TAIR presentations from the 2014 ICAR conference.

1. TAIR Workshop schedule
• 4:30 – 4:55 A New Funding Model for Academic Resources
(Eva Huala)
• 4:55 – 5:20 TAIR: A Sustainable Community Database for
International Arabidopsis Research (Donghui Li)
• 5:20 – 5:30 Questions

2. Rise of the Phoenix
a New Funding Model
for Academic Resources

3. 1. Importance of TAIR
1. Ways to fund curation
2. TAIR’s new funding model

4. 1. Importance of TAIR
1. Ways to fund curation
2. TAIR’s new funding model

5. Computable
Not
Computable
Data Knowledge
Lab notebook
Gene ontology annotation
(gene function)
Plant ontology annotation
(gene expression pattern)
Research article
Microarray dataset
RNA-seq reads
Metabolite levels in
seeds of a mutant
Gene function
inferred from mutant
phenotype
Free text mutant
phenotype
cDNA sequence
Research seminar

6. Computable
Not
Computable
Data Knowledge
Lab notebook
Gene ontology annotation
(gene function)
Plant ontology annotation
(gene expression pattern)
Research article
Microarray dataset
RNA-seq reads
Metabolite levels in
seeds of a mutant
Gene function
inferred from mutant
phenotype
Free text mutant
phenotype
cDNA sequence
Research seminar
TAIR’s area of emphasis

7. TAIR has 2 main roles
1. Collect, convert and integrate information 2. Search, display, and analyze information
TAIR DB
Research
Articles
TAIR Curator Article Author
TAIR DB
Unique to TAIR Shared with many other sites
Unique Not Unique

8. TAIR DB
Research
Articles
Gene function
Gene symbol
Allele name
Phenotype
GO annotation
PO annotation
Publications
Etc…
AIP
TAIR’s unique role relative to
other resources – gathering
information from literature:

9. New Gene Ontology annotations
made by a TAIR curator

10. New Gene Ontology annotations
contributed by an author

11. New Gene Symbol and Full Name

12. New Mutant Alleles

13. New Publications

14. 1. Importance of TAIR
1. Ways to fund curation
2. TAIR’s new funding model

15. Funding models for biological databases – pros and cons
Type of Support:
Pros and cons:
Direct federal
funding
Federal or
foundation
grants
User fees
(for profit)
User fees
(nonprofit)
Budget scales with
usage and need
No No Yes Yes
Directly responsive to
community needs
No No Yes Yes
Accessible to all Yes Yes No ???
Unlimited lifespan Yes No Yes Yes

16. Type of Support:
Pros and cons:
Direct federal
funding
Federal or
foundation
grants
User fees
(for profit)
User fees
(nonprofit)
Budget scales with
usage and need
No No Yes Yes
Directly responsive to
community needs
No No Yes Yes
Accessible to all Yes Yes No ???
Unlimited lifespan Yes No Yes Yes
Funding models for biological databases – pros and cons

17. http://www.phoenixbioinformatics.org/
New nonprofit Phoenix Bioinformatics
(founded by the TAIR team)

18. What does it mean to be a nonprofit?
• Motivated by mission, not profit
• Income must be used for nonprofit goals
• Governed by board of directors
“Develop an economically
and technologically
sustainable business model
and platform that provides
the resources to allow
scientific databases to
persist….”

19. What does it mean to be a nonprofit?
• Motivated by mission, not profit
• Income must be used for nonprofit goals
• Governed by board of directors
www.phoenixbioinformatics.org

20. Other
DBs
Other
tools
Shared tools and expertise:
• Fundraising
• Subscriptions
• Ad revenue
• Donations
• Technical help
Forecast: Stormy weather in Washington DC...
Many projects under one umbrella…

21. 1. Importance of TAIR
1. Ways to fund curation
2. TAIR’s new funding model

22. Options for user fees:
Type of User Fee Pros Cons
Open Access model
(charge submitters to
deposit data)
No one is shut out from data
access
Researchers have
Insufficient motivation to
pay for data submission.
No reward structure
analogous to promotion
based on articles listed in
CV.
Subscription model
(charge users to access
data)
People value access to TAIR
Many have said they would
be willing to pay for it to
sustain the database
Some people may lose
access
Data sharing – delay in
releasing data to other
sites
Can we make it fair?
Can we mitigate any drawbacks?

23. Institution-wide subscriptions:
• Cover all faculty, staff and students
• Allow access based on IP address of the institution
• Provide access to casual users (students looking up information, researchers
working on other organisms)
• Shift the cost from grants or personal funds to university library budgets
• Allow easy access to students and casual users of the database
Individual or lab subscriptions:
• Will require login with a username and password
• Will provide access method for researchers who can’t get an institutional
subscription
1. Provide several ways to subscribe
2. Make each option fair and affordable

24. $7500/year
$5000/year
$2500/year
$500/year
5000
10,000
15,000
20,000
25,000
30,000
35,000
40,000
45,000
Visits/yearbyInstitution
685 Academic institutions, sorted by usage
$7500 $5000 $2500 $500
Institutional subscription - 4 price tiers:

25. 2014 subscription prices:
Company subscriptions (based on size of company):
• Over $5B annual sales: $25,000/year
• Under $5B annual sales: $5,000/year
Institutional subscriptions (based on institution-wide usage):
• Tier 1 (over 5000 visits/year): $7500/year
• Tier 2 (2501-5000 visits/year):$5000/year
• Tier 3 (1001-2500 visits/year): $2500/year
• Tier 4 (less than 1000 visits/year): $500/year
Lab/individual subscriptions ($85/$95 per person, single seat)
Free subscriptions for students enrolled in a course using TAIR
Free subscriptions for countries with lowest GDP

26. Metered access – allows infrequent
users to access TAIR without paying
Free pages:
• Home
• Search pages
• ABRC stock and ordering
• News
Metered pages:
• Locus page
• Analysis tools
Pages requiring subscription:
• View job postings
• Data download
Limited number of
pages per month
What else can we do to ensure everyone has access?

27. Free pages
LoHome page
LoList of search results
LoSearch page

28. Free pages
LoStock ordering

29. Metered pages
LoLocus page LoBLAST
LoGBrowse

30. Subscription
required
LoFTP site
LoData download tool

31. Progress on subscriptions – excellent!
Large companies:
5 subscribed
1 declined
Academic institutions:
~ 110 academic institutions have subscribed, mainly via the library
All academic institutions in China via NSTL (National Science and
Technology Library)
Large consortium subscriptions being pursued for other countries

33. Next up: Donghui Li