Criteria for Data Entry into ALFRED
Data submission to ALFRED - guidelines
Use of ALFRED
How to create URL to ALFRED
OverviewALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. (Researchers wishing to have their data entered into ALFRED should contact us. If suitable data can be sent in appropriate electronic format, it will be much easier to include them in ALFRED, see "Criteria" below.) ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching.
ALFRED is a work in progress. The structure and functionality of ALFRED are being revised in an ongoing process as time allows improvements to be implemented. We are also routinely adding new data and links to other databases. Those of us on the ALFRED staff hope these data will be useful to others. We welcome comments on content, structure, and the interfaces available.
ALFRED is maintained by the ALFRED Staff.
Criteria for Data Entry into ALFREDWe feel that gene frequency data are only meaningful if a population sample is reasonably well defined and large enough for a reasonably accurate frequency estimate and if the polymorphism is sufficiently defined to be replicable. Therefore, not all published gene frequency data will be included in ALFRED. Currently, there is no absolute minimum sample size since samples that are small but come from sparsely represented areas and/or have data on multiple polymorphisms can be very useful. (The Nasioi sample is a specific example of such small sample (22 individuals) studied for multiple markers.) We are only including samples that can be reasonably specified as to ethnicity though this includes some highly heterogeneous groups such as "United States whites", which is the equivalent of "mixed European".
Because ALFRED focuses on gene frequency variation among populations, we are generally including frequency estimates only for polymorphisms that have been studied in at least six distinct population samples. Of course, there are exceptions, especially if a sample generally studied for multiple polymorphisms that meet the ">6 populations" criterion also has data on some unique polymorphisms. Similarly, various small sets of data are being entered when we know or expect there are additional data becoming or already available for eventual entry into ALFRED. Our available resources to enter data from the literature are quite limited but if researchers can provide suitable electronic versions of their appropriate data we will be happy to add them to ALFRED.
The above criteria for inclusion in ALFRED are subject to change. We welcome comments from the scientific community interested in these data and will attempt to follow any consensus that emerges.
Data submission to ALFRED - guidelinesOnly data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. If the submitted data lack any of this information, the data lose much of their value. Therefore, we are looking for the most complete set of information for each population sample. As an aid in your ALFRED submission we have listed below guidelines that you should follow in order to provide the necessary data. In addition to the actual frequencies, we will need further information regarding your publications, samples, loci and sites. Below you will find what type other information we will need to input your data into ALFRED.
We need any citations for publications that contain the allele frequencies that you are submitting.Your data will be linked to these publications. If your data are unpublished the data will be referred to the researcher’s name saying they are unpublished. If they are published in the future, you will need to send us the new citation in order for the data to be linked to the appropriate publication.
ALFRED distinguishes samples of a population (a particular set of individuals) from the population. This allows future researchers to consider whether differences of whatever sort, shown by different loci, for example, can be attributed to the loci because the same set of individuals was tested for both loci or might be attributed to sampling differences because different sets of individuals were tested.
To describe the sample sufficiently, we need to know about certain elements concerning your specific sample. The information you provide will also be used to aid in a complete description of the population from which the sample was collected. The following information is most important:
Please provide the official name and symbol for the gene in which the site is located. For the official gene symbol, go to the HGNC website http://www.genenames.org/cgi-bin/hgnc_search.pl.
If you cannot find an official gene symbol for the site, please give us as much information as possible. For intergenic sites it is helpful to have the name of the closest gene and an indication of the distance from the gene 5' or 3'Site (polymorphism):
The excel spreadsheet provided, can be used for submitting data to the ALFRED Staff at firstname.lastname@example.org . The information that has be provided in the spreadsheet are as follows:
Sample, locus, and site information can be submitted via a Word file or other comparable word processing file. If you have problems using the excel spreadsheet provided please let us know and we will work with you to come up with a more useful method of submitting your data. If you have any questions, comments or suggestions about any aspect of ALFRED, please feel free to contact us.
Use of ALFREDHelp is available within ALFRED and we hope the searching procedures are fairly intuitive; we welcome comments if you find some aspect is not obvious or does not work as expected. The following are some hints about ways we think you can get a quick overview of what is in ALFRED.
The Keyword Search function helps a user to query the database using a list of keywords separated by semi-colons. There are 2 types of searches one can perform.
Data display and accessibility
There are several ways allele frequency data can be viewed and downloaded from ALFRED. Allele frequency data for individual polymorphisms can be displayed in
ALFRED offers multiple summary tables which includes
The ALFRED team puts together a newsletter which is emailed to all the registered users on a regular basis. The newsletter includes several types of information which keeps the user up-to-date with any new functions, recent data uploads, and friendly tips on using ALFRED. Other documentation files available from ALFRED's 'Documentation' tab are
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How to create URLs to ALFRED description pagesCreating URL links to access description pages in ALFRED is very straight forward.
URL to locus description page
URL to site description page
© 2018 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.