HbVar: A Database of Human Hemoglobin Variants and Thalassemias
Frequently Asked Questions (FAQ)

I found a new variant. How do I get it added to HbVar?

Send data in a human readable format to the HbVar database curators from the contact us page. The types of data to send are the same as those in the query form, or what is in the page displays of other mutations. Also include a researcher ID for yourself, to ensure you get full credit for the submission.

What is a researcher ID?

It is an unique ID assigned to an individual. It helps in uniquely identifing someone when giving credit for work done. Peoples names are not unique and can change. An example of a source for such an ID is Thomson Reuters researcher ID. There is no cost involved in getting a researcher ID from Thomson Reuters. For more information on the use of researcher IDs, read this paper.

What reference sequence and numbering conventions are used?

Go here for details on numbering systems.

How can I tell if the SNP I found is novel, or has been seen before?

This tool will look up the SNP by its position in HbVar and dbSNP. The position can be entered using the numbering systems described above.

I found a SNP that is not associated with a phenotype other than normal, can I enter it in HbVar?

No, HbVar does not include these. But you are encouraged to submit these to dbSNP as well as the fact that the phenotype is normal.

If it is unknown whether a mutation is located in alpha1 or alpha2 (or Agamma vs. Ggamma), where is it listed in the database?

These are listed under both sections. For example if it is unknown whether it is alpha1 or alpha2 you will find the entry when you query on either alpha1 or alpha2.

How can I get the HbVar variants from NCBI's dbSNP?

Search dbSNP by submitter handle HBVAR or click here. From there you can click on a batch ID and get all the variants submitted or updated with the batch.

How do I query on more than one name of a variant?

You can type an "OR" between 2 names or parts of names to look for more than 1 variant or a variant where you are not sure of the name or spelling. If you type "AND" between the names you will be looking for a variant with both the names listed. See also the Help page for more information on querying using the text boxes.

What I want to query on is not listed in the selection box.

Try looking in a different selection box or for a synonym. If what you want is not on the query form then it is not in the database or it is stored only as a comment.

How do I query on a name/word with an accent mark?

The names of the variants and thals are the only fields where accent marks are used. Just type the characters without the accent mark when doing a query, the program will search the names as plain text. Many of the references come from PubMed and they do not use accent marks for author names so we do not store the accents for author names.

How do I say NOT?

This is not easily done with the form. You can select everything in the box except the one you don't want. The problem with this is that it will treat the entries that have no entry in that field the same as ones that have the entry you don't want.

How should I query ranges under laboratory findings or for residues?

To look for an exact value enter that value in both boxes. To query for values between 2 numbers put the lower number in the first box and the higher number in the second box. To query on anything greater than a particular number enter the number in the first box. Then either leave the second box blank or enter a number greater than what you believe the highest number to be. To query on anything less than a particular number enter the number in the second box. Either leave the first box blank or enter a number smaller than the smallest number in this field. (for example, laboratory findings is not likely to be less than 0)

Why is there a NULL in the selection box?

The NULL allows you to query on entries that have no data in this field of the database. Sometimes this can be useful on its own such as querying on all entries with Jaundice that are mild, moderate, or don't mention any degree. The NULLs can also be used to build a "NOT" query. If you want all the entries which are NOT unstable, select all the other choices including the NULL. If the NULL were not there you would not get the entries with no stability data.

When I try to go back to the Summary table I get an error message saying the page has expired.

This is because the page was not done downloading the first time. To use the browsers back button wait until the Summary table is done downloading before clicking on any hyperlinks.

Where can I get the Syllabi in book form?

Obtaining a printed copy

Can I use HbVar output in Galaxy?

Ask for the tab-separated text output, then save the result to your computer. Go to the Galaxy page and upload the file. The file will have chromosome coordinates so it should work well with many of the Galaxy tools.

What if I need an output format that the query page doesn't provide?

Send an email to Belinda from the contact us page. She will in most cases either provide the needed file or consider adding the format to the output options.