cv_annotations.txt

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        neXtProt
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Description: Ontology annotation (general annotation / feature)
Name:        cv_annotations.txt
Release:     00.0 of 23-Apr-2014

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  This document lists the controlled vocabulary used to defined a bio-sequence 
  annotation type in the neXtProt database

  The definition of the CV is provided in the following format:

  ---------  ---------------------------     ----------------------
  Line code  Content                         Occurrence in an entry
  ---------  ---------------------------     ----------------------
  ID         Identifier (annotation type)    Once; starts a keyword entry
  AC         Accession (CVAN_xxxx)           Once
  DE         Definition                      Once or more
  HI         Hierarchy                       Optional; once (only the parent)
  //         Terminator                      Once; ends an entry

The AC with a xxxx < 100 are reserved for CVs with a nextprot.cv_terms.cv_id prefixed
Next accession CVAN_0176
__________________________________________________________________________
ID   annotation
AC   CVAN_0001
DE   Biological sequence general annotation or feature (region of interest)
//
ID   feature
AC   CVAN_0002
DE   Region of interest in a biological sequence
HI   annotation
//
ID   general annotation
AC   CVAN_0003
DE   Biological sequence general annotation (function, subcelleluar location, etc.)
HI   annotation
//
ID   ontology annotation
AC   CVAN_0004
DE   Biological sequence ontology annotation (go, ec, keywords, etc.)
HI   annotation
//
ID   molecule processing
AC   CVAN_0010
DE   Cleavage processing of the sequence
HI   feature
//
ID   region of interest
AC   CVAN_0011
DE   Region of interest in the sequence
HI   feature
//
ID   site
AC   CVAN_0012
DE   Interesting single amino acid site on the sequence
HI   feature
//
ID   amino acid modification
AC   CVAN_0013
DE   Modified residues
HI   feature
//
ID   secondary structure
AC   CVAN_0014
DE   Protein secondary structure
HI   feature
//
ID   variant
AC   CVAN_0015
DE   Protein variant site
HI   feature
//
ID   misdefined region
AC   CVAN_0016
DE   Uncertain or uncomplete region
HI   feature
//
ID   expression
AC   CVAN_0017
DE   Expression annotation; expression level as measured in tissues or cell lines
HI   annotation
//
ID   initiator methionine
AC   CVAN_0100
DE   Cleavage of the initiator methionine
HI   molecule processing
//
ID   signal peptide
AC   CVAN_0101
DE   Sequence targeting proteins to the secretory pathway or periplasmic space
HI   molecule processing
//
ID   transit peptide
AC   CVAN_0102
DE   Extent of a transit peptide for organelle targeting
HI   molecule processing
//
ID   maturation peptide
AC   CVAN_0103
DE   Part of a protein that is cleaved during maturation or activation
HI   molecule processing
//
ID   mature protein
AC   CVAN_0104
DE   Extent of an active peptide or a polypetide chain in the mature protein
HI   molecule processing
//
ID   transmembrane region
AC   CVAN_0105
DE   Extent of a membrane-spanning region
HI   topology
//
ID   domain
AC   CVAN_0106
DE   Position and type of each modular protein domain
HI   region of interest
//
ID   repeat
AC   CVAN_0107
DE   Positions of repeated sequence motifs or repeated domains
HI   region of interest
//
ID   calcium-binding region
AC   CVAN_0108
DE   Position(s) of calcium binding region(s) within the protein
HI   region of interest
//
ID   zinc finger region
AC   CVAN_0109
DE   Position(s) and type(s) of zinc fingers within the protein
HI   region of interest
//
ID   DNA-binding region
AC   CVAN_0110
DE   Position and type of a DNA-binding domain
HI   region of interest
//
ID   nucleotide phosphate-binding region
AC   CVAN_0111
DE   Nucleotide phosphate binding region
HI   region of interest
//
ID   coiled-coil region
AC   CVAN_0112
DE   Positions of regions of coiled coil within the protein
HI   region of interest
//
ID   short sequence motif
AC   CVAN_0113
DE   Short (up to 20 amino acids) sequence motif of biological interest
HI   region of interest
//
ID   compositionally biased region
AC   CVAN_0114
DE   Region of compositional bias in the protein
HI   region of interest
//
ID   topological domain
AC   CVAN_0115
DE   Location of non-membrane regions of membrane-spanning proteins
HI   topology
//
ID   active site
AC   CVAN_0116
DE   Amino acid(s) directly involved in the activity of an enzyme
HI   site
//
ID   metal ion-binding site
AC   CVAN_0117
DE   Binding site for a metal ion
HI   site
//
ID   binding site
AC   CVAN_0118
DE   Binding site for any chemical group (co-enzyme, prosthetic group, etc.)
HI   site
//
ID   non-standard amino acid
AC   CVAN_0119
DE   Occurence of non-standard amino acids (selenocysteine and pyrrolysine) in the protein sequence
HI   amino acid modification
//
ID   lipid moiety-binding region
AC   CVAN_0120
DE   Lipidation: covalently attached lipid group(s)
HI   amino acid modification
//
ID   glycosylation site
AC   CVAN_0121
DE   Covalently attached glycan group(s)
HI   amino acid modification
//
ID   disulfide bond
AC   CVAN_0122
DE   Cysteine residues participating in disulfide bonds
HI   amino acid modification
//
ID   cross-link
AC   CVAN_0123
DE   Residues participating in covalent linkage(s) between proteins
HI   amino acid modification
//
ID   helix
AC   CVAN_0124
DE   Helical regions within the experimentally determined protein structure
HI   secondary structure
//
ID   turn
AC   CVAN_0125
DE   Turns within the experimentally determined protein structure
HI   secondary structure
//
ID   beta strand
AC   CVAN_0126
DE   Beta strand regions within the experimentally determined protein structure
HI   secondary structure
//
ID   sequence variant
AC   CVAN_0127
DE   Natural variant of the protein
HI   variant
//
ID   mutagenesis site
AC   CVAN_0128
DE   Site which has been experimentally altered by mutagenesis
HI   variant
//
ID   sequence conflict
AC   CVAN_0129
DE   Sequence discrepancies of unknown origin
HI   variant
//
ID   unsure residue
AC   CVAN_0130
DE   Regions of uncertainty in the sequence
HI   misdefined region
//
ID   non-consecutive residues
AC   CVAN_0131
DE   Indicates that two residues in a sequence are not consecutive
HI   misdefined region
//
ID   non-terminal residue
AC   CVAN_0132
DE   The sequence is incomplete. Indicate that a residue is not the terminal residue of the complete protein
HI   misdefined region
//
ID   function
AC   CVAN_0133
DE   General function(s) of a protein
HI   general annotation
//
ID   catalytic activity
AC   CVAN_0134
DE   Reaction(s) catalyzed by an enzyme
HI   general annotation
//
ID   cofactor
AC   CVAN_0135
DE   Non-protein substance required for enzyme activity
HI   general annotation
//
ID   enzyme regulation
AC   CVAN_0136
DE   Enzyme regulatory mechanism
HI   general annotation
//
ID   subunit
AC   CVAN_0138
DE   Subunit structure: interaction with other protein(s)
HI   general annotation
//
ID   pathway
AC   CVAN_0139
DE   Associated metabolic pathways
HI   general annotation
//
ID   subcellular location
AC   CVAN_0140
DE   Subcellular location of the mature protein
HI   general annotation
//
ID   tissue specificity
AC   CVAN_0141
DE   Expression of the gene product in different tissues
HI   general annotation
//
ID   developmental stage
AC   CVAN_0142
DE   Expression of the gene product according to the cell stage and/or tissue or organism development
HI   general annotation
//
ID   induction
AC   CVAN_0143
DE   Effects of environmental factors on gene expression
HI   general annotation
//
ID   domain information
AC   CVAN_0144
DE   Relevant information on protein domain(s)
HI   general annotation
//
ID   PTM
AC   CVAN_0145
DE   Post-translational modifications
HI   general annotation
//
ID   polymorphism
AC   CVAN_0146
DE   Description of polymorphism(s)
HI   general annotation
//
ID   disease
AC   CVAN_0147
DE   Involvement in disease: disease(s) associated with protein defect(s)
HI   general annotation
//
ID   disruption phenotype
AC   CVAN_0148
DE   Description of the effects caused by the disruption of a protein-encoding gene
HI   general annotation
//
ID   allergen
AC   CVAN_0149
DE   Allergenic properties: information relevant to allergenic proteins
HI   general annotation
//
ID   toxic dose
AC   CVAN_0150
DE   Lethal, paralytic, effect dose or lethal concentration of a toxin
HI   general annotation
//
ID   biotechnology
AC   CVAN_0151
DE   Biotechnological use: use in a biotechnological process
HI   general annotation
//
ID   pharmaceutical
AC   CVAN_0152
DE   Pharmaceutical use: use of as a pharmaceutical drug
HI   general annotation
//
ID   miscellaneous
AC   CVAN_0153
DE   Any relevant information that doesn't fit in any other defined sections
HI   general annotation
//
ID   similarity
AC   CVAN_0154
DE   Sequence similarities: description of the sequence similaritie(s) with other proteins and family attribution
HI   general annotation
//
ID   caution
AC   CVAN_0155
DE   Warning about possible errors and/or grounds for confusion
HI   general annotation
//
ID   expression info
AC   CVAN_0156
DE   Expression annotation to summarize expression levels measured in a series of experiments
HI   general annotation
//
ID   sequence caution
AC   CVAN_0157
DE   Errors concerning the protein sequence
HI   caution
//
ID   alignment conflict
AC   CVAN_0158
DE   differences between the sequence in swissprot and the genome
HI   variant
//
ID   coding sequence
AC   CVAN_0159
DE   Coding sequence on dna sequence
HI   region of interest
//
ID   family name
AC   CVAN_0160
DE   Family classification
HI   similarity
//
ID   domain name
AC   CVAN_0161
DE   Domain classification
HI   similarity
//
ID   go molecular function
AC   CVAN_0162
DE   Ontology annotation by go molecular function
HI   ontology annotation
//
ID   go biological process
AC   CVAN_0163
DE   Ontology annotation by go biological process
HI   ontology annotation
//
ID   go cellular component
AC   CVAN_0164
DE   Ontology annotation by go cellular component
HI   ontology annotation
//
ID   uniprot keyword
AC   CVAN_0165
DE   Ontology annotation by uniprot keyword
HI   ontology annotation
//
ID   enzyme classification
AC   CVAN_0166
DE   Ontology annotation by enzyme classification
HI   ontology annotation
//
ID   topology
AC   CVAN_0167
DE   Describes the topology of regions for transmembrane proteins that span membrane compartments.
HI   region of interest
//
ID   cleavage site
AC   CVAN_0168
DE   Cleavage site on the sequence.
HI   site
//
ID   interacting region
AC   CVAN_0169
DE   Region interacting with another macromolecule.
HI   region of interest
//
ID   subcellular location info
AC   CVAN_0170
DE   Subcellular location information of the mature protein
HI   general annotation
//
ID   self-association
AC   CVAN_0171
DE   Subunit structure: protein self-association
HI   subunit
//
ID   binary interaction
AC   CVAN_0172
DE   Subunit structure: binary interaction between proteins
HI   subunit
//
ID   complex
AC   CVAN_0173
DE   Subunit structure: proteins complex
HI   subunit
//
ID   3D structure
AC   CVAN_0174
DE   Protein 3D structure
HI   region of interest
//
ID   cofactor information
AC   CVAN_0175
DE   Relevant information on protein cofactor(s)
HI   general annotation
//