The documents in this section provide details on how DOI registration and update can be performed using the two available methods: batch upload (for registration only) and System-to-System integration based on a XML protocol supporting both registration and update. We provide full technical assistance to users for DOI registration, just send an email to [email protected]
- Batch registration documentation 1.7 This zipped archive contains a document explaining how to fill-in the included Excel template
- GLIS XML Integration Protocol 3.8 The document explains in detail the XML messages to be sent to GLIS to register a new DOI or update DOIs that have been already registered. If you prefer not to implement the XML protocol directly, The Integration Toolkit described below could be of interest for you.
- Integration Toolkit 2.04 installation and operation manual The Integration Toolkit is a lightweight Java application with an embedded database that you can easily deploy in your IT environment to facilitate DOI registration and update using the GLIS XML Integration Protocol. The document describes the architecture of the Toolkit, the structure of the database that it uses, its installation and configuration and how to operate it.
- Vademecum for DOI registrants This document describes what you can do with the GLIS DOIs you have just obtained to make the most out of them.
Short documents explaining specific aspects of the GLIS system for those interested in getting more details. Some of the notes have been written to address requests received from users and stakeholders. If you would like other areas of the GLIS system be described by a new note, please send us your request using the button "Feedback" above.
- Referencing GLIS DOIs in publications and datasets
- Links to websites
- PGRFA-DOI relationships
- Standard codes
- Tips and tricks for batch registration
- XML protocol how-to
- Genesys integration
This section provides references to background information on Digital Object Identifiers and their use in the context of Plant Genetic Resources.
- International DOI Foundation a not-for-profit membership organization that is the governance and management body for the federation of Registration Agencies providing Digital Object Identifier (DOI) services and registration, and is the registration authority for the ISO standard (ISO 26324) for the DOI system. The DOI system provides a technical and social infrastructure for the registration and use of persistent interoperable identifiers, called DOIs, for use on digital networks.
- DataCite is a Registration Agency authorized by the International DOI Foundation to provide DOI registration services. DOIs assigned by GLIS are registered by DataCite.
This section provides leads to information on the descriptors adopted by GLIS in association to its DOIs.
- Digital Object Identifiers for food crops This booklet incorporates the two reference documents for adopting DOIs in your organization: "Guidelines for the optimal use of Digital object Identifiers as permanent unique identifiers for Plant Genetic Resources for Food and Agriculture - v.2" describing concrete use cases for DOI adoption and their impacts on existing processes and procedures and "Data required for the assignation of Digital Object Identifiers in the Global Information System v.2.1" wchi describes the descriptors associated to GLIS DOIs, especially in relation to the Multi-Crop Passport Descriptors Standard (see below)
- Multi-Crop Passport Descriptors The MCPD, developed jointly by Bioversity International (formerly IPGRI) and FAO, is a widely used international standard to facilitate germplasm passport information exchange. These descriptors are compatible with Bioversity's crop descriptor lists, with the descriptors used by the FAO World Information and Early Warning System (WIEWS) on plant genetic resources (PGR), and with the GENESYS global portal. GLIS descriptors are largely based on MCPD.
- Descriptors for Crop Wild Relatives Conserved in situ It is an updated list of passport descriptors for crop wild relatives conserved in situ that provides an international standard to ensure consistency in the way data about CWRI is collected and exchanged. It is also available in Arabic, French and Spanish
- Descriptors for specific crops The uniformity in data description, collection and documentation is instrumental for the conservation and use of the plant material. These descriptors are an essential tool to enable information sharing for crops covered under Annex 1 of the International Treaty.
- Other descriptors and guidelines
Taxonomy is a critical aspect of effective conservation and research on Plant Genetic Resources. Yet, it is often cause of inconsistencies and sub-optimal data quality. GLIS adopts the GRIN Taxonomy as reference list to offer synonymy search and validation services. There is also a number of Web sites that offer spell checking and validation. GLIS users are ecnouraged to submit their data to any of the services listed below to check their taxonomic information before requesting DOI registration in GLIS.
- GRIN Taxonomy The National Plant Germplasm System of the Agricultural Research Service, U.S. Department of Agriculture maintains a computer database, the Germplasm Resources Information Network, GRIN-Global, for the management of and as a source of information on its 599,842 germplasm accessions. The taxonomic portion of GRIN-Global provides the classification and nomenclature for these genetic resources and many other economic plants on a worldwide basis. Included in GRIN-Global Taxonomy are scientific names for 27,666 genera (14,514 accepted), 1,422 infragenera (1,360 accepted), and 122,164 species or infraspecies (66,755 accepted) with common names, geographical distributions, literature references, and economic importance. Generally recognized standards for abbreviating authors' names and botanical literature have been adopted in GRIN-Global. The scientific names are verified, in accordance with the international rules of botanical nomenclature, by taxonomists of the National Germplasm Resources Laboratory using available taxonomic literature and consultations with taxonomic specialists. Included in GRIN-Global Taxonomy are federal- and state-regulated noxious weeds and federally and internationally listed threatened and endangered plants. Since 1994, GRIN-Global taxonomic data have been searchable on the Internet.
- Taxonomic Name Resolution Service This website accepts batch submissions of names anche checks them against a variety of reference lists, including GRIN Taxonomy. The resulting score indicates whether each name is correct or not.
- Mansfeld Database on Agricultural and Horticultural Crops
- Diversity Assessment Tool for Agrobiodiversity and Resilience (DATAR) is a new open-source pilot software platform with a web interface, the DATAR Web Portal, and an Android App that will allow the integration of diverse crop varieties, livestock breeds, and aquatic farmed-types into decision-making plans.
- GRIN-Global Wizard for assigning DOIs with GLIS This plug-in wizard allows GRIN-Global users to assign Digital Object Identifiers from the Global Information system, free of charge. It is a component of the "Curator Tool" and it requires to be configured as explained in the accompanying documentation. Among other parameters, the configuration includes the Permanent Unique Identifier (PID) provided by the International Treaty. The source files and the documentation for “GLIS-DOI Manager Wizard" are available online.
Ontologies are a representation, including formal names and category definitions, properties and relations between the concepts, data and entities related to a specific field. In other words, an ontology is a way of representing the entities in a given field and how they are related, by defining a set of concepts and categories that establish relationships among them.
- Crop ontology The Crop Ontology project is the creation of the Generation Challenge Programme (GCP), which understood from its inception the importance of controlled vocabularies and ontologies for the digital annotation of data. The project will continue the incremental validation and refinement of the Crop Ontology, which involves adding methods of trait measurement and experiments to enable the mapping of ontology terms onto measured, stored or published variables.The Crop Ontology is a key element of the Integrated Breeding Platform