Biotechnology - Genomic and Proteomics/Data, narratives and tools produced by the BGP field

Report April 2009

Answer the questions:

1. Define what kind of data, narratives and tools constitute the outputs of the field and its dynamics (e.g.: data in science may get better if open once it receives annotations and can be improved by other scientist).

Data

• Foundational Data
  • Big players:

• Observational Data
  • Big Players:

BGP Company Profiles - Data

Amgen

Genentech

Genzyme

Gilead Sciences

Biogen Idec

Cephalon

MedImmune

Celgene

Abraxis BioScience

ImClone Systems

For more information on these companies, see: BGP Table of Biggest For-Profit Companies

Narratives

BGP Company Profiles - Narratives

• JOURNALS
  • INCUMBENTS
    • Elsevier
    • Springer
    • Wiley Blackwell
    • Thomson Reuters Science
  • CHALLENGERS
    • PubMed
    • Nature
    • BioMedCentral
      • BioMed Central is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Science+Business Media, a leading global publisher in the STM sector.
    • Public Library of Science

• ONTOLOGIES
  • US National Center for Biomedical Ontology
  • Open Biomedical Ontologies
  • Gene Ontology

• ANNOTATIONS
  • Gene Ontology Annotation
  • Distributed Annotation System
  • Gene Wiki

Tools

Biological Materials

Steam cells

• Concept: Steam cells are cells with the ability to divide for indefinite periods in culture and to give rise to specialized and different cell types. In addition, in many tissues they serve as a sort of internal repair system, dividing essentially without limit to replenish other cells as long as the person or animal is still alive. Stem cells are distinguished from other cell types by two important characteristics. First, they are unspecialized cells capable of renewing themselves through cell division, sometimes after long periods of inactivity. Second, under certain physiologic or experimental conditions, they can be induced to become tissue- or organ-specific cells with special functions.

• From the NIH Stem Cell Basics Site:

1. What are stem cells, and why are they important?
2. What are the unique properties of all stem cells?
3. What are embryonic stem cells?
4. What are adult stem cells?
5. What are the similarities and differences between embryonic and adult stem cells?
6. What are induced pluripotent stem cells?
7. What are the potential uses of human stem cells and the obstacles that must be overcome before these potential uses will be realized?
8. Where can I get more information?

• Embryonic Steam Cells Bibliography under reading:
  • http://wistechnology.com/articles/3157/
  • http://blogs.nature.com/reports/theniche/2008/02/one_of_the_warf_patents_on_hum.html
  • http://www.genengnews.com/articles/chitem.aspx?aid=2180&chid=0
  • http://ezinearticles.com/?MIT-Technology-Review-Concern-Over-WARF-Patent-Royalty-Demand-To-CIRM-Over-Stem-Cells-Is-Misguided&id=184620
  • http://www.signonsandiego.com/uniontrib/20060730/news_1n30stems.html

Mice

• SPONTANEOUS MOUSE
  • Research:
  • Funds:
  • Patent: not subject to patents
  • Patent Owner: N/A
  • Use: general research tool
  • Historic of patent license strategy: N/A
  • Biobank:
  • Results on Innovation:
• KNOCK-OUT MOUSE
  • Research: University of Utah
  • Funds:
  • Patent:
  • Patent Owner: University of Utah
  • Use: general purpose research tool
  • Historic of patent license strategy: "the University of Utah received a patent in 1987 but never sought to enforce the patent against follow-on researchers using the knock-out methodology. Instead, Knock-out mice were made available at (essentially) marginal cost through the Jackson Laboratory (i.e., these mice were distributed as JAX mice)." (pg 12) (Murray at all 2009)
  • Biobank: Jax Labs
  • Results on Innovation:
    • Knockout Mouse Project: KOMP Data Coordination Center and KOMP Repository
• ONCO-MOUSE
  • Research: Harvard
  • Funds: partially financed by DuPont and public fund of ???
  • Development: Internally by DuPont
  • Patent:
  • Patent Owner: DuPont
  • Use:general purpose research tool
  • Historic of patent license strategy: "As a result of their partial funding of Harvard's Oncomouse discoveries and their internal development of Cre-Lox technology, DuPont gained exclusive control over patents for these two technologies. In contrast to the University of Utah, DuPont exercised strict control over the distribution and use of mice that exploited the techniques covered by their patent portfolio. During the early 1990s, researchers (and their institutions) who wanted "freedom to operate" were obliged to obtain a license from DuPont when they sought to receive and use an Onco or Cre-Lox mouse.The detailed licensing agreement required annual disclosure to DuPont regarding experimental progress, limits on informal mouse exchange among academic researchers, and "reach through" rights allowing DuPont to automatically receive licensing revenue from any commercial applications developed using either Cre-Lox or Onco technology." (pg 12) (Murray at all 2009)
  • Community reaction to patent license strategy and high transaction costs of legal access and lack of "freedom to operate" exception:
    • protest: patent invalidation proceedings (which did not work)
    • informality: formation of VIP sharing networks in the shadow of most University's official policy rules and under the constant possibility of law suits
    • institutional reaction toward openness: Jax Laboratory made mice available without the necessity of a license
    • institutional reaction toward closedness (fear): restrictions from Universities on researches advising the non-use of the mice - University's official policy rules
    • redundant development: development of mice during the research process, bringing high costs (time - delays of 18 months were reported by Murray 2009 and money)
    • new research lines: researches that saw barriers to access the mice took new directions (Murray 2009)
  • Biobank: Jax Labs
  • Results on Innovation before NIH MoU: Delay on research for almost 2 years were faced here. Plus, since these are general purpose technologies, high potential to impact vertical and horizontal academic research.
  • Results on Policy: NIH MoU and others see: NIH EFFORTS
  • Results on Innovation after NIH MoU: Vertically, an average increase of citations of 21% (pg 23). Horizontally, average increase of 25% of new last-authors citations, average of 20% citations from new institutions and 20% increase on diversity of key words (pg 23-26) (Murray at all 2009)
• CRE-LOX MOUSE
  • Research: Harvard, partially financed by DuPont
  • Funds: partially financed by DuPont and public fund of ???
  • Development: Internally by DuPOnt
  • Patent:
  • Patent Owner: DuPont
  • Use: general purpose research tool
  • Historic of patent license strategy: same as "Onco-Mouse"
  • Community reaction to patent license strategy and high transaction costs of legal access and lack of "freedom to operate" exception: same as Onco-Mouse, with exception for the access through Jax Labs (see Murray at all, pg 27 for more detailed analysis). So, higher dependence in VIPs and resulting higher transaction costs (eg: requisites of co-authorship).
  • Biobank: Jax Labs
  • Results on Innovation: similar to Onco-mouse
  • Results on Policy: NIH MoU and others see: NIH EFFORTS
  • Results on Innovation after NIH MoU: Vertically, an average increase of citations of 18% (pg 23) Horizontally, average increase of 22% of new last-authors citations, average of 20% citations from new institutions and 30% increase on diversity of key words (pg 23-26) (Murray at all 2009)

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Bibliography for Item 3 in BGP
Biotechnology_-_Genomic_and_Proteomics