workshop will be the 12th to 16th March 2007. The first day will be for coordination and planning and 4 days for coding in groups.
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d44 1
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a44 1
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The proposed place for the workshop is CRIA (to be confirmed) in Campinhas, Brazil.
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d48 5
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a52 5
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References:
|
||
|
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1 OGC: Open Geospatial Consortium
|
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2 WFS: Web Feature Service
|
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3 WMS: Web Map Service
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4 CSW: Web Catalog Service
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d54 3
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d60 3
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@
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1.2
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%META:TOPICINFO{author="TimSutton" date="1163539263" format="1.1" version="1.2"}%
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d3 52
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d56 9
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a64 1
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The newly formed as-yet-unnamed Geospatial subgroup task group on application-interoperablity is interested in submitting a proposal for the TDWG Infrastructure Project.
|
||
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d68 2
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a69 1
|
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|
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In biodiversity conservation easy access to geographic information and distribution maps in re-usable formats has been identified as a major need in many end-user and stakeholders surveys. Recent species observational data are usually accurately georeferenced by GPS devices. Older records, which originally had no geographic coordinates can be properly georeferenced by using available gazetteers, maps and additional information to accurately pinpoint the sampling sites. Numerous atlases have been published showing species distribution ranges. Many are completed by valuable habitat description layers like protected areas, soil occupation, geological or meteorological information. This existing information is of high value for a large number of stakeholders in nature conservation. Several activities in recent and ongoing projects have successfully enabled access to geographic information for specific groups of end-users, by implementing GIS webportals using OGC (INSPIRE) compliant GIS software. The goal of this task group is to provide global and generalized access to biodiversity-linked geographical data. It will offer open and non-proprietary standard GIS services (like WMS, WFS or WCS) in an user-friendly and interoperable way in form of a Biogeography Spatial Data Infrastructure (BioGeoSDI?).
|
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d71 4
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a74 1
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We would like to create a workflow of interconnected projects which use existing TDWG and other well-accepted standards and technologies, such as OGC, DiGIR, TAPIR, GBIF Portal, SEEK TOS, TCS, DataTester, openModeler, TDWG Ontologies ... From this project we expect to determine where the weaknesses and holes in the existing Bioinformatics Infrastructure, fix the simple ones and extend standards where it is appropriate.
|
||
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d79 1
|
||
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a79 1
|
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|
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A biodiversity website which integrates existing projects, technologies, and standards into a workflow and data exploration interface. The initial objective of the workflow will be to create distribution ranges of a species. Data exploration can occur at every step of the process, allowing data visualization and display of metadata for datasets, individual data components, and data providers.
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d81 1
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a81 1
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The workflow begins with a query on a simple species name. The Name/Concept Resolution service will return a list of LSIDs/namestrings and information on how they relate to the original query term. The researcher selects the LSIDs/namestrings to be used in the analysis. This list is then sent to the Data Harvester which returns a set of occurrences for the list. Each occurence includes the latitude, longitude and a globally unique identifier. The interface allows map visualization and metadata queries of some or all of the returned data. The interface also allows the resercher to discard occurrences s/he does not wish to use. In addition there are options to let the researcher use DataTester and Biogeomancer to explore and perhaps improve the data quality of the returned data.
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d83 1
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d86 4
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d91 8
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a98 1
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Preparatory discussions would occur via the wiki and the listserv to map out what standards/technologies would be represented and the developers/institutions who will do the work.
|
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d100 1
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a100 1
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Our first objective would be a workshop with to map out exactly how these developers will connect the pieces. Shall we enumerate other concrete goals of this workshop?
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d102 4
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a105 1
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Given the structure of the group, the work will be distributed among several institutions with one or more working meetings to keep the focus.
|
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a106 1
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|
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We should have a list of active contributers here.
|
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@
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1.1
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%META:TOPICINFO{author="AimeeStewart" date="1163111274" format="1.1" version="1.1"}%
|
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d19 1
|
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a19 1
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The occurrence data can then be sent to OpenModeller to perform an fundamental ecological niche analysis. When the researcher submits this request, the job is assigned a unique id/link which is sent to the researcher when the job is complete. Clicking a link in the email takes him to a page that lets him download the model via WCS, and download the original occurence points via WFS, or visualise the model in an interactive web mapping application with the original occurrence points overlaid.
|
||
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d39 1
|
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a39 1
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|
|
* List of candidate standards/technologies/projects to be used at each stage of the workflow
|
||
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a45 1
|
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@
|