ALFRED
      The ALlele FREquency Database   
A resource of gene frequency data on human populations
supported by the U. S. National Science Foundation.

Data Structure in ALFRED

As of 6/19/02

Graphical representations of general and detailed table relationships are also available.


Frequencies
Describes a single allele frequency for a single sample typed on a single population
Field Name Field Description
freq_id Primary key
frequency Frequency of a single allele in a single population
allele_id Foreign key for alleles
typed_sample_id Foreign key for a typed sample
standard_error Standard error for the frequency
fdate Record entry date
contributor Foreign key for the contributor
typing_method Foreign key for the typing_method
visible Flag to set the public visibility statusof a record. Used instead of deleting records


Typed Sample
A juncture between a sample and the site it was typed on
Field Name Field Description
typed_sample_id Primary key
sample_id Foreign key for sample
site_id Foreign key for the site
number_chromosomes The number of chromosomes typed in the sample for this site
typingdate Redundant storage of the date the sample was typed for this site
description Description of the typed sample
visible Flag to set the public visibility statusof a record. Used instead of deleting records


Samples
Describes a sample of a population
Field Name Field Description
sample_id Primary key
population_id Foreign key for the population
description Description of the sample
number_chromosomes 2N individuals in the sample.
sample_uidUnchanging Universal IDentifier for the sample
relation_to_other_samplesDefines the relationship between this sample and other samples
sample_name Name of the sample
visible Flag to set the public visibility statusof a record. Used instead of deleting records


Populations
Describes a single population.
Field Name Field Description
pop_id Primary key.
pop_name Name of the population.
description Description of the population.
maxlongitude Maximum longitude. Used to generate a rough rectangle within which the population is located or originally from
minlongitude Minimum longitude. Used to generate a rough rectangle within which the population is located or originally from
maxlatitude Maximum latitude. Used to generate a rough rectangle within which the population is located or originally from
minlatitude Minimum latitude. Used to generate a rough rectangle within which the population is located or originally from
geographic_region An abbreviation used to identify the rough geographic region within which the population is located or originally from
graphsort_idDecimal based system for ordering populations during dynamic graphing
primary_languageLanguage primarily spoken by the population
language_familyLanguage family primary language belongs to
pop_uidUnchanging Universal IDentifier for the population
visibleFlag to set the public visibility statusof a record. Used instead of deleting records


Alleles
Describes a single allele for a single site.
Field Name Field Description
allele_id Primary key
site_id Foreign key for the site
allele_name Name of the allele
allele_symbol Symbol used for the allele
description Description of the allele (size, etc)
visible Flag to set the public visibility statusof a record. Used instead of deleting records


Sites
Describes a single site from a single locus
Field Name Field Description
site_id Primary key
locus_id Foreign key for a locus
site_description Description of the site
site_name Name of the site
ancestral_allele Ancestral allele name
ancestral_basis Basis for determination of the ancestral allele
site_uidUnchanging Universal IDentifier
visible Flag to set the public visibility statusof a record. Used instead of deleting records


Loci
Describes a single locus. May be, but is not limited to being, a gene
Field Name Field Description
locus_id Primary key
locus_name Name of the locus
locus_symbol Symbol used to represent the locus
chromosome Which chromosome the locus is on
band_position Chromosomal band position of the locus if known.
locus_uidUnchanging locus Universal IDentifier
locus_description Description of the locus
symbol_check Should the symbol be checked automatically to see if it is official
visible Flag to set the public visibility statusof a record. Used instead of deleting records


Typing Method
Describes the general procedure used to type the site.
Field Name Field Description
id Primary key
typing_method_name Name of the general typing method (ASO, PCR_RFLP, STRP, etc)
typing_method_description A brief description of the typing method
visible Flag to set the public visibility statusof a record. Used instead of deleting records


Publications
Describes a single publication
Field Name Field Description
pub_id Primary key
authors List of authors
title Title of the publication
journal Journal the publication is printed in
volume Volume the publication is printed in
issue Issue the publication is printed in
pages Pages of the journal the publication is printed in
year Year the article was printed
pub_uidUnchanging Universal IDentifier for publications
puburl_idurl_id from table urls for making link to PubMed
visible Flag to set the public visibility statusof a record. Used instead of deleting records


urls
Details of a single URL
Field Name Field Description
url_id Primary key
url The complete url
remote_uid Remote datebase Unique IDentifier
remotedbname The name of the remote database the url links to
url_type The type of data the url links to
visible Flag to set the public visibility statusof a record. Used instead of deleting records


Contributor
Provides information on a single contributor.
Field Name Field Description
contrib_id Primary key
name Name of the contributor
fax Fax number
phone Phone number
address Address
country Country of residence
email Email address
preferred_contact_method Preferred contact method
public Is the contributor information public or not?
contrib_uidUnchanging Universal IDentifier for the contributor information
homepageWWW home page for the contributor


Typing Protocol
Details of the typing protocol by which a site is typed
Field Name Field Description
typing_protocol_id Primary key
protocol Typing Protocol or a link to the typing protocol
typingprot_uidUnchanging Universal IDentifier for the typing protocol
visible Flag to set the public visibility statusof a record. Used instead of deleting records


pubfreq
Link table between frequencies and publications. Every frequncy value in the database should have a publication linked to it.
Field Name Field Description
pubfreq_id Primary key
pub_id Foreign key for the publications
freq_id Foreign key for the frequencies


pubpop
Link table between populations and publications
Field Name Field Description
pubpopid Primary key
popid Foreign key for the populations
pubid Foreign key for the publications


pubsample
Link table between publications and samples
Field Name Field Description
pubsample_id Primary key
pub_id Foreign key for the publications
sample_id Foreign key for the samples


publocus
Link table between locus and publications
Field Name Field Description
publocus_id Primary key
pub_id Foreign key for the publications
locus_id Foreign key for the locus


pubsites
Link table between publications and sites
Field Name Field Description
pubsite_id Primary key
pub_id Foreign key for the publications
site_id Foreign key for the sites


pop_url
Link table between populations and urls
Field Name Field Description
popurl_id Primary key
pop_uid Foreign key for the populations
url_id Foreign key for the urls


locus_url
Link table between locus and urls
Field Name Field Description
locus_url_id Primary key
locus_id Foreign key for the locus
url_id Foreign key for the urls


site_url
Link table between sites and urls
Field Name Field Description
site_url_id Primary key
site_id Foreign key for the sites
url_id Foreign key for the urls


synonyms
Stores all the names from tables sites, loci, populations, samples and synonyms to ALFRED names.
Field Name Field Description
syn_id Primary key
alfred_uid UIds from the above mentioned tables.
syn_name ALFRED names and synonyms
comments Source of the synonym


© 2018 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan