Trove like Classifiers for Database Catalog - mauriceling/mauriceling.github.io GitHub Wiki
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:
data:: intron/exon Collects data on introns and exons [relates to data:: sequence, data:: structure]
data:: coding/non-coding DNA Collects data on coding and/or non-coding DNA [relates to data:: sequence, data:: structure]
data:: mutations and polymorphisms Collects data on mutations and polymorphisms
data:: short tandem repeats Collects data on short repeating sequences, including microsatellites.
data:: complements Collects data on complementary strands of genes or its expression. This includes antisense expressions and RNA interference transcripts.
data:: transposons Collects data on transposable gene elements.
data:: probes and primers Collects data on probes and primers
data:: RNA Collects data on RNA
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]
data:: transcriptome Collects data on transcrip-tome
data:: protein Collects data on protein
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]
data:: protein-protein interactions Collects data on protein-protein interactions
data:: protein-nucleic acid interactions Collects data on protein-nucleic acid interactions, such as DNA/RNA binding proteins like transcription fac-tors.
data:: antibodies Collects data on antibodies
data:: post-translational modifications Collects data on post-translational modifications of peptides, such as glycosylation and lipidation.
data:: proteome Collects data on proteome
data:: metabolome Collects data on metabolome [relates to data:: pathways]
data:: lipids Collects data on lipids
data:: carbohydrates Collects data on carbohy-drates and sugars
data:: chemicals and small molecules Collects data on chemical compounds and small molecules
data:: drugs and drug targets Collects data on drugs and drug targets [relates to data:: diseases]
data:: ligand activity and pairs Collects data on binding of proteins by chemical compounds, and its associated activities [relates to data:: protein-protein interactions]
data:: structure Collects data on structures
data:: sequence Collects data on DNA, RNA, or-protein sequences
data:: promoters and regulators Collects data on promoters and regulators [relates to data:: structure]
data:: motif Collects data on specific motifs [re-lates to data:: protein, data:: structure]
data:: enzymatic sites / complexes Collects data on enzymatic sites, such as enzymes and ribozymes [relates to data:: structure]
data:: metal ion binding / interactions Collects data on binding of proteins by metallic ions, and its associated activities [relates to data:: protein-protein interactions]
data:: localization Collects data on targeting and localization
data:: classification Database on classification of different entities
data:: properties and annotation Collects data on properties and descriptors of items, such as mole-cules
data:: genetic similarity and/or conservation Collects data on sequence homology and conserved regions [relates to data:: DNA, data:: RNA, data:: protein, data:: sequence]
data:: pathways Collects data on metabolic pathways
data:: diseases Collects data on diseases
data:: clinical Collects clinical data
data:: literature Collects data from literature
data:: statistics Collects statistical data, such as accidents
data:: ancient Collects ancient data, such as data of extinct animals
data:: comparative Collects data of comparative work, such as orthologous genes
data:: high-throughput Collects data from high-throughput technologies
data:: microarray Collects microarray data
data:: NGS Collects data from next-generation sequencing technologies, such as DNA-seq, RNA-seq, ChIP-seq
data:: mass spectrometry Collects data from mass spectrometry
data:: crystallography Collects data from crystal-lography
data:: images Collects image data
data:: images:: microscopic Collects images from microscopy
data:: model Collects data models
data:: model:: 3D Collects 3 dimensional models of single entities, such as protein 3D structures or DNA 3D structures (eg, hairpin loops)
data:: model:: interactions Collects models of in-teractions, such as pathways (eg, SBML metabolic rate models) or enzymatic rates (eg, Michaelis-Menten equations)
data:: inferred Data inferred from other primary data sources (secondary data sources), or used pri-mary data sources to make predictions, calculations, or inferences
system:: organelles Data concerning specific or-ganelles
system:: nucleus Data concerning nucleus
system:: cytoplasm Data concerning cytoplasm
system:: mitochondria Data concerning mito-chondria
system:: chloroplast Data concerning chloroplast
system:: ribosome Data concerning ribosome
system:: extracellular Data concerning extracellular, microscopic compartments, such as extracellular matrix
system:: whole cell Data concerning entire cell
system:: tissues Data concerning specific tissues
system:: organs Data concerning specific organs
system:: organ systems Data concerning specific organ systems, such as nervous system
system:: organism Data concerning on the entire organism
system:: population Data concerning populations
access:: web forms/applications Data access via web form or web applications
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.
access:: data download Data files can be down-loaded from the website
access:: submission Allows user to submit data
status:: alive The database is accessible
status:: dead The database is not accessible over a period of 3 months and/or URL is no longer active
status:: unknown The database is not accessible over a period of less than 3 months