Board on Research Data and Information, National Research Council“Changing Roles of Libraries in Support of Scientific Data Activities”

June 3, 2010

More Data, More Use, Less Lead Time:Scientific Data Activities at the

National Library of Medicine

Betsy L. HumphreysDeputy Director

National Library of Medicinewww.nlm.nih.gov

NLM & Scientific Data

• Data categories– Substances– Sequences– Clinical Research– Taxonomies/Nomenclatures/Ontologies

NLM & Scientific Data

• Challenges (aka Problems)– Much more data

• Greater NIH/other investment in generating data• High throughput methods• New, unfunded mandate(s)

– Much less lead time• Need to achieve standardization more rapidly

Growth In PubChem Tested Substances

start to

12

/31

/20

05

1/3

0/2

00

53

/6/2

00

54

/10

/20

05

5/1

5/2

00

56

/19

/20

05

7/2

4/2

00

58

/28

/20

05

10

/2/2

00

51

1/6

/20

05

12

/11

/20

05

1/1

5/2

00

62

/19

/20

06

3/2

6/2

00

64

/30

/20

06

6/4

/20

06

7/9

/20

06

8/1

3/2

00

69

/17

/20

06

10

/22

/20

06

11

/26

/20

06

12

/31

/20

06

2/4

/20

07

3/1

1/2

00

74

/15

/20

07

5/2

0/2

00

76

/24

/20

07

7/2

9/2

00

79

/2/2

00

71

0/7

/20

07

11

/11

/20

07

12

/16

/20

07

1/2

0/2

00

82

/24

/20

08

3/3

0/2

00

85

/4/2

00

86

/8/2

00

87

/13

/20

08

8/1

7/2

00

89

/21

/20

08

10

/26

/20

08

11

/30

/20

08

1/4

/20

09

2/8

/20

09

3/1

5/2

00

94

/19

/20

09

5/2

4/2

00

96

/28

/20

09

8/2

/20

09

9/6

/20

09

10

/11

/20

09

11

/15

/20

09

12

/20

/20

09

1/2

4/2

01

0

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

80,000

90,000

100,000

Week of

R

ec

ord

s

7

ICMJE

FDAAA 801

~25-30 / wk

~250 / wk

~320 / wk

Number of Studies Registered at ClinicalTrials.gov since May 1, 2005

2,317 Results Records submitted (Sept 2008 – March 2010)– About 30 new results records per week; 80 re-submissions per week

– Anticipate increase in rate as rules become clear and outreach continues

UMLS Metathesaurus – May 2010 version

NLM & Scientific Data• Strengths

– Mission & Track Record• Curation, Storage, Permanent Access, Standards, R & D

– Robust Infrastructure• Staff Expertise, Advisory Structure, Computing, Communications

– Connections between different kinds of data, information– Strong US partnerships and international collaborations– Heavy use

• Weaknesses– The “defects of our qualities”– Limited resources– Less user outreach/training than desirable

Hazardous Substances Data, 1978-

Toxic Release Inventory Data, 1987-

National Center for Biotechnology Information, 1988-

– Design, develop, implement, and manage automated systems for collection, storage, retrieval, analysis, & dissemination of knowledge concerning molecular biology, biochemistry, & genetics

– Perform research into advanced methods of computer-based information processing capable of representing and analyzing the vast number of biologically important molecules and compounds

– Enable persons engaged in biotechnology research and medical care to use these systems & methods

– Coordinate, as much as is practicable, efforts to gather biotechnology information on an international basis

Benzene – PubChem Bioassay Results

300,000

200,000

100,000

Entrez Web Traffic (Unique IP Addresses): 1999 - 2009

400,000

19

98

500,000

600,000

700,000

19

99

20

00

20

01

20

02

20

03

20

04

20

05

20

06

800,000

20

07

900,0002

00

8

20

09

1,000,000

- ~2 million users a day - 100 million hits a day - 5 terabytes of data a day - 3,500 web hits a second (peak)

17

PubChem Users per Day

Current Activities/Future Plans

• Continued emphasis on:– Improving the input

• Tagging, standardization, explicit links (e.g., GenBank #s, NCT #s)

– Increasing data curation efficiency– Use of “influentials” to promote standards, best

practices– US Partnerships & International collaborations – Computer center efficiency, security– Better discovery, retrieval, display methods

21

0 times2%

1 time8%

2 times4%

3-5 times8%

6-10 times8%

11-100 times41%

100+ times28%

PubMed Central Article Request Frequency - cal-endar 2009

Available: 1.9 Million Articles Used: 98%, Used > 10 times: 69%