Documentation

DOI registration

• Batch registration documentation 1.7 This zipped archive contains a document explaining how to fill-in the included Excel template.
• GLIS XML Integration Protocol 3.9 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.

GLIS technical notes

• Referencing GLIS DOIs in publications and datasets This note describes the connection between GLIS DOIs publications and datasets and how data citation can be done through the Global Information System on PGRFA.
• Links to websites This note explains how links to external websites and resources are included in and managed in the DOI metadata and how keywords are assigned to them.
• PGRFA-DOI relationships This technical note describes the relationship between two or more PGRFA through the assignation of DOIs and explores some potential uses, such as the identification of ancestors and other information associated with them.
• Standard codes This document describes in detail the codes adopted in the GLIS System for a wide range of information (e.g. individuals or institutions conserving PGRFA, countries, dates, coordinates and other PGRFA attributes), and provides guidance about how to use them.
• Tips and tricks for batch registration of DOIS in GLIS This document provides suggestions on how to best access and fill in the templates for the batch registration of DOIS, which is recommended in GLIS for medium-size collections.
• XML protocol how-to This document describes the early experiences with adopting the XML protocol to assign DOIS to PGRFA material in GLIS. The XML protocol is especially suited for large collections, and the document explains the various implementing options available.
• Genesys integration This document explains the information exchange between Genesys and GLIS, particularly the addition to the GLIS DOI page of the link to the Genesys page on the same accession and the GLIS update from Genesys.

• International DOI Foundation It is 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 It is a Registration Agency authorized by the International DOI Foundation to provide DOI registration services. DOIs assigned by GLIS are registered by DataCite.

Descriptors

• 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" which includes 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 the Alliance of Bioversity International and CIAT, 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.
• ICRAF/FAO descriptors In collaboration with national and international academic and research partners, the World Agroforestry (ICRAF) and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture, have developed various booklets containing sets of minimum descriptors for characterization and evaluation of multipurpose fruit trees native to Africa and Asia. These strategic sets of descriptors facilitate standard documentation, access to information, and use of the species.
• UPLB/FAO pili nut descriptors In collaboration with academic and research partners, the University of the Philippines Los Baños (UPLB) and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture, have developed this key set of descriptors for characterization and evaluation of Canarium ovatum. It is expected to support studies focusing on the genetic and morphological diversity of pili nut, conservation of its genetic resources, domestication, and increase production and use of its products.
• ILRI/FAO descriptors for forage legume species The International Livestock Research Institute (ILRI) and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture, in collaboration with academic and research partners, have developed the Key set of descriptors for characterization and evaluation of forage legumes species. While these descriptors have been developed for some herbaceous small tropical species, they may also be helpful for the characterization of other similar forage legumes.
• ILRI/FAO descriptors for fodder trees The International Livestock Research Institute (ILRI) and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture, in collaboration with academic and research partners, have developed the Key set of descriptors for characterization and evaluation of fodder trees. These descriptors have been developed for some fast-growing species that are already being adopted by smallholder farmers worldwide
• ILRI/FAO descriptors for forage grasses The International Livestock Research Institute (ILRI) and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture, in collaboration with academic and research partners, have developed the Key set of descriptors for characterization and evaluation of fodder trees. These descriptors have been developed for various tropical species of the family Poaceae that are already being adopted by smallholder farmers worldwide
• ICAR-IIMR/ICAR-NBPGR/ICRISAT and FAO descriptors for foxtail millet In collaboration with national and international academic and research partners, the ICAR-Indian Institute of Millets Research, the International Crops Research Institute for the Semi-Arid Tropics, the ICAR-National Bureau of Plant Genetic Resources and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture has developed a booklet containing a key strategic set of characterization and evaluation descriptors for Setaria italica and Setaria pumila. This minimum set aims to support studies focusing on genetic and morphological diversity of foxtail millet and its wild and weedy relatives, as well those on conservation, domestication and use.
• ICAR-IIMR, ICAR-NBPGR, ICRISAT and FAO descriptors for fonio millets The ICAR-Indian Institute of Millets Research, the ICAR-National Bureau of Plant Genetic Resources, the International Crops Research Institute for the Semi-Arid Tropics, and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture has developed key descriptors of characterization and evaluation descriptors for Digitaria exilis Stapf and Digitaria iburua Stapf of the family Poaceae. This strategic set aims at facilitating access to and utilization of these species, and it does not exclude the addition of other descriptors later.

Resources for developing descriptors

• Developing crop descriptor lists: guidelines for developers To increase international exchange of material, a minimum element of uniformity is critical in data collection, recording, storage and retrieval. These guidelines assist genebank curators, breeders, networks and users of genetic resources to develop their own descriptor lists to characterize their material and make information available to others in a systematic and unambiguous form.
• Key characterization and evaluation descriptors: methodologies for the assessment of 22 crops The methodology describes the development process for each key set of descriptors and was designed to facilitate access to and utilization of plant genetic resources information. It includes strategic key sets of characterization and evaluation descriptors for 22 crops included in Annex I of the International Treaty.
• CWR Descriptor Tool v.1 This open data collection tool helps document Crop Wild Relatives conserved in situ conditions. The tool is based on the Descriptors for Crop Wild Relatives Conserved in situ (CWRI v.1.1), and it is composed of various spreadsheets with information and data-entry functions. It helps users to collect and structure CWR data in a standardized manner as a first step to developing national databases of populations conserved in situ.

Other descriptors

• Descriptors for genetic marker technologies This descriptor list is targeted to researchers using genetic marker technologies to generate and exchange genetic marker data that are standardized and replicable. This initial proposed set of descriptors was reviewed widely by international experts from national research institutions, universities and CGIAR centres.
• Descriptors for farmers’ knowledge This list of descriptors aims to capture key characteristics, uses and values of cultivated and wild plants as described by farmers and other people in farming communities.
• Alliance of Bioversity and CIAT - Crop descriptors for various crops The Alliance of Bioversity International and CIAT in collaboration with partners has developed descriptors for various crops. They are targeted at farmers, curators, breeders, scientists and users and facilitate the exchange and use of resources
• UPOV Technical Guidelines Technical Guidelines for the examination of Distinctness, Uniformity and Stability (DUS) and the Development of Harmonized Descriptions of New Varieties of Plants.
• GRIN Global Descriptors It provides the classification and nomenclature for genetic resources and for many other economic plants on a worldwide basis. Included in GRIN-Global Taxonomy are scientific names for 28,094 genera (14,723 accepted), 1,422 infragenera (1,350 accepted), and 129,994 species or infraspecies (71,326 accepted) with common names, geographical distributions, literature references, and economic importance.

Taxonomy

• 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 It is an online database developed at IPK since 1998. It contains information on 6,100 crop plant species, excluding forestry and ornamental plants. Each species entry provides nomenclature and synonymy, common names in different languages, spontaneous distribution and regions of cultivation, uses, images, references, but also the ancestral species and notes on the phylogeny, variation and history.
• Diversity Assessment Tool for Agrobiodiversity and Resilience (DATAR) It 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.
• Cichorieae Systematics Portal It provides access to the existing knowledge about cichorieae plants, based on authoritative phylogenetic and taxonomic information as far as available.
• Euro+Med PlantBase It covers all native and introduced vascular plants from Europe, the Mediterranean and the Caucasus.
• EDIT Platform for Cybertaxonomy It is a collection of open source tools and services which together cover all aspects of the workflow in biology for describing, classifying and naming groups of organisms.

Ontologies

• 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

• PLAZA It is a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.
• AgBioData It is a consortium of agricultural biological databases with the mission of consolidating standards and best practices for acquiring, displaying, and reusing genomic, genetic, and breeding (GGB) data.
• Breeding Management System It is a data management software specifically designed to meet the needs of modern plant breeders.
• Breedbase It is a comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping samples in a field, store large amounts of high density genotypic information, and provide Genomic Selection related analyses and predictions.
• Sol Genomics Network It is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.
• OECD Variety List Query It is the official list of varieties that have been accepted as being eligible for certification by the National Designated Authorities of countries participating in the OECD Seed Schemes.
• EUPVP - Common catalogue The common catalogues of varieties of agricultural plant and vegetable species list the varieties which can be marketed in the EU.
• IBG-4 Plant biotechnology Information This website attempts to track sequenced plant genomes which have been published in peer-reviewed journals.