Trove like Classifiers for Database Catalog

• occurrence:: initial --> First occurrence of the database. New database.
• occurrence:: update --> Updated version of previous database.
• taxonomy:: single species --> Collects data only pertaining to one species, such as drosophila. Also implies more than one strain of the species.
• taxonomy:: single strain --> Collects data only pertains to one strain of a species.
• taxonomy:: multi-species --> Collects data across more than one species
• taxonomy:: virus --> Collects data on viruses
• taxonomy:: eubacteria --> Collects data on eubacteria (prokaryotes)
• taxonomy:: archaebacteia --> Collects data on archaebacteria (prokaryotes)
• taxonomy:: eukaryotes --> Collects data on eukaryotes
• taxonomy:: vertebrate --> Collects data on vertebrate
• taxonomy:: invertebrate --> Collects data on invertebrate
• taxonomy:: unicellular eukaryotes --> Collects data on unicellular eukaryotes, such as yeast
• taxonomy:: plants --> Collects data on plants
• taxonomy:: fungi --> Collects data on fungi
• taxonomy:: mammals --> Collects data on mammals
• taxonomy:: human --> Collects data on human
• 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/models/) and National Institute of General Medical Sci-ences (NIGMS; http://www.nigms.nih.gov/Research/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)
• data:: DNA --> Collects data on DNA
• 2. data:: genes  Collects data on genes
• 3. data:: genome  Collects data on genome
• 4. data:: intron/exon  Collects data on introns and exons [relates to data:: sequence, data:: structure]
• 5. data:: coding/non-coding DNA  Collects data on coding and/or non-coding DNA [relates to data:: sequence, data:: structure]
• 6. data:: mutations and polymorphisms  Collects data on mutations and polymorphisms
• 7. data:: short tandem repeats  Collects data on short repeating sequences, including microsatellites.
• 8. data:: complements  Collects data on complementary strands of genes or its expression. This includes antisense expressions and RNA interference transcripts.
• 9. data:: transposons  Collects data on transposable gene elements.
• 10. data:: probes and primers  Collects data on probes and primers
• 11. data:: RNA  Collects data on RNA
• 12. 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]
• 13. data:: transcriptome  Collects data on transcrip-tome
• 14. data:: protein  Collects data on protein
• 15. 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]
• 16. data:: protein-protein interactions  Collects data on protein-protein interactions
• 17. data:: protein-nucleic acid interactions  Collects data on protein-nucleic acid interactions, such as DNA/RNA binding proteins like transcription fac-tors.
• 18. data:: antibodies  Collects data on antibodies
• 19. data:: post-translational modifications  Collects data on post-translational modifications of peptides, such as glycosylation and lipidation.
• 20. data:: proteome  Collects data on proteome
• 21. data:: metabolome  Collects data on metabolome [relates to data:: pathways]
• 22. data:: lipids  Collects data on lipids
• 23. data:: carbohydrates  Collects data on carbohy-drates and sugars
• 24. data:: chemicals and small molecules  Collects data on chemical compounds and small molecules
• 25. data:: drugs and drug targets  Collects data on drugs and drug targets [relates to data:: diseases]
• 26. data:: ligand activity and pairs  Collects data on binding of proteins by chemical compounds, and its associated activities [relates to data:: protein-protein interactions]
• 27. data:: structure  Collects data on structures
• 28. data:: sequence  Collects data on DNA, RNA, or-protein sequences
• 29. data:: promoters and regulators  Collects data on promoters and regulators [relates to data:: structure]
• 30. data:: motif  Collects data on specific motifs [re-lates to data:: protein, data:: structure]
• 31. data:: enzymatic sites / complexes  Collects data on enzymatic sites, such as enzymes and ribozymes [relates to data:: structure]
• 32. data:: metal ion binding / interactions  Collects data on binding of proteins by metallic ions, and its associated activities [relates to data:: protein-protein interactions]
• 33. data:: localization  Collects data on targeting and localization
• 34. data:: classification  Database on classification of different entities
• 35. data:: properties and annotation  Collects data on properties and descriptors of items, such as mole-cules
• 36. data:: genetic similarity and/or conservation  Collects data on sequence homology and conserved regions [relates to data:: DNA, data:: RNA, data:: protein, data:: sequence]
• 37. data:: pathways  Collects data on metabolic pathways
• 38. data:: diseases  Collects data on diseases
• 39. data:: clinical  Collects clinical data
• 40. data:: literature  Collects data from literature
• 41. data:: statistics  Collects statistical data, such as accidents
• 42. data:: ancient  Collects ancient data, such as data of extinct animals
• 43. data:: comparative  Collects data of comparative work, such as orthologous genes
• 44. data:: high-throughput  Collects data from high-throughput technologies
• 45. data:: microarray  Collects microarray data
• 46. data:: NGS  Collects data from next-generation sequencing technologies, such as DNA-seq, RNA-seq, ChIP-seq
• 47. data:: mass spectrometry  Collects data from mass spectrometry
• 48. data:: crystallography  Collects data from crystal-lography
• 49. data:: images  Collects image data
• 50. data:: images:: microscopic  Collects images from microscopy
• 51. data:: model  Collects data models
• 52. data:: model:: 3D  Collects 3 dimensional models of single entities, such as protein 3D structures or DNA 3D structures (eg, hairpin loops)
• 53. data:: model:: interactions  Collects models of in-teractions, such as pathways (eg, SBML metabolic rate models) or enzymatic rates (eg, Michaelis-Menten equations)
• 54. data:: inferred  Data inferred from other primary data sources (secondary data sources), or used pri-mary data sources to make predictions, calculations, or inferences
• 1. system:: organelles  Data concerning specific or-ganelles
• 2. system:: nucleus  Data concerning nucleus
• 3. system:: cytoplasm  Data concerning cytoplasm
• 4. system:: mitochondria  Data concerning mito-chondria
• 5. system:: chloroplast  Data concerning chloroplast
• 6. system:: ribosome  Data concerning ribosome
• 7. system:: extracellular  Data concerning extracellular, microscopic compartments, such as extracellular matrix
• 8. system:: whole cell  Data concerning entire cell
• 9. system:: tissues  Data concerning specific tissues
• 10. system:: organs  Data concerning specific organs
• 11. system:: organ systems  Data concerning specific organ systems, such as nervous system
• 12. system:: organism  Data concerning on the entire organism
• 13. system:: population  Data concerning populations
• 1. access:: web forms/applications  Data access via web form or web applications
• 2. 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.
• 3. access:: data download  Data files can be down-loaded from the website
• 4. access:: submission  Allows user to submit data
• 1. status:: alive  The database is accessible
• 2. status:: dead  The database is not accessible over a period of 3 months and/or URL is no longer active
• 3. status:: unknown  The database is not accessible over a period of less than 3 months