NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!

1. NCBI Tools for
Information and
Scientific Discovery
July 25, 2012 RML Rendezvous
webcast
Jackie Wirz, PhD

2. Welcome to RML Rendezvous
• *6 to mute your phone, especially for
noisy backgrounds, *6 also unmutes
• Please don’t place your phone on hold
• Feel free to ask public questions via
phone or ‘Everyone’ in chat box
• For private questions, select
‘Presenters’ from the chat box
•Additional questions?

3. Where are you from?
https://www.surveymonkey.com/s/PNRinfo
•USA - ZIP code, international – country name
•Click as many job categories as apply
•Used for demographics reporting only
Thank you!

4. 1. databases
2. discovery!
3. real example
4. poll/Q&A

5. asdf
science
can be
complex

6. science
can be
amazing

7. science
is about
discovery

8. NCBI
is about
discovery

9. NCBI

10. NCBI
“ ...advances science and
health by providing ”
access to biomedical and
genomic information

11. NCBI Sequences
Expression
Genome maps
Structures
Protein Domains
Homology (gene, protein, structure)
Pathways
Genetic Variation

12. NCBI
http://www.ncbi.nlm.nih.gov/

13. NCBI
http://www.ncbi.nlm.nih.gov/gquery/

14. NCBI

15. NCBI

16. NCBI?

17. NCBI
tools
databases

18. NCBI
tools
databases

19. NCBI
tools
( nex
t ti me
databases

20. databases

21. databases

22. databases*
*a brief survey of selected dbs

23. 1
literature

24. PubMed
Bookshelf
OMIM

25. PubMed
http://www.ncbi.nlm.nih.gov/pubmed
21,953,042
2,491,646
5,632

26. PubMed
21,953,042
2,491,646
5,632
http://blogs.discovermagazine.com/discoblog/category/ncbi-rofl/ 1

27. Bookshelf
http://www.ncbi.nlm.nih.gov/books
1027

28. Bookshelf

29. OMIM
http://www.ncbi.nlm.nih.gov/omim

30. OMIM

31. Lesch-Nyhan
OMIM

32. Lesch-Nyhan
OMIM

33. PubMed
Bookshelf
OMIM

34. 2 sequences

35. Nucleotide
GenBank
RefSeq

36. DNA RNA Protein

39. NCBI

40. NCBI

41. NCBI
SNP
Databases
Primary
GEO
GenBank
Protein

42. http://www.ncbi.nlm.nih.gov/nuccore

43. attggctgccgcgcggggcggggagcggggtcggctcagtggccctgagaccctagctctgctctcggtccgct
cgctgtccgctagcccgctgcgatgttgcgcgctgccgcccgcttcgggccccgcctgggccgccgcctcttgt
cagccgccgccacccaggccgtgcctgcccccaaccagcagcccgaggtcttctgcaaccagattttcataaac
aatgaatggcacgatgccgtcagcaggaaaacattccccaccgtcaatccgtccactggagaggtcatctgtca
ggtagctgaaggggacaaggaagatgtggacaaggcagtgaaggccgcccgggccgccttccagctgggctcac
cttggcgccgcatggacgcatcacacaggggccggctgctgaaccgcctggccgatctgatcgagcgggaccgg
acctacctggcggccttggagaccctggacaatggcaagccctatgtcatctcctacctggtggatttggacat
ggtcctcaaatgtctccggtattatgccggctgggctgataagtaccacgggaaaaccatccccattgacggag
acttcttcagctacacacgccatgaacctgtgggggtgtgcgggcagatcattccgtggaatttcccgctcctg
atgcaagcatggaagctgggcccagccttggcaactggaaacgtggttgtgatgaaggtagctgagcagacacc
cctcaccgccctctatgtggccaacctgatcaaggaggctggctttccccctggtgtggtcaacattgtgcctg
gatttggccccacggctggggccgccattgcctcccatgaggatgtggacaaagtggcattcacaggctccact
gagattggccgcgtaatccaggttgctgctgggagcagcaacctcaagagagtgaccttggagctgggggggaa
gagccccaacatcatcatgtcagatgccgatatggattgggccgtggaacaggcccacttcgccctgttcttca
accagggccagtgctgctgtgccggctcccggaccttcgtgcaggaggacatctatgatgagtttgtggagcgg
agcgttgcccgggccaagtctcgggtggtcgggaacccctttgatagcaagaccgagcaggggccgcaggtgga
tgaaactcagtttaagaagatcctcggctacatcaacacggggaagcaagagggggcgaagctgctgtgtggtg
ggggcattgctgctgaccgtggttacttcatccagcccactgtgtttggagatgtgcaggatggcatgaccatc
gccaaggaggagatcttcgggccagtgatgcagatcctgaagttcaagaccatagaggaggttgttgggagagc
caacaattccacgtacgggctggccgcagctgtcttcacaaaggatttggacaaggccaattacctgtcccagg
ccctccaggcgggcactgtgtgggtcaactgctatgatgtgtttggagcccagtcaccctttggtggctacaag
atgtcggggagtggccgggagttgggcgagtacgggctgcaggcatacactgaagtgaaaactgtcacagtcaa
GenBank
agtgcctcagaagaactcataagaatcatgcaagcttcctccctcagccattgatggaaagttcagcaagatca
gcaacaaaaccaagaaaaatgatccttgcgtgctgaatatctgaaaagagaaatttttcctacaaaatctcttg
ggtcaagaaagttctagaatttgaattgataaacatggtgggttggctgagggtaagagtatatgaggaacctt
ttaaacgacaacaatactgctagctttcaggatgatttttaaaaaatagattcaaatgtgttatcctctctctg
aaacgcttcctataactcgagtttataggggaagaaaaagctattgtttacaattatatcaccattaaggcaac
tgctacaccctgctttgtattctgggctaagattcattaaaaactagctgctcttaacttacaaaaaaaaaaaa

44. GenBank Format
GenBank

45. LOCUS
Locus name, size, type, division,
modification date
Search tips:
Locus names can change!
Division names are historical,
not taxonomical!

46. DEFINITION
As the author sees fit…
Search tip: No Controlled Vocabulary in
Definitions!

47. CESSION/Version
Accession numbers do not
change, even if information in
the record is changed at the
author's request.
Version and GI numbers
change

48. s, Source, Organism
Organism: Tied into Taxonomy Browser
Search tip: Keywords are often blank
When performing a “keyword” style search,
use [all] , [word] or [title]

49. cted References
Newest First
Last reference covers submission information

50. eatures I
Source, gene,
misc features

51. eatures II
CDS: links, translation

52. equence

53. GenBank Format
GenBank
(also for protein)

54. 132,015,054

55. 132,015,054
+ HARD WORK
- redundancy

56. 132,015,054
+ HARD WORK
- redundancy
RefSeq

57. RefSeq

58. RefSeqs
provides a single record for each
natural biological molecule for
major organisms ranging from
viruses to bacteria to eukaryotes

59. RefSeqs
bio mol
provides a single record for each
DNA molecule for
natural biological
RNA
major organisms ranging from
viruses to bacteria to eukaryotes
Protein

60. RefSeqs
bio mol
provides a single record for each
HELLO
DNA molecule for
my name is
natural biological
RNA
major organisms ranging from
XX_123456
viruses to bacteria to eukaryotes
Protein

61. bio molecules
Incomplete Genomic DNA
(NC)
(NG)
mRNA
Model mRNA (NM)
(XM)
Model protein Curated Protein
(XP) (NP)

62. NG_012250.1
NM_000690.2
AY621070.1
EU414258.1
EU414257.1
EU414256.1
EU414255.1
EU414254.1
EU414253.1
EU414252.1
EU414251.1
EU414250.1
EU414249.1
AF164120.1
EU373813.1 NG_012250.1
EU373812.1
EU373811.1
EU373810.1 NM_000690.2
NP_000681.2
EU373809.1
EU373808.1
EU373807.1
EU373806.1
EU373805.1
EU373804.1
AH002599.1
M20456.1 M20455.1
M20454.1 M20453.1
M20452.1 M20451.1
M20450.1 M20449.1
M20448.1 M20447.1
M20446.1 M20445.1
M20444.1
CR456991.1
AB385105.1
CU678321.1
CU678320.1
AF073514.1
http://www.ncbi.nlm.nih.gov/nuccore

63. Nucleotide
GenBank
RefSeq

64. 3
genes/genome

65. Genome/BioProject
Gene
HomoloGene

66. Genome/BioProject

67. http://www.ncbi.nlm.nih.gov/genome

71. Regulatory
Gene
Intron
Exon
Intron
http://www.ncbi.nlm.nih.gov/gene

72. Regulatory
11,043,299
Intron
Exon
Intron

75. External
links

76. HomoloGene

77. P3H1
http://www.ncbi.nlm.nih.gov/homologene

79. Protein of Interest
(P3H1)

80. Genome
Gene
HomoloGene

81. 4 expression
& structure

82. UniGene
EST, GEO
Structures
CDD, MMDB, PubChem…

83. UniGene
…an organized
view of the
transcriptome

84. UniGene
HOW MUCH,
WHERE IS IT?

85. http://www.ncbi.nlm.nih.gov/unigene

86. SELECTED PROTEIN SIMILARITIES
MAPPING POSITION
SEQUENCES
mRNA
EST

87. GENE EXPRESSION
EST: estimated counting
GEO: assayed

88. Structures
CDD, MMDB, PubChem…

90. http://www.ncbi.nlm.nih.gov/structure

93. http://www.ncbi.nlm.nih.gov/cdd

95. http://pubchem.ncbi.nlm.nih.gov/

97. http://www.ncbi.nlm.nih.gov/biosystems

99. UniGene
EST, GEO
Structures
CDD, MMDB, PubChem…

101. databases

102. discovery

103. bucket loads
of library
databases

104. lots of tools

105. Word weight
PubMed
Taxonomy 3-D
3D
Structure
VAST
Phylogeny Gene
BLAST Nucleotide Protein BLAST
sequences sequences

106. Word weight
PubMed
SI MP LE 3-D
3D
OO
Taxonomy VAST
T
Structure
Phylogeny Gene
BLAST Nucleotide Protein BLAST
sequences sequences

107. 10M 1M 100k 10k 1k

109. S tilltoo
IM PL E*
S
* This chart is 9 years old

110. NCBI
discovery
initiative

111. NCBI
discovery
initiative

112. NCBI
high quality DB
discovery tools

113. Information Hubs
• BioProject
• Genome
• Gene
Analysis Hubs
• HomoloGene
• UniGene
• BLAST/VAST

115. where
do I
start?

116. anywhere*

117. *but gene acts as a good hub

118. Apolipoprotein E
APOE

119. HYPOTHESIS:
A structural defect in
APOE protein causes
early onset
Alzheimer’s disease

120. What Genetics
To Disease Variants
Expression
Do Homologus
Structure
? Analysis

121. How Gene and RefSeq
To Genome Maps
Allelic Variants
Do Expression
Homologus G/P
It! Structure

122. APOE
Sequence Viewer
Gene
Genes and More

128. Links in
Gene
Record

129. L

130. Links to
Outside
Sources

144. .0016

146. (many databases here)

149. Dis ease
DY S ITE S State
BO
e lo p ment
Dev

152. liver
brain

153. (many databases here)

171. Apolipoprotein E
APOE

172. HYPOTHESIS:
A structural defect in
APOE protein causes
early onset
Alzheimer’s disease

173. CONCLUSION:
The Cys130Arg
mutation does not
produce a significant
structural variant

175. asdf
science
can be
complex...

176. …NCBI can
help you
with that.

177. thank
you

178. NCBI Tools for
Information and
Scientific Discovery
July 25, 2012 RML Rendezvous
webcast
Jackie Wirz, PhD wirzj@ohsu.edu

179. Now it’s
your turn…

180. Now It’s Your Turn
What database other than PubMed do you
think your patrons will find most useful?
• Gene
• BioProject
• OMIM
• PubChem

181. Now It’s Your Turn
Reminder: Where are you from?
https://www.surveymonkey.com/s/PNRinfo

182. Thank You!
See you next time on…
August 22, 2012 1:00 PM Pacific
https://webmeeting.nih.gov/rendezvous