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Cover slide Documentation of Genetic Resources Global Information Systems SEEDNet Training Course May 28, 2008 NordGen, Alnarp Dag Terje Filip Endresen Nordic Genetic Resource Center/ Bioversity International
The GCP Mission: To use advanced genomics science and plant genetic diversity to overcome complex agricultural bottlenecks that condemn millions of the world’s neediest people to a future of poverty and hunger .
The GCP Vision: A future where plant breeders have the tools to breed crops in marginal environments with greater efficiency and accuracy for the benefit of the resource-poor farmers and their families.
Scenario: You have a dataset of genebank accessions with pointers to the source datasets of the holding genebanks. You produce phenotypic evaluation data on accessions in this dataset. You find evaluation data from other sources on some of the accessions in your dataset. Some of the evaluation data are produced in areas of different day length, rainfall, soils… Some of the accessions in your dataset originate from areas of higher population densities other accessions originate from more natural habitats. Unfortunately most of the different sources of information is located on different web sites and it is difficult to bring the information together.
You would need to go through more or less the same process as other researchers in many domains of gathering heterogeneous data from multiple sources, combining and analysing it. This is the challenge that faces the web as a whole and is being addressed by the Semantic Web project.
RDFs can assist you to relate information from different sources.
A RDF triplet looks like this: subject-predicate-object
anytime approximate case study diagnosis inconsistent kads banana apples stem color knowledge based systems knowledge level knowledge management knowledge representation LSID accession number GUID unitID ontology owl parametric design Full Scientific Name peer to peer systems problem solving landrace traditional cultivar 300 methods rdf rdf WEB2 ABCD SDD semantic web semantics specification languages web based web ontology INSTCODE plant genetic resources germplasm agricultural traits Aegilops
Crop Wild Relatives ARM LKA BOL MDG UZB National Datasets are shared with the central CWR data index. The national datasets as well as access to other International datasets are provided from the CWR data portal. EURISCO SINGER [ http://www.cropwildrelatives.org ]
The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community.
Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.
Use of GBIF technology and integration of PGR collection data into GBIF allows PGR users to simultaneously search PGR collections and other biodiversity collections, and to get access to the data (and possibly the material) of relevant biodiversity collections.
The establishment of new data portals on a specific crop, a regional thematic network or similar subset of the total global biodiversity datasets; can be done with rather few efforts! This requires only that all the relevant datasets are provided by GBIF compatible web services (like the BioCASE PyWrapper).
In taxonomy, descriptive data takes a number of very different forms.
Natural-language descriptions are semi-structured, semi-formalised descriptions of a taxon (or occasionally of an individual specimen). They may be simple, short and written in plain language (if used for a popular field guide), or long, highly formal and using specialised terminology when used in a taxonomic monograph or other treatment.
The goal of the SDD standard is to allow capture, transport, caching and archiving of descriptive data in all the forms shown above, using a platform- and application-independent, international standard. Such a standard is crucial to enabling lossless porting of data between existing and future software platforms including identification, data-mining and analysis tools, and federated databases.
Hagedorn, G.; Thiele, K.; Morris, R. & Heidorn, P. B. 2005. The Structured Descriptive Data (SDD) w3c-xml-schema, version 1.0. http://www.tdwg.org/standards/116/ . [Last retrieved 05-May-2007]