ALFRED

ALFRED (the ALelle FREquency Database) is an Internet-accessible database designed to store and make available frequencies of alleles of DNA-based human polymorphisms for multiple populations, primarily for the population genetics and molecular anthropology communities. The emphasis remains on populations typed for multiple polymorphisms and polymorphisms typed on multiple populations. Allele frequencies at each site are linked to the specific populations and specific samples of those populations with descriptions. When available, haplotype frequencies are also included. Each polymorphism site is linked to molecular definitions and to molecular databases.

As of January 2005, ALFRED had data on 1,051 polymorphisms, 399 populations and 23,179 frequency tables (one population typed for one site). ALFRED is accessible from http://www.alfred.med.yale.edu. Data in ALFRED come from two sources: They are extracted from the literature, or they are submitted by researchers. From either source, data included in ALFRED are carefully curated and multiple links established, making it possible to retrieve data through many pathways. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching.

[Page 46]Populations are organized by geographic regions, and each population record is annotated with alternate names (synonyms),linguistic, geographical location information, and links to external databases. The population descriptions in ALFRED are meant to be helpful but not fully comprehensive. The ability to retrieve additional information on populations is provided by active links to linguistic and ethnographic databases. Population samples are organized by populations and annotated with sample information such as sample size and relation to other samples. Genetic polymorphisms are defined primarily by their locus and allele. Loci are organized by chromosome, and each locus record is annotated with alternate names (synonyms), chromosomal position, a valid locus symbol, and links to external databases. Polymorphisms and haplotypes are organized by locus, and each polymorphism record is annotated with dbSNP rs#, alternate names (synonyms), ancestral allele, and links to external databases for expanded molecular information. Thus, ALFRED provides links to both molecular and anthropologic databases. Each allele frequency record is linked to the population sample information, polymorphism information, typing method, and the publication the frequency was extracted from. All publication entries are linked to PubMed. Every record in ALFRED has a unique identifier (UID) that can be used in publications to reference specific data.

Flexible methods of querying ALFRED are available. The queries can start with loci, population, publication author, ALFRED UID, dbSNP ID (rs#, ss#), geographic region, or a combination of gene name and population name. The results of frequency searches can be viewed both in graphical and tabular format. The graphical stacked-bar format offers a quick visual display of the frequency variation among populations. On the other hand, the tabular format offers frequency values and related information, which can be used in analysis tools.

Several other means of retrieving data are being developed. One is a geographic interface that displays populations on maps and can also display graphics of data at the map location of the population.

Data in ALFRED are available for downloads in different user-friendly formats. Allele frequency data for individual polymorphisms can be downloaded in semicolon-delimited format. The entire database can be downloaded in XML format by following the link provided in the Web site(http://www.alfred.med.yale.edu/alfred/xmldatadump.asp). Depending on requirements, a researcher can download the entire database with or without the descriptions or have the tables separately downloaded in XML format. In addition, the allele frequencies, polymorphism, and population information tables in ALFRED are also provided in downloadable text files. Data in these files can be seamlessly imported into Excel spreadsheets for further analysis.

...