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Next: Transcription data in table Up: Guide to the EpoDB Previous: Complex Attributes in Nucleotide

Protein data in table form

 
aa_seq        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
protein_unit_id table_id no pointer to protein unit none
extent string no indicates whether sequence is complete or not COMPLETE
seq string no amino acid sequence none
   
SWISS-PROT_base_info        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
protein_unit_id table_id no pointer to protein unit none
sp_id string no SWISS-PROT entry name none
status string no SWISS-PROT data class none
primary_accession string no SWISS-PROT accession number none
secondary_accessions string set yes SWISS-PROT secondary accessions none
gene_name string yes gene names none
first_created string no SWISS-PROT date of creation none
last_sequence_update string no SWISS-PROT date of last seq update none
last_annotation_update string no SWISS-PROT date of last annot update none
organism_scientific string no genus species none
organism_common string yes common name none
tax_classification string no taxonomic classification none
db_xref record set yes database cross-references none
embl_xref record set yes EMBL cross-references none
key_words string set yes keywords none
   
protein_unit        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
name string no protein name none
synonyms string set yes alternative names none
family string yes protein family none
gene_origin string no gene origin (organelle or nuclear) nuclear
amino_acids int no length in amino acids none
mol_weight int no MW (rounded to nearest gram) none
cyclic_redundancy_check string no 32-bit cyclic redundancy check CRC32 none
post_translational_modification string yes post translational modification none
caution string yes warning about possible errors and/or confusion none
comments string set yes OTHER comments none
references string set no references none
   
protein_feature        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
protein_unit_id table_id no pointer to protein unit none
category string no class of feature none
name string no name of feature none
description string yes description of feature none
start int no start of feature none
end string no end of feature none
feature_source string yes place of feature addition _
   
protein_mass_spec        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
protein_unit_id table_id no pointer to protein unit none
method string no method none
mass real no MW none
mass_error real yes MW error none
mass_start int no start of protein sequence for which MW was determined 1
mass_end int no end of protein sequence for which MW was determined length
   
protein_function        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
protein_unit_id table_id no pointer to protein unit none
function_description string yes general function description none
domain string yes description of the domain structure of a protein none
subunit string yes description of the quaternary structure none
catalytic_activity string yes description of the reaction(s) catalysed by an enzyme none
pathway string yes description of the metabolic pathway(s) in which protein participates none
   
protein_genetics        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
protein_unit_id table_id no pointer to protein unit none
disease_association string yes description of the disease(s) associated with a deficiency of a protein none
polymorphism string yes description of polymorphism(s) none
similarity string yes description of the similariti(es) (sequence or structural) of a protein with other proteins none
database record yes cross reference to mutation db none
   
protein_expression        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
protein_unit_id table_id no pointer to protein unit none
alternative_products string yes dscription of the existence of related protein sequence(s) produced by alternative splicing of the same gene(s) or by the use of alternative initiation codons none
induction_of_synthesis string yes description of the compound(s) which stimulate the synthesis of a protein none
rough_developmental_stage string yes description of the developmental specific expression of a protein none
tissue_specificity string yes description of the tissue specificity of a protein none
subcellular_location string yes description of the subcellular location of a mature protein product none
   
enzyme_properties        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
protein_unit_id table_id no pointer to protein unit none
mechanism string yes description of an enzyme regulatory mechanism none
cofactor string yes description of an enzyme cofactor none
 
enzymatic_reaction        
Attribute Type Undefined Description Default
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
ec_number string yes EC number none
catalyzed_by string no name of protein_unit none
left string list yes left side of written reaction none
left_coefficients int list no coefficients for left side of reaction none
right string list no right side of written reaction none
right_coefficients int list no coefficients for right side of reaction none
 

next up previous
Next: Transcription data in table Up: Guide to the EpoDB Previous: Complex Attributes in Nucleotide

Fidel Salas
1/15/1998