Unique Identifiers in an Online Permit and Monitoring System to support the Nagoya Protocol

Country Code Identifiers

All countries possess a unique two letter country code defined in international standard ISO3166-1 alpha 2 (e.g. see this Wikipedia entry and the ISO browsing platform and select Country codes and search).

For example, the standard two letter country code for the Bahamas is BS, Kenya is KE, Uganda is UG and South Africa is ZA. If these country codes are combined with a date (YYYYMMDD) and a unique number (1234) a unique identifier will be generated. In this case we will simply use the year (YYYY) to generate the following identifiers.

• BS20151234
• KE20151234
• UG20151234
• ZA20151234

What is clear from this is that a single and distinctive unique identifier (country - year - number) has been created for each permit and corresponding MAT that is immediately distinguishable using the country code from similar numbers issued by other authorities. The combination of the country code, the date and a numeric identifier (country - YYYMMDD - number) is already used very successfully to keep track of approximately 90 million patent documents in countries around the world and is recommended. The example below is for a patent application from the United States that makes reference to collections from the Bahamas and can be viewed on the main worldwide patent database espacenet operated by the European Patent Office here.

In this example we can see that the unique document identifier US2001049387A1 consists of the following [US] – the country code – [2001] the year of application – [049387] – the unique numeric identifier, and [A1] known as the “kind code” for the type of document (in this case a patent application).

The strength of this system is that the components combine into a unique identifier that is:

1. distinctive, and;
2. easy to retrieve.

The relevance of this type of numbering system becomes apparent when we consider the section of this patent application that makes reference to biological collections in a country. In this case the example is from the Bahamas (See the first paragraph highlighted or read directly here).

In this case, the applicants make reference to a sponge specimen 23-XI-98-3-002 and a HBOI CatNo. 003:00973. Under the proposal advanced in this document the ABS domestic legislation, permit and associated MAT could require recipients of a permit to disclose the permit number (e.g. BS20151234) in the description section of any patent application arising from the research.².

Unique Identifiers and Registers

An important feature of this system as deployed within patent databases is that the unique identifier is used to store all documents that relate to a particular application over time. In this case the United States application was also filed in Europe at the European Patent Office and this document can be identified in the patent family of the US document. European Patent Application EP1259502A2 was filed prior to the introduction of the year into the identifier. However, for our purposes the document is important because in Europe it is possible to access all documents linked to that application, including formal communications between the patent office and applicants in the European Patent Register. The figure below displays the list of documents linked to this identifier and can be accessed here.

It is immediately clear that the use of this unique identifier system allows all documents related to that identifier to be linked together into an electronic register (file history) for each application. We propose a very similar system where a unique identifier is used to link all documents arising from a permit application both internally within the system and for samples, publications and patent applications arising from the research. Specifically, the use of the unique identifier in labels for samples and specimens would facilitate the monitoring of compliance by users.

This type of unique identifier is simple, easy to use and robust over time. For that reason it is recommended as the first component of a triple system.

DNA and Amino Acid Sequences

Additional options include a requirement to use the basic unique identifier (BS20151234) in the documentation entered into databases for DNA and amino acid sequence data or html embed codes (for web publications).

In the case of DNA data an example of the existing use of identifiers, and the ability to monitor DNA sequence and amino acid information is provided by the Barcode of Life Database (BOLD).

Information using species names or identifiers can be retrieved using the taxize package in R using RStudio which generates the following link for a search for a species name.

library(taxize) # load the taxize package
get_boldid(searchterm = "Prunus africana") # search for the dna barcode id for a species

## 
## Retrieving data for taxon 'Prunus africana'

## [1] "191949"
## attr(,"class")
## [1] "boldid"
## attr(,"match")
## [1] "found"
## attr(,"multiple_matches")
## [1] FALSE
## attr(,"pattern_match")
## [1] FALSE
## attr(,"uri")
## [1] "http://boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=191949"

More information from the URL can then be accessed in R as a data table or through the BOLD website. On the BOLD website this produces a list of sequence related records. The image below is viewable here.

Selecting Access Published & Released Data produces the following list of records.

The final record in this list includes a specimen image and the following information.

A significant amount of information is contained in this record, including the record number, sample ID, Museum ID, where the specimen is located along with where the material was collected, by whom, along with the sequence listing. A link is also provided to the Sequence ID and GenBank Accession number as seen below.

As this demonstrates, it is increasingly possible to rapidly access sequence and associated record information for a particular species or list of species. Given the presence of multiple ID fields it appears reasonable to assume that the simple permit identifier (e.g. BS21051234) in sequence records arising from research could be included in the conditions of the permit and associated MAT. This could readily lead to the creation of an archive of electronic records for biodiversity in a country that contain known sequence data. Uses of such sequences could then become amenable to monitoring using the relevant IDs or sequence searching for identical or similar sequences using BLAST (Basic Local Alignment Search Tool) and associated tools.