What is GLIS?

GLIS is the Global Information System on Plant Genetic Resources for Food and Agriculture (PGRFA) referred to in Article 17 of the International Treaty. It is a system that facilitates the exchange of information on scientific, technical and environmental matters related PGRFA, by building on and linking existing information systems. The Vision and Programme of Work for the development of GLIS were adopted by the Governing Body of the Treaty in 2015. GLIS includes a web-based portal. Read more at www.fao.org/plant-treaty/areas-of-work/global-information-system/links/en/.

What is being done during the inception phase of GLIS?

With the generous support of the Government of Germany, the implementation of the Programme of Work started with setting up the IT infrastructure (e.g. the GLIS Portal), and the development of standards for the identification and documentation of  PGRFA. The implementation also facilitated the promotion of tools to foster interoperability among systems, and the organization of workshops and capacity strengthening activities in selected developing countries.

Who provides guidance and advice on the development of GLIS?

The Governing Body of the International Treaty provides guidance, while a Scientific Advisory Committee provides advice to the Secretariat on GLIS implementation. In addition, inputs are sought from a broad range of stakeholders in order to cater for the needs of the global PGRFA community.

What is the GLIS Portal?

It is a web-based global entry point for users and third-party systems to access information and knowledge on scientific, technical and environmental matters to strengthen PGRFA conservation, management and utilization activities. The Portal also enables recipients of PGRFA to make available all non-confidential information and the results of their research and development on germplasm according to the provisions of the Treaty and the Standard Material Transfer Agreement (SMTA). FAO launched GLIS in October 2017.

What types of PGRFA can be documented through GLIS?

GLIS can incorporate all types of PGRFA, including genebank accessions, breeding lines, PGRFA under development, released varieties, material held by farmers, in community seed banks or informal working or research collections, and all other research materials such as mapping populations, purified genetic stocks, etc.

What is the added value that GLIS brings to existing systems?

GLIS adds value to existing systems by connecting information on genebank accessions, breeding, and research on varieties maintained on farm or in natural environments and already available in those systems. GLIS reaches out to research institutions, national inventories, herbaria and the private sector making available a collection of organized links to websites where the information is produced and maintained up to date. FAO is exploring the best technical options to facilitate searches across multiple data sources by users and third-party information systems and the development of data visualization tools across existing systems and databases.

Which standards does GLIS promote?

GLIS promotes the use of DOIs as a common standard to uniquely and permanently identify PGRFA and facilitate interoperability.

The second version of the GLIS descriptors (Data required for the assignation of Digital Object Identifiers in the Global Information System) was published in 2017 along with the first version of the Guidelines for the optimal use of DOIs for germplasm samples. These documents serve as reference guides to enrich and refine further as their development is an evolving process based on users’ needs. The latest versions are available online.

How do DOIs relate to existing identifiers?

DOIs are designed to coexist with other identifiers. Data curators can keep their current sample identifiers, continue to use them as they currently do, and use them as search keys in GLIS. This minimizes the impact of adopting DOIs on existing systems and established procedures. The use of DOIs is recommended for all purposes that are beyond the intended scope of existing identifiers, such as information sharing across different information systems and different communities.

What do DOIs add to existing identifiers?

DOIs: 

• Enable the development of additional functionalities for data integration across systems;
• Provide a single standard for the identification of PGRFA of any kind, in contrast to existing identifiers designed for particular communities such as genebanks and breeders.

Will Accession Identifiers be replaced by DOIs?

DOIs are not intended to replace Accession Identifiers, widely used in the genebank community, or any other identifier that is currently being used within your organisation. You can continue using the identifiers you are most comfortable with. However, when material is transferred outside your institution, using DOIs ensures that the material is properly tagged and provides access to the advantages provided by GLIS and DOIs.

Does the use of DOIs help to comply with the information-sharing provisions under the Treaty?

Yes. It helps providers of material to comply with their obligations under the Treaty to make available all non-confidential information about their PGRFA. It also enables recipients of material under a Standard Material Transfer Agreement (SMTA) to comply with their obligations to make available all non-confidential information that results from research and development carried out on the material received. DOIs can be used when reporting on SMTA transfers through Easy-SMTA.

Can assigning DOI to plant material help to define royalties in Material Transfer Agreements?

DOI itself does not have any direct implication on royalties.

Will DOIs be added as a reporting requirement to Easy-SMTA?

It is not mandatory to use DOIs in SMTA reporting. However, it is possible to voluntarily use DOIs in the Sample ID field of the Annex 1 to the SMTA (i.e. the list of material being transferred with the SMTA) to identify the material transferred.

Am I required to obtain DOIs for the PGRFA that I manage?

No, there is no obligation to obtain DOIs: use of the system is entirely voluntary. However, obtaining DOIs gives you access to new functionalities provided by GLIS, so if you need any such functionality you will need to obtain DOIs.

Is there an obligation of users within a Centre, to use the DOIs of materials distributed for internal purposes?

No. However, the Centre may choose to establish its own obligatory standard operating procedures.

Have protocols been established to enable DOI assignment in GRIN Global?

The Secretariat is collaborating with USDA, CIMMYT and other users of GRIN Global to ensure that future versions of GRIN-Global interoperate with GLIS to obtain DOIs.

How is it possible to take into account farmers who are in fact the first/true provider of plant materials?

Farmers are invited to join the GLIS initiative either by themselves, through associations or through other forms of coordination. We are analysing the needs of farmers as well as of other user communities to make GLIS as useful and effective as possible.

Do you think associating farmers to publications and institutes is a good way to recognize their effort of PGR conservation?

Yes. Farmers can join the GLIS initiative and assign DOIs for their own material, exactly as any other GLIS user. There can be technical issues in joining GLIS from remote rural areas of developing countries, but in this case farmer associations or other coordination bodies can act as proxies.

Why DOIs were selected as the GLIS identifiers?

DOIs were identified as the most effective technology for Permanent Unique Identifiers (PUIDs). They are used to unambiguously and permanently identify PGRFA being exchanged not only in the context of the ITPGRFA and its Multilateral System but also outside. Once a DOI is assigned, a PGRFA sample and associated information can be referenced easily, unambiguously and permanently across organizations.

With DOIs, non-confidential information about PGRFA made available by different organizations and in multiple databases may be gathered and harvested more efficiently. Assigning a DOI is a critical first step towards more organized, manageable, effective and available information on PGRFA at global level to support plant breeding, research and training.

What main advantages can we expect from the use of DOIs?

The adoption of DOIs is expected to bring several major advantages to PGRFA users:

• easier discovery and access to information related to PGRFA material;
• more effective harvesting of such information through automated means;
• more accurate identification of the material, associated information and related rights and obligations;
• more reliable association of research outcomes to the material;
• access to advanced services such as identification of publications mentioning specific materials.

What is the difference between DOIs and finger printing for identification of crop varieties?

These are entirely different. The DOI is a digital identifier, like a passport number or social security ID, whereas a DNA “fingerprint” is a record of a characteristic part of the genetic composition of an organism. Validation of a DOI requires cross-referencing associated metadata, whereas validation of a DNA fingerprint requires re-extraction and re-analysis of a DNA sample.

Is there any feasibility or pilot study assessing the implementation of DOIs in genebanks?

The Treaty Secretariat, in collaboration with partner institutions, is currently implementing some pilot projects to facilitate the adoption of DOIs in real-world situations. One example is a project led by Indonesia that is validating the GLIS infrastructure and processes at the regional level. Additionally, the Treaty is promoting the adoption of DOIs through various national and international genebanks and research communities.  In just one month since its operations, GLIS assigned DOIs to more than 560,000 genebank accessions.

What is the cost of using DOIs?

The Secretariat of the International Treaty provides DOI registration free-of-charge for the entire PGRFA community.

How can I link my system to GLIS?

You can contact the Secretariat of the International Treaty at [email protected] indicating the material you would like to register and the contact details of the main data curator in your organization.

What does a DOI look like? How many digits will it be?  Will it fit in labels and shipping lists?

A GLIS DOI looks like 10.18730/12A2E. Even when there will be 1 billion DOIs, the actual string will look like 10.18730/3D2ZQ6, making it quite compact.

Can there be any “meaning” immediately obvious within a DOI (human intelligible and readable)?

DOIs assigned by GLIS are fully opaque: no meaning can be extracted by just looking at the DOI. Resolving the DOI (i.e. entering it into the GLIS search function or in any other DOI Resolution Service) is the correct way to get any information about the PGRFA associated to the DOI.

Is a DOI a URL, and where does it point?

A DOI, by itself, is not a URL. However, it can be easily converted to a URL by using the form: https://doi.org/<doi> (e.g. https://doi.org/10.1109/5.771073). When converted to a URL, the DOI points to the landing page provided by the system that registered the DOI. For GLIS DOIs, it will be a page served by GLIS with the information associated to the PGRFA as well as the link to the owner’s website, if provided.

How is material identified?

Users can register the identifier they normally use according to their community, such as accession ID, Selection ID, Selection Number, Derivative name, Population ID, Seed lot ID, Catalogue entry, etc., or even a sample ID created by a collector when collecting a sample from in situ conditions.

How can I register my PGRFA into the GLIS portal?

Three options are available to register your PGRFA in GLIS. The first one, for small numbers of records, is to use the web form offered by the portal. The next option is based on batch files (essentially Excel documents) that you will compile according to our specifications. However, being error prone and time-consuming, this option should be considered just a stop-gap solution. The recommended approach is to adopt the published XML integration protocol that ensures much more effective and reliable integration with the GLIS framework. You are welcome to create your own implementation of the protocol, but the Secretariat also provides a free-of-charge, easily deployable Toolkit providing all the functions required to register your material in GLIS. Please contact the Secretariat of the International Treaty at [email protected] for further information.

How long could it take to get a DOI for a plant material?

Once access to GLIS is granted, registering a DOI boils down to populating a web form and pressing the “Submit” button. The assignment of the DOI is instantaneous and the newly assigned DOI can be immediately used in publications. For DOIs obtained through the XML protocol, once the successful response is obtained the DOI contained therein is ready to use. For batch registrations, the file that is returned by the Treaty Secretariat contains the DOIs that can be used immediately.

It seems the registration process depends on the collection size. How do you define the size?

The XML-based protocol is recommended for any collection, regardless of its size. However, the registration can be performed using any of the three options: manually through a web form, using batch files or through the XML-based protocol. An Integration Toolkit is also available for easy installation of the XML-based protocol. The choice of which option to choose rests on the user. We recommend the web form for small collections where manual registration can be performed by an individual in a matter of hours or days (200 accessions is a small collection in this sense). When the number of accessions reaches the thousand, registering manually one by one would be time consuming. In this case, the batch registration is more appropriate. For larger collections, the XML-based protocol is the preferred option, as it minimizes human intervention.

Will there be a link at FAO between the DOIs and the PIDs?

Users wishing to register DOIs through GLIS will need to acquire a PID from Easy-SMTA where they will maintain their account information. Easy-SMTA provides user management services to GLIS.

Is there any support during the registration process?

The Secretariat will provide support during development and testing of the implementation of the integration layer between your system and GLIS. To further facilitate adoption of the XML-based protocol, a free of charge Toolkit is offered that can be easily deployed and configured to provide not only the GLIS integration services but also the SMTA reporting workflow, if required.

At the national level there are many accessions holders, what institution will be eligible to assign DOIs or how to organise them?

Each holder should register DOIs independently. If central coordination is desired, then the coordinating institution may register DOIs on behalf of the individual holders. GLIS allows for proxy registration to support these cases.

Are DOIs associated with a germplasm sample or with their description?

A DOI in GLIS is associated with the germplasm sample within its context, i.e. the holding individual or institution, not with its description.

Can centres assign their own DOIs independently of the mechanism provided by GLIS?

Yes. However, centres should consider the consequences before deciding whether to assign DOIs on their own. First, to participate in GLIS and gain the associated benefits, the PGRFAs would still need to be registered in GLIS; GLIS will not assign a new DOI if the centre’s own DOI is provided. Second, assigning DOIs independently implies that the registrant complies with the obligations set forth by the DOI System, e.g. provide a landing page, and commit to maintaining that landing page permanently. Third, registering DOIs using a system other than GLIS requires mapping the PGRFA descriptors to the DOI metadata structure. Fourth, the International Treaty provides DOIs free of charge to material being registered in GLIS whereas registering DOIs using other services generally implies some cost.

Can DOIs refer to historical samples?

Yes, DOIs are normally assigned to existing material. If the material is subsequently lost or becomes unavailable for reproduction or transfer, the DOI will continue to exist because other DOIs may reference the material or it may be referred to in publications or datasets. A specific DOI descriptor was developed to indicate in the future that the sample does not exist anymore.

It is also possible to assign DOIs to material that is historical even at the moment of registration. This is recommended if information about the historical material is relevant to extant material. For example, suppose a genebank or collector gave copies of the same material to two different genebanks and then lost the original material. By assigning a DOI to the original material, both receiving genebanks could specify the same original DOI as the progenitor of their accessions, and thus clearly document the association between the two accessions.

Do DOIs cover genetic variability?

Yes, if the genetic composition of the material changes, the holder can request a new DOI. DOIs provide more flexibility as it takes into account basic methods of creation of the material, thus making them suitable for application in situations other than genebanks.

What happens if some information supplied when requesting the DOI is found to have errors or to be incomplete at a later stage?

It can be amended by the data curator as appropriate, in a way similar to existing identifiers, for example changes in taxonomy or of the name or code of the holding institution. This is because the DOI is associated to the physical material and not to the set of descriptors.

How do you prevent transcription errors in DOIs?

Each DOI incorporates a “checksum”. If you make a transcription error when entering a DOI, the DOI will be invalid. You can check on GLIS server whether the DOI is valid.

In addition, best practice is to avoid typing or writing DOIs manually as much as possible by reading and writing them electronically, for example by scanning bar-coded DOIs.

Of course this does not protect against all errors, so there is still a need to verify that the correct DOI is used for each PGRFA.

Is there any possibility to have DOI duplicates?

There is no way that two identical DOIs are ever created. DOIs are assigned by GLIS and guaranteed unique. When GLIS registers the DOI to DataCite, a further uniqueness check is performed, and again when the DOI is later propagated to the Global DOI System.

If we assign a DOI to a sample that later turns out to be an internal duplicate, can we just ignore the extra DOI?

Yes, you could just ignore the extra DOI. To help make sure it is not used, and to stop it being misused in aggregating statistics about genebanks, it would be desirable to mark it as an historical record.

Should a recipient document and use the provider’s DOI?

The Guidelines for the optimal use of DOIs for PGRFA provide guidance on the situations under which a recipient should use the provider’s DOI or obtain a new DOI.

Why do we allow recipients of material NOT to provide the provider’s DOI thus preventing accession tracking?

The condition set out in the International Treaty in its article 12.3(b) (“Access shall be accorded expeditiously, without the need to track individual accessions”) is interpreted to mean that linking a recipient’s DOI to the Provider’s DOI cannot be made mandatory. The Governing Body of the International Treaty may choose to reconsider this. Currently, as indicated in the Guidelines, we can only encourage all users to acquire new DOIs for the PGRFA they receive and properly relate such DOIs to provider’s DOIs. The benefits of maintaining the links should be sufficient to encourage most recipients to properly relate DOIs.

When should a DOI be initially assigned to an accession?

A DOI should be assigned to an accession as soon as the genebank manager wishes to make its existence publicly known. The Guidelines for the optimal use of Digital Object Identifiers as permanent unique identifiers for PGRFA available at http://www.fao.org/plant-treaty/areas-of-work/global-information-system/guidelines provide further information.

Can DOIs be assigned to pure lines for access by others?

Yes.

Most genebank accessions are genetically heterogeneous and change over time. What are the implications for the management of DOIs?

The genetic variability of accessions is a major factor in a genebank manager’s decisions in managing a genebank; measures to address it are documented in the FAO/Bioversity genebank management standards. A genebank manager will normally keep the accession ID unchanged, but will assign a new accession ID if a genetic change is observed that is unreasonably large given the breeding system of the material. In certain circumstances (for example for DNA sequencing and gene discovery) it is necessary to be more rigorous, for example purifying an accession to reduce its genetic variability, assigning a new accession ID to the purified sample, applying more rigorous checks on its genetic composition, or using more specific identifiers for components of an accession. The same principles apply to DOIs: a curator may assign a new DOI only when a significant genetic change is obvious, or may apply more stringent criteria requiring more frequent assignment of new DOIs, or may apply DOIs to components of an accession.

Can DOI be assigned to intermediate material in breeding programs?

Yes, DOIs can be assigned to intermediate material in breeding programs, but it is not mandatory and may often be not appropriate.

The “rule of thumb” is that DOIs are assigned to anything whose existence the holder wishes make publicly known; breeding material is no exception. Only a small fraction of breeding materials is shared outside the breeder’s organization while the vast majority is destroyed. Hence the recommendation is to assign DOIs only where the breeding material or associated information is shared outside the breeder’s organization. Details on the origin of the material with DOIs will be still available in the breeding management system and can be made available to the public by providing a suitable link associated to the DOI.

If an accession is sub-sampled, will a new DOI need to be assigned?

A new DOI does not need to be assigned, but can be if appropriate.

If the sub-sample is intended to be the same genetic entity as the parent, the same DOI may be used for the sub-sample. Alternatively, since DOIs can be assigned at any desired degree of precision and granularity that a registrant deems to be appropriate, a new DOI would be assigned if the genebank manager has reason to make publicly known the existence of the specific subsample as a distinct entity. It would be important to specify that subsample was taken from the accession, by providing the DOI of the accession as the progenitor of the subsample.

On the other hand, if the sub-sample is intended to be different – for example if it contains one particular component of a mixed accession – then the original DOI should not be used for the sub-sample: if a DOI is needed for it, a new DOI should be obtained. Again, it would be important to specify that subsample was taken from the accession, by providing the DOI of the accession as the progenitor of the subsample.

When does a DOI change?

A DOI does never change by definition.

Is there any guidance for genebank managers for the mapping of multi-crop passport data with core GLIS descriptors?

The Secretariat developed in 2017 a first use case for genebanks. A table mapping the core GLIS descriptors to the corresponding MCPD 2.1 descriptors is available as an Annex to the GLIS descriptors.

Why is the country of provenance not mandatory?

Country of provenance cannot be mandatory as it is often unknown for older materials, and the very concept of a single country of provenance is often not applicable for modern breeding materials and released varieties. Tracing the pedigrees of modern varieties back to varieties collected from farmers may reveal 20 or more countries in their ancestry; and the ongoing processes of hybridising, testing and selecting are typically undertaken in multiple countries. In these cases a “country of provenance” has no meaning.

If the need for DOIs is to identify each sample by its holder as well as by its genetic identity, how can cultivars which are grown by many farmers be treated?

Cultivars are treated in the same was as all other types of PGRFA. A farmer who maintains a cultivar could obtain a DOI for his/her version of the cultivar. A seed company that maintains a cultivar for commercial sale could obtain a DOI for the material it maintains. A national regulatory body responsible for testing and releasing new cultivars could obtain DOIs for the material it tests, maintains or releases.

How should we promote that recipients of materials from genebanks perpetuate and use the assigned DOIs?

You can promote the use of DOIs by informing recipients of the benefits of using DOIs, such as: using DOIs will give them easy access to all up-to-date online information on the material;  if they use DOIs in their publications and online datasets, they will automatically comply with their obligations under article 6.9 of the SMTA; inform them that they can use the provider’s DOI, but that it is recommended to obtain a new DOI for their copy of the accession and relate it to the provider’s DOI by specifying the provider’s DOI as the progenitor of their new DOI. Help them by listing the DOIs alongside the accession IDs, and by providing the DOIs electronically or in bar-coded format so that they do not have to type them manually.

Should we recommend DOIs as the principle means of recognition of materials in publications?

Yes, accurate, unique identification of PGRFA is increasingly being requested by publishers and DOIs address this. It is recommended that the DOI of the material is referenced in the publication’s metadata to allow advanced services offered by the DOI System. In the text, recommended usage could be like acronyms (at the first usage specify both the DOI and a more easily intelligible name, and thereafter use only the intelligible one) or like DOIs of publications (use only the intelligible IDs in the text, and provide a list of associated DOIs at the end).