The document discusses various databases that contain biological data including genes, proteins, genomes, protein domains, gene expression, interactions, pathways, and models. It mentions several specific databases such as GenBank, UniProt, PDB, SGD, TAIR, Ensembl, InParanoid, HomoloGene, COG, OrthoMCL, Entrez, eggNOG, TreeFam, CDD, Pfam, SMART, InterPro, SCOP, CATH, GEO, ArrayExpress, Cyclebase, BioGRID, DIP, IntAct, MINT, Prosite, ELM, Domino, Phospho.ELM, PhosPhAt, Phosida, CORUM,

1. Data and databases Lars Juhl Jensen EMBL Heidelberg

2. a lot of data

4. a lot of databases

5. Duncan Hull, nodalpoint.org

6. genes and proteins

7. GenBank

10. UniProt

13. PDB

16. genomes

17. SGD Saccharomyces Genome Database

20. TAIR The Arabidopsis Information Resource

23. GeneDB

26. Ensembl

30. and many others

31. homology

32. orthology and paralogy

34. InParanoid

35. model organism databases

39. HomoloGene

40. Entrez

43. COG Clusters of Orthologous Groups

44. deep orthology

45. functional classes

47. OrthoMCL

48. high resolution

52. YOGY

53. meta-database

56. eggNOG

57. multiple resolutions

62. TreeFam

63. phylogenetic trees

67. protein domains

68. CDD Conserved Domain Database

69. NCBI BLAST

72. Pfam

73. high coverage

77. SMART

78. signal transduction

81. InterPro

82. meta-database

86. structural classification

87. SCOP

88. manual assignments

90. CATH

91. automatic assignments

93. cell cycle

94. evolution of expression

96. gene expression

97. microarrays

99. dynamics

100. GEO Gene Expression Omnibus

103. ArrayExpress

106. cell cycle

109. Cyclebase.org

113. SCEPTRANS

116. interactions

117. affinity purification

119. yeast two-hybrid

121. synthetic lethality

123. repositories

124. BioGRID

127. DIP Database of Interacting Proteins

131. IntAct

134. MINT Molecular Interactions Database

138. cell cycle

139. dynamic network

141. linear motifs

142. less than 10 residues

144. Prosite

146. ELM

148. Domino

151. PepCyber P~Pep

155. Phospho.ELM

158. PhosphoSite

161. PhosPhAt

165. Phosida

168. cell cycle

169. evolution of phosphorylation

171. complexes

172. CORUM

175. Gene Ontology

178. cell cycle

179. regulation of assembly

181. pathways

182. KEGG

183. broad coverage

186. iPath

189. EcoCyc

190. MetaCyc

191. metabolism

194. Reactome

195. elegant data model

197. PID Pathway Interaction Database

198. meta-database

201. models

202. BioModels

205. cell cycle

206. Cyclonet

211. CCDB

216. integration

217. STRING

219. benchmarking

221. transfer by orthology

224. Bayesian framework

226. signaling networks

227. NetworKIN