ad hoc open-ended working group on access and benefit sharing

Ad hoc Open-Ended Working Group on Access and Benefit SharingSeventh Meeting, Paris, 2-8 April 2009

Convention onBiological Diversity

Excerpts from: Studies on the Identification, Tracking and

Monitoring of Genetic ResourcesGeorge M. Garrity

Michigan State UniversityEast Lansing, MI USA

Lorraine Thompson, USADavid Ussery, Denmark

Norman Paskin, UKDwight Baker, USA

Philippe Desmethe, BelgiumDavid Schindel, USA

Perry Ong, Philippines



The study

Our charge To review of recent methods of identifying genetic resources directly base on DNA sequences

To identify methods of tracking and monitoring genetic resources through the use of persistent globally unique identifiers, including practicality, feasibility, costs, and benefits of different options.Our approach A design exercise to help develop baseline requirements for such a global tracking system to aid users and providers in complying with CBD ABS objectives.



Key questions and definitions

How are genetic resources defined?Are genetic resources different from biological

resources?

Is the concept universal?

What metadata are associated with genetic resources and how is that metadata defined and supplied?

What are the ramifications of new genomic methods on identifying genetic resources?

What are persistent identifiers?Which persistent identifiers are used widely?

How do persistent identifiers differ?

Have tracking systems for genetic resources been deployed elsewhere?

What existing knowledge and technologies can be “leveraged” in creating such a system?

Questions



Key events in parallel to the CBD timeline

1980 1985 2005200019951990 2010

AHWGBiodiversity

CBD entersinto force

UNECDRio de Janeiro

COP I

2 2

COP II

2

COP III

2

COP IV

2

COP V

2

COP VI

2

COP VII

2

COP VIII

2

COP IX

2

TCP/IP

Nameserver

DNS

Internet

WWW

UN goesonline

Netscape

VoIP

Google/Napster

Internetviruses & worms

blogsbegin

YouTube

PubMed

PubMedCentral

PMC OAIcompliant

PMCOAI

requirement

UKPMC

PCR

US Supreme

Court Decision

GenBank

GeneticFinger-printing

ABISequence

HumanGenomeInitiative

INSCDCreated

RDPCreated

HGPbegins

BLAST

NIHdata

directive

H. influenzagenome

M. jannaschiigenome

E. coligenome

C. elegansgenome

M. tuberculosisgenome

Drafthuman

genome

100,00016S rDNA

CBOLbegins

Human genomefinished

750,00016S rDNA

NGS

URNURN

PURLPURLARKARK

NNGS

LIMSLIMS

1000bacterialgenomes



An example of a tracking system



Cascading workflow

All genetic resource types

Processed to yield multiple derivative samplesMost yield small numbers of samples that are

discarded. Others can yield 100-1000s, some of which may be retained for decades.

Each sample follows a predictable path through the system.

Derivative samples may be stored and reprocessed in the future for a variety or purposes.

Each sample is associated with one or more unique identifiers.*

Each sample is associated with various types of metadataSample source, testing history, contractual rights

and obligations, etc.Entire sample history can be reconstructed “on-the-

fly” if identifiers are actionable



Examples of tracking identifiers

Centrally controlled numbering scheme, but semantically laden

General properties

Microorganisms

B325,797-001-001

Sequentialseries

leadnumber

batchnumber

samplenumber

Screening number

Culture collection number (internal/external)

0534-605F

year/week assay.series

XX-YYYYz

collection identifier sequential number



Lessons learned



Impact of genome sequencing



Service (2006, 311: 1544) in Science. Reproduced with permission.



The “surprises” keep coming...



Impact of 2nd and 3rd generation sequencing

Method Read length (bp)Cost/human

genomeRun time (h/GB) Ease of use

ABI Solid 35 60,000 42 difficult

Solexa 35 60,000 56 difficult

454-FLX 240-400 1,000,000 75 difficult

Helicos tSMS 30 70,000 ~12 easy

PacBio SMRT 100,000 Low <1 easy

Nanoporemethods

Potentially unlimited

Low >20 easy

ZS Genetics TMPotentially unlimited

Low ~14 easy

From: Gupta, PK, Trends in Biotechnology, (2008) 22: 602-611



Cumulative number of published genomes

Source - Liolios et al.



A job unfinished

Source - D. Ussery



A job undone is still worth something...

Source - P. Chain



“Although used every day, identifiers are a mystery to many people, including people responsible for building complex information systems.”

Report of the NISO Identifiers Roundtable, 2006



Essential elements inHuman - human communications

Human - machine communications

Machine - machine communications

Identifiers

Ideally… Exist as an unambiguous string

Context and application dependentActionable

Resolvable

Other points to considerSemantically opaque

Global or local

Unique or non-unique

Unanticipated uses



A name or an identifier for a resource that uniquely identifies that resource and will be forever associated with that resource. It will never be reassigned to any other resource and will not change regardless of where the resource is located or whatever protocol is used to access it.

Use of a well managed persistent identifier rather than a location will ensure that when a document is moved, or its ownership changes, the links to it will remain actionable.

Persistentidentifiers

From: Diana Dack, Persistence is a Virtue Information Online Conference, Sydney. January 2001



The concept of name resolution

PID URLPID1

PID2

PID3

URL1

URL2

URL3

Resource

Identifies LocatesName resolution



Name registration&

Name resolution

Name registration&

Name resolution

AuthorityAuthority

PID URLPID1

PID2

PID3

URL1

URL2

URL3

ResourceMetadata

PID URL

IdentifiesIdentifies LocatesLocates

UserUser

Key metadataKey metadata

Global registryGlobal registry



The identifier gradient

A single unambiguous string

A numbering scheme

A label that identifies an entityISBN 0-387-98771-1

ATCC 27126

A method of providing consistent syntax to denote class membership of an entity.

An arbitrary internal system

A formal standard or industry convention

Key point is establishing a 1:1 correspondence between labels and members

Enumeration

The numbers or labels are simply strings




A syntax by which an identifier can be expressed in a form suitable for use within a specific infrastructure.

Actionable identifiers

URI (URN and URL)

ISBN numbers as UPC/EAN identifiers

Does not mandate a method of creating labels

Does not create a managed environment

An infrastructure specification




Includes

Unique identifiers

A formalized infrastructureManagement policies for registration,

structured interoperable metadata, policy, and governance mechanisms.

Examples

UPC/EAN barcodes and RFID tagsDigital object identifiers (digital identifiers of

objects)

A fully implementedidentifier system



<Handle>::=<Handle Prefix> "/"<Handle Suffix>

http://hdl.handle.net/10.1099/ijs.0.64483-0

LSIDLSID Life ScienceIdentifiers

<purl>::=<protocol>/<resolver>/<name>http://purl.oclc.org/OCLC/OCLC/PURL/FAQ

urn:<LSID>:<AuthorityID>:<Namespace>:<Object>:<Rev>

http://lsid.biopathways.org/resolver/data/urn:LSID:ncbi.nlm.nih.gov:GenBank/accession:NT_001063:2

Syntax of some other PIDs in “common” use

PersistentURLs

http://hdl.handle.net/10.1099/ijs.0.64483-0



Two implementations using DOIsIndependent membership association,founded and

directed by STM publishers. Mission is to connect users to primary research literature through a DOI RA that performs reference cross-linking, subject to publisher-access controls.

The largest and most successful implementation of DOI services.

NamesforLife is an experimental semantic resolution service for dynamic terminologies. It provides a method for persistently linking the occurrence of a biological name or other technical term in third party content to managed information about its origins, formal definition, current usage, and related information.



On-the-fly look-up services using DOIs



A proposed tracking system



Our recommendations

• Promptly establish the minimum information required for compliance with the IR Stipulate which documents are mandatory and which are optional.

• Adopt a well-developed and widely used PID system that leverages an existing infrastructure and derives support from multiple sources.

• Consider current and future needs of genetic resource providers and users. Biological and functional diversity and both must be accommodated.

• Deploy light-weight applications that use browser technology for interactive use. Publish application program interfaces to support other web services. Develop strong policies governing access and use of the resource to avoid data abuse. Trust is a key element.

• Deploy prototype tracking systems to validate underlying concepts and refine critical elements that will be needed in a fully operational system.

ad hoc open-ended working group on access and benefit sharing

Documents

openended working group

benefit sharingseventh

genetic resources different

biological resources

methods of tracking

persistent identifiers

tracking systemad

global tracking system