Trove like Classifiers for Database Catalog

occurrence:: initial --> First occurrence of the data-base. New database. occurrence:: update --> Updated version of previous database.

1. taxonomy:: single species  Collects data only per-taining to one species, such as drosophila. Also im-plies more than one strain of the species.
2. taxonomy:: single strain  Collects data only per-tains to one strain of a species.
3. taxonomy:: multi-species  Collects data across more than one species
4. taxonomy:: virus  Collects data on viruses
5. taxonomy:: eubacteria  Collects data on eubacteria (prokaryotes)
6. taxonomy:: archaebacteia  Collects data on archae-bacteria (prokaryotes)
7. taxonomy:: eukaryotes  Collects data on eukary-otes
8. taxonomy:: vertebrate  Collects data on vertebrate
9. taxonomy:: invertebrate  Collects data on inverte-brate
10. taxonomy:: unicellular eukaryotes  Collects data on unicellular eukaryotes, such as yeast
11. taxonomy:: plants  Collects data on plants
12. taxonomy:: fungi  Collects data on fungi
13. taxonomy:: mammals  Collects data on mammals
14. taxonomy:: human  Collects data on human
15. taxonomy:: model organism  Collects data on model organisms. We used National Institute of Health list of model organisms for biomedical re-search (NIH; http://www.nih.gov/science/ mod-els/) and National Institute of General Medical Sci-ences (NIGMS; http://www.nigms.nih.gov/ Re-search/Models/), consisting of the following model organism: Mouse (Mus musculus; NIH, NIGMS) Rat (Rattus norvegicus; NIH, NIGMS) Budding yeast (Saccharomyces cerevisiae; NIH, NIGMS) Fission yeast (Schizosaccharomyces pombe; NIH, NIGMS) African clawed frog (Xenopus; NIH; NIGMS) Filamentous fungus (Neurospora crassa; NIGMS) Round worm (Caenorhabditis elegans; NIH, NIGMS) Water flea (Daphnia pulex; NIH, NIGMS) Fruit fly (Drosophila melanogaster; NIH, NIGMS) Zebra fish (Denio rerio; NIH, NIGMS) Arabidopsis thaliana (NIH, NIGMS) Social amoeba (Dictyostelium discoideum; NIGMS) Chicken (Gallus gallus; NIH) Chlamydomonas (NIGMS) Ascidian (Ciona spp., NIGMS) Dog (Canis lupus familiaris; NIGMS) Escherichia coli (NIGMS) Honey bee (Apis mellifera; NIGMS) Hydra (NIGMS) Malaria parasite (Plasmodium falciparum; NIGMS) Tetrahymena (NIGMS)
16. data:: DNA  Collects data on DNA
17. data:: genes  Collects data on genes
18. data:: genome  Collects data on genome
19. data:: intron/exon  Collects data on introns and exons [relates to data:: sequence, data:: structure]
20. data:: coding/non-coding DNA  Collects data on coding and/or non-coding DNA [relates to data:: sequence, data:: structure]
21. data:: mutations and polymorphisms  Collects data on mutations and polymorphisms
22. data:: short tandem repeats  Collects data on short repeating sequences, including microsatellites.
23. data:: complements  Collects data on complementary strands of genes or its expression. This includes antisense expressions and RNA interference transcripts.
24. data:: transposons  Collects data on transposable gene elements.
25. data:: probes and primers  Collects data on probes and primers
26. data:: RNA  Collects data on RNA
27. data:: ribozymes  Collects data on ribozymes. This differs from data:: enzymatic sites which collects data on catalytic sites [relates to data:: enzymatic sites, data:: sequence, data:: structure]
28. data:: transcriptome  Collects data on transcrip-tome
29. data:: protein  Collects data on protein
30. data:: enzymes  Collects data on enzymes. This differs from data:: enzymatic sites which collects data on catalytic sites [relates to data:: enzymatic sites, data:: sequence, data:: structure]
31. data:: protein-protein interactions  Collects data on protein-protein interactions
32. data:: protein-nucleic acid interactions  Collects data on protein-nucleic acid interactions, such as DNA/RNA binding proteins like transcription fac-tors.
33. data:: antibodies  Collects data on antibodies
34. data:: post-translational modifications  Collects data on post-translational modifications of peptides, such as glycosylation and lipidation.
35. data:: proteome  Collects data on proteome
36. data:: metabolome  Collects data on metabolome [relates to data:: pathways]
37. data:: lipids  Collects data on lipids
38. data:: carbohydrates  Collects data on carbohy-drates and sugars
39. data:: chemicals and small molecules  Collects data on chemical compounds and small molecules
40. data:: drugs and drug targets  Collects data on drugs and drug targets [relates to data:: diseases]
41. data:: ligand activity and pairs  Collects data on binding of proteins by chemical compounds, and its associated activities [relates to data:: protein-protein interactions]
42. data:: structure  Collects data on structures
43. data:: sequence  Collects data on DNA, RNA, or-protein sequences
44. data:: promoters and regulators  Collects data on promoters and regulators [relates to data:: structure]
45. data:: motif  Collects data on specific motifs [re-lates to data:: protein, data:: structure]
46. data:: enzymatic sites / complexes  Collects data on enzymatic sites, such as enzymes and ribozymes [relates to data:: structure]
47. data:: metal ion binding / interactions  Collects data on binding of proteins by metallic ions, and its associated activities [relates to data:: protein-protein interactions]
48. data:: localization  Collects data on targeting and localization
49. data:: classification  Database on classification of different entities
50. data:: properties and annotation  Collects data on properties and descriptors of items, such as mole-cules
51. data:: genetic similarity and/or conservation  Collects data on sequence homology and conserved regions [relates to data:: DNA, data:: RNA, data:: protein, data:: sequence]
52. data:: pathways  Collects data on metabolic pathways
53. data:: diseases  Collects data on diseases
54. data:: clinical  Collects clinical data
55. data:: literature  Collects data from literature
56. data:: statistics  Collects statistical data, such as accidents
57. data:: ancient  Collects ancient data, such as data of extinct animals
58. data:: comparative  Collects data of comparative work, such as orthologous genes
59. data:: high-throughput  Collects data from high-throughput technologies
60. data:: microarray  Collects microarray data
61. data:: NGS  Collects data from next-generation sequencing technologies, such as DNA-seq, RNA-seq, ChIP-seq
62. data:: mass spectrometry  Collects data from mass spectrometry
63. data:: crystallography  Collects data from crystal-lography
64. data:: images  Collects image data
65. data:: images:: microscopic  Collects images from microscopy
66. data:: model  Collects data models
67. data:: model:: 3D  Collects 3 dimensional models of single entities, such as protein 3D structures or DNA 3D structures (eg, hairpin loops)
68. data:: model:: interactions  Collects models of in-teractions, such as pathways (eg, SBML metabolic rate models) or enzymatic rates (eg, Michaelis-Menten equations)
69. data:: inferred  Data inferred from other primary data sources (secondary data sources), or used pri-mary data sources to make predictions, calculations, or inferences
70. system:: organelles  Data concerning specific or-ganelles
71. system:: nucleus  Data concerning nucleus
72. system:: cytoplasm  Data concerning cytoplasm
73. system:: mitochondria  Data concerning mito-chondria
74. system:: chloroplast  Data concerning chloroplast
75. system:: ribosome  Data concerning ribosome
76. system:: extracellular  Data concerning extracellular, microscopic compartments, such as extracellular matrix
77. system:: whole cell  Data concerning entire cell
78. system:: tissues  Data concerning specific tissues
79. system:: organs  Data concerning specific organs
80. system:: organ systems  Data concerning specific organ systems, such as nervous system
81. system:: organism  Data concerning on the entire organism
82. system:: population  Data concerning populations
83. access:: web forms/applications  Data access via web form or web applications
84. access:: programmatic  Data access via program-matic interface. For example, the data-base/application provides an interface for users to query it using a program/script.
85. access:: data download  Data files can be down-loaded from the website
86. access:: submission  Allows user to submit data
87. status:: alive  The database is accessible
88. status:: dead  The database is not accessible over a period of 3 months and/or URL is no longer active
89. status:: unknown  The database is not accessible over a period of less than 3 months