marine genetic resources in patent data

Marine Genetic Resources in Patent Data

Paul Oldham, Stephen Hall & Colin Barnes

United Nations University & One World Analytics

Image: Available GBIF coordinates for 3,432 marine species appearing in patent data

The Problem of Scale• Patents provide a window into human innovations

involving biodiversity but present challenges of scale;

• An estimated +1.2 million accepted species and 8.7 million predicted species (+/-1.3 million) (Mora 2011). 219,714 marine accepted species in WoRMS;

• Over 60 million patent documents in multiple languages;

• Digital data in the form of taxonomic databases (GBIF) and electronic patent data provide a means to map and monitor activity involving marine biodiversity;

Mora et al (2011) How Many Species are There on the Earth and in The Ocean? PLoS Biology.

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001127

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001127

GBIF is the key international data

depository for taxonomic data and

linked to the CoL and EOL

Marine data from OBIS. Provides

access to geographicaloccurrences

ABSPAT INDEX

Patent data can be mined using parallel computing to identify

6 million species names from the

Global Name Index

ABSPAT = Access and Benefit Sharing Patent Index. An offline index of species in patent documents.

Publication Year19

7619

7719

7819

7919

8019

8119

8219

8319

8419

8519

8619

8719

8819

8919

9019

9119

9219

9319

9419

9519

9619

9719

9819

9920

0020

0120

0220

0320

0420

0520

0620

0720

0820

0920

10

0K

2K

4K

6K

8K

10K

Num

ber of Pub

lications

Trends

Application Grant 0K 2K 4KNumber of Publications

0 200 400 600Occurrences in Claims

kluyveromyces drosophilarumaequorea victoria

beneckea parahaemolyticarenilla reniformis

chaetomium globosumsulfolobus solfataricus

thermoplasma acidophilumportulaca oleraceamodulus moduluseuglena gracilis

chondrus crispusbeneckea alginolytica

salmo salaroncorhynchus mykisslimulus polyphemus

debaryomyces hanseniiserenoa repens

668

688

702

723

741

852

930

1,195

1,638

1,806

2,097

2,293

3,825

4,157

262

140

88

103

170

73

2

185

368

82

571

595

281

30

Marine Species (Ranked on Patent Publications)

0K 2K 4KPublications

0 500 1000Claims

GENENTECH (﴾ROCHE)﴿

UNIVERSITY OF CALIFORNIA REGENTS

BASF AKTIENGESELLSCHAFT

E. I. DU PONT DE NEMOURS AND COMPANY

BAYER CROPSCIENCE AG

BAYER AKTIENGESELLSCHAFT

BASF PLANT SCIENCE GMBH

MARTEK BIOSCIENCES CORPORATION

BASF SE

NOVOZYMES A/S

MONDOBIOTECH LABORATORIES AG

STAUFFER CHEMICAL COMPANY

THE SCRIPPS RESEARCH INSTITUTE

SUMITOMO CHEMICAL COMPANY, LIMITED

L'OREAL

CROPDESIGN N.V.

INVITROGEN CORPORATION 146

157

163

165

173

178

197

206

241

259

283

285

296

501

538

601

3,456

7

1

28

10

69

9

9

10

1

84

8

6

2

14

8

152

6

Applicants

IPC Sub Class

20K 40KPublications

0K 20K 40KClaims

Genetic EngineeringPharmaceuticals/Medicinal Preparations

PeptidesFermentation/Enzyme Using Chemical Synthesis

Testing Enzymes/Microorganisms - DNA SequencingAnalysing Chemical/Physical Properties

Nucleic AcidsBiocides

New PlantsHeterocyclic Compounds

Animals (new varieties)Foodstuf fs & Non Alcoholic Beverages

CosmeticsCarbocyclic Compounds

Animal Feedstuf fsApparatus for Microbiology

Combinatorial Libraries

Technology Areas

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

��

�

��

��

��

��

��

��

��

��

��

��

��

��

��

�

��

��

��

�

�

��

��

��

��

�

�

�

�

�

�

�

��

Patent family data allows patents

linked to MGRs to be identified

worldwide over time

First Draft of Global

Occurrences of Marine Species in

Patent Data

Species Name:Aequorea victoria

Kingdom:AnimaliaKingdom:Animalia

Brief Description of the species:A bioluminescent jellyfish Brief Description of the species:A bioluminescent jellyfish Brief Description of the species:A bioluminescent jellyfish

Occurrences in Claims: 281Occurrences in Claims: 281 Number of Publications: 3825Number of Publications: 3825

A bioluminescent jellyfish found along the western coast of north America including Vancouver Island. A species most noted for the production of Green Fluorescent Protein.The primary source of GFP which is used as a reporter of gene expression.




Species Name:trichodesmium erythraeum

Kingdom:BacteriaKingdom:Bacteria

Brief Description of the species:‘Sea Sawdust’, a marine filamentous cyanobacteria that is nitrogen fixing.




They are among the most important of the marine varieties of nitrogen fixing bacteria, and are being extensively studied for their role in nutrient cycling in the ocean. Trichodesmium is thought to fix nitrogen on such a scale that it accounts for almost half of the nitrogen-fixation within marine systems on a global scale. Occurs between China, Japan, South Korea and tip of western Australia.




Species Name:Riftia pachyptila

Kingdom:AnimalKingdom:Animal

Brief Description of the species:Giant Tube WormBrief Description of the species:Giant Tube WormBrief Description of the species:Giant Tube Worm


Large tubeworms which live around hydrothermal vents. With sunlight not available directly as a form of energy, the tubeworms rely on bacteria in their habitat to oxidize hydrogen sulphide using dissolved oxygen in the water for respiration. Occurs off coast of Ecuador & Galapagos, Pacific Coast of Mexico




Species Name:Euphausia superba.

Kingdom:AnimalKingdom:Animal

Brief Description of the species:Antarctic Krill. Brief Description of the species:Antarctic Krill. Brief Description of the species:Antarctic Krill.

Occurrences in Claims: 33 (Krill = 337)Occurrences in Claims: 33 (Krill = 337) Number of Publications: 109 (Krill = 2234)Number of Publications: 109 (Krill = 2234)

The keystone species for Antarctic ecosystems. The waters around the Antarctic continent harbour possibly the largest plankton assemblage in the world upon which the krill feed. The biomass of Antarctic krill is estimated to be 125 to 725 million tonnes.




MGR occurrence records outside

the EEZ and Hydrothermal

VentsSource: Hydrothermal Vents, InterRidge Vents Database. www.interridge.org

http://www.interridge.org/irvents/

http://www.interridge.org/irvents/

Identifying Origins• Disclosure of origin debates involve two issues:

• a) Technical disclosure of the origin or source of genetic resources in a patent application;

• b) The consequences of disclosure or a failure to disclose;

• In practice samples may be obtained from sources such as: commercial suppliers, public collections, genomics databases (in silico), universities, or through in situ collection.

Oldham & Burton (2010) Defusing Disclosure in Patent Applications. UNU study. UNEP/CBD/COP/10/INF/44

M. jannaschii genome. Univ

Illinos, TIGR, Univ John Hopkins 2003.

Granted only for gene fragments

The 1980 Bayh-Dole Act Disclosure Statement for

Federal Funding Facilitates Monitoring

Non-Monetary Benefit-Sharing

• Patents provide a good proxy indicator for intended commercial research and development;

• In debates on access and benefit-sharing considerable emphasis is also placed on non-monetary benefit sharing. However, this is difficult to quantify and to ‘see’;

• A way forward is provided by examining the data that accompanies scientific literature to reveal networks of collaboration, knowledge transfer and funding in scientific research on marine genetic resources.

Country Collaboration Network for

publications on Marine Genetic

Resources 2011-2013.

Organization Network for

Marine Genetic Resources

2011-2013. Sample Data

1DWLRQDO�6FLHQFH�)RXQGDWLRQ

'DYLG�DQG�/XFLOH�3DFNDUG�)RXQGDWLRQ

&HQVXV�RI�0DULQH�/LIH

1DWXUDO�(QYLURQPHQW�5HVHDUFK�&RXQFLO��8.�

1HZ�=HDODQG�)RXQGDWLRQ�IRU�5HVHDUFK�6FLHQFH�DQG�7HFKQRORJ\

6FULSSV�,QVWLWXWLRQ�RI�2FHDQRJUDSK\

:RRGV�+ROH�2FHDQRJUDSKLF�,QVWLWXWLRQ

&156

*HUPDQ�5HVHDUFK�)RXQGDWLRQ��')*

,)5(0(5

-DSDQ�6RFLHW\�IRU�WKH�3URPRWLRQ�RI�6FLHQFH

1DWLRQDO�+LJK�7HFKQRORJ\�5�'�3URJUDP�RI�&KLQD��$$��

1HZ�=HDODQG�0LQLVWU\�RI�)LVKHULHV

12$$

$OIUHG�:HJHQHU�,QVWLWXWH��$:,

$15��O�$JHQFH�1DWLRQDOH�GH�OD�5HFKHUFKH��)UDQFH

$15�'HHS2DVHV

$XVWUDOLDQ�5HVHDUFK�&RXQFLO

&H'$0DU��&HQVXV�RI�WKH�'LYHUVLW\�RI�$E\VVDO�0DULQH�OLIH�

&+(0(&2��(6)�(852'((3

&KLQD�2FHDQ�0LQHUDO�5HVRXUFHV�5HVHDUFK�DQG�'HYHORSPHQW�$VVRFLDWLRQ��'<;0��

&RQVRUWLXP�1DWLRQDO�GH�5HFKHUFKH�HQ�*HQRPLTXH

')*

(XURSHDQ�&RPPLVVLRQ

)UHQFK�$15

-DSDQHVH�0LQLVWU\�RI�(GXFDWLRQ��&XOWXUH��6SRUWV��6FLHQFH�DQG�7HFKQRORJ\

-RLQW�2FHDQRJUDSKLF�,QVWLWXWLRQV��-2,��,QF

/DQG�,QIRUPDWLRQ�1HZ�=HDODQG

0D[�3ODQFN�6RFLHW\

1DWLRQDO�2FHDQLF�DQG�$WPRVSKHULF�$GPLQLVWUDWLRQ��12$$��2IILFH�RI�2FHDQ�([SORUDWLRQ�*UDQW��1$��2$5��1$�2$5��1$��2$5��

1(5&��1(�&��

1HZ�=HDODQG�0LQLVWU\�RI�6FLHQFH�DQG�,QQRYDWLRQ

1,:$

12$$�2FHDQ�([SORUDWLRQ�2IILFH��1$��2$5��

2DN�)RXQGDWLRQ

5R\DO�6RFLHW\�RI�1HZ�=HDODQG

6ORDQ�)RXQGDWLRQ

8�6��1DWLRQDO�6FLHQFH�)RXQGDWLRQ��16)

8QLYHUVLW\�RI�7URPVR

86�'HSDUWPHQW�RI�(QHUJ\�2IILFH�RI�6FLHQFH��%LRORJLFDO�DQG�(QYLURQPHQWDO�5HVHDUFK�3URJUDP

1HWKHUODQGV�2UJDQLVDWLRQ�IRU�6FLHQWLILF�5HVHDUFK��1:2��

8.�1DWXUDO�(QYLURQPHQW�5HVHDUFK�&RXQFLO

(XURSHDQ�6RFLDO�)XQG

$15�'HHS�2DVHV

(XURSHDQ�8QLRQ

5XVVLDQ�)RXQGDWLRQ�IRU�%DVLF�5HVHDUFK��D

$]RUHDQ�5HJLRQDO�*RYHUQPHQW

)&7��)RXQGDWLRQ�IRU�6FLHQFH�DQG�7HFKQRORJ\��3RUWXJDO

1DWXUDO�6FLHQFHV�DQG�(QJLQHHULQJ�5HVHDUFK�&RXQFLO�RI�&DQDGD

7RWDO�)RXQGDWLRQ��$E\VV��

&6,52�0DULQH�5HVHDUFK

$OH[DQGHU�YRQ�+XPEROGW�)RXQGDWLRQ

$15�'((3�2$6(6��$15��%'9��

*'5�(&&+,6

&13T��&RQVHOKR�1DFLRQDO�GH�'HVHQYROYLPHQWR�&LHQWLILFR�H�7HFQRORJLFR

0LQLVWU\�RI�(GXFDWLRQ�DQG�6FLHQFH�RI�5XVVLDQ�)HGHUDWLRQ��*��

7RWDO�)RXQGDWLRQ

$OIUHG�3��6ORDQ�)RXQGDWLRQ

$XVWUDOLDQ�*RYHUQPHQW�LQLWLDWLYH

&RPPRQZHDOWK�(QYLURQPHQW�)DFLOLWLHV��&(5)��SURJUDPPH

'HSDUWPHQW�RI�&RQVHUYDWLRQ

)567��822;��

0LQLVWU\�RI�)LVKHULHV

SURJUDP��&RDVWV�2FHDQV�2%,��&��;��

&HQWUH�1DWLRQDO�GH�OD�5HFKHUFKH�6FLHQWLILTXH��&156

$17520$5(��&70��&��0$5

%,20$5(��&70��&��0$5

1DWLRQDO�,QIUDVWUXFWXUH�RI�1DWXUDO�5HVRXUFHV�IRU�6FLHQFH�DQG�7HFKQRORJ\�3URJUDP�RI�&KLQD��'.$��

1DWLRQDO�1DWXUDO�6FLHQFH�)RXQGDWLRQ�RI�&KLQD��

6FLHQWLILF�5HVHDUFK�)RXQGDWLRQ�RI�7KLUG�,QVWLWXWH�RI�2FHDQRJUDSK\��62$��

1DWLRQDO�6FLHQFH�&RXQFLO��7DLZDQ��5�2�&

&205$��'<;0��

1(5&

*HUPDQ�5HVHDUFK�)RXQGDWLRQ��')*��,167��/DZUHQFH�/LYHUPRUH�1DWLRQDO�/DERUDWRU\��'(�$&��1$��

/RV�$ODPRV�1DWLRQDO�/DERUDWRU\��'(�$&��1$��2DN�5LGJH�1DWLRQDO�/DERUDWRU\��'(�$&��25��

8QLYHUVLW\�RI�&DOLIRUQLD��/DZUHQFH�%HUNHOH\�1DWLRQDO�/DERUDWRU\��'(�$&��&+��

&RXQFLO�RI�6FLHQWLILF�DQG�,QGXVWULDO�5HVHDUFK��&6,5

)RQGV�1DWLRQDO�GH�OD�5HFKHUFKH��)15��/X[HPERXUJ��$)5��

6SDQLVK�6FLHQFH�DQG�7HFKQRORJ\�0LQLVWU\��&70��&��0$5��&70��(�0$5

Draft Funding Network Marine Research Sample Web of Science.

Size = Publication Counts

Best Practices for Monitoring• Improving coverage of marine species in analysing patent

data (i.e. using WoRMS);

• Evidence based analysis of origins/sources in patents;

• Improving coverage & validating geocoding in GBIF data to remove noise;

• Using existing geocoded resources for deep sea locations;

• Using existing best practice and technical advice in patent analysis from the WIPO Patent Landscaping Group;

• Making indexed data available in an accessible and useful format;

Thank-you The research in this presentation was made possible

with support from:

The UK Intellectual Property Office

Department for Environment, Food and Rural Affairs (DEFRA), UK

Institute of Advanced Studies, United Nations University

Contact: [email protected]

Background Image: Copyright Kate Whitley/Wellcome Trust, London

One World Analytics is a trading name of POMC Consulting Ltd., UK.

mailto:[email protected]

mailto:[email protected]

marine genetic resources in patent data

Documents