Linking to the Genome Browser with just an ID

[Solomon Shorser]

Hello,

I am trying to link to the Genome Browser, with just a UCSC ID.

I will get a list of UniProt IDs and use the UniProt mapping service (http://www.uniprot.org/mapping/) to map them to UCSC IDs. I get results that look like this:

From    To
P34947    uc001led.4
Q8TCW9    uc010yqj.3
P08235    uc003ilk.5
P16254    uc008lsa.1
Q8K4Z5    uc007hup.2
E9Q414    uc007mzf.2

From here, I need to create links to UCSC. All I have is the UCSC ID such as "uc001led.4". I've looked at the document about linking to the Genome Browser (https://genome.ucsc.edu/FAQ/FAQlink.html#link1) but it states that I need values for "org", "position", and "db". I have tried using the UCSC ID for "position", and it works for some but not others.

For example: 

http://genome.ucsc.edu/cgi-bin/hgTracks?position=uc003ilk.5

seems to work OK,

but this URL:

http://genome.ucsc.edu/cgi-bin/hgTracks?position=uc007mzf.2

yields an error:

•  
• Sorry, couldn't locate uc007mzf.2 in Human Dec. 2013 (GRCh38/hg38)

I know that not all of the UniProt identifiers that I map will be human, but I won't know the details of which identifiers will be for which species - right now all I can get is a flat list of identifiers.

Is there a way to link to the genome browser with just a UCSC ID, or is there some way to query some other tool based on UCSC ID to determine which "org" or "db" I should use before constructing the URL?

Thanks,
Solomon Shorser.

Solomon Shorser
Software Developer

Ontario Institute for Cancer Research
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[Jairo Navarro Gonzalez]

Hello Solomon,

Thank you for using the UCSC Genome Browser and your inquiry.

You can link to the Genome Browser using the UniProt identifiers without the need to map them to UCSC IDs.
To create these links, simply edit the following template URL:

https://genome.ucsc.edu/cgi-bin/hgLinkIn?resource=uniprot&id=[UniProt ID]

For example, you can use the following links to view a couple of UniProt identifiers you provided:

https://genome.ucsc.edu/cgi-bin/hgLinkIn?resource=uniprot&id=P08235
https://genome.ucsc.edu/cgi-bin/hgLinkIn?resource=uniprot&id=E9Q414

I would also like to note that hgLinkIn is a brand new feature that we're just now rolling out, so there may be little to no documentation on it yet.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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[Solomon Shorser]

Hi Jairo,

Thanks, I'll try using the hgLinkIn.

Solomon Shorser.

[Solomon Shorser]

Hi Jairo,

I had a look at this feature and I think it will work for what I am doing. Thanks for letting me know about it!

I'm just curious: if I only had a list of UCSC IDs (and no list of corresponding UniProt IDs), how could I properly link to the Genome Browser? Does the Genome Browser have any mapping capabilities so that I could map a UCSC ID to a proper URL? Or would it actually be better to seek out a mapping service to map the UCSC IDs to a "other" IDs that I could then use with this hgLinkIn feature?

Thanks,
Solomon Shorser.

On 2017-10-10 03:45 PM, Jairo Navarro Gonzalez wrote:

[Christopher Lee]

Hi Solomon,

Thank you for your question about linking to the UCSC Genome Browser
with only a UCSC ID. If you knew the assembly that corresponds to a
particular ucID, like hg38 for Human GRCh38 or mm10 for Mouse GRCm38,
then you could use your ucID's in a url like so:
hgTracks?db=assembly&position=ucID

If you don't know the assembly name then unfortunately there is no way
to create the correct links. If you at least know the organism, but
not the assembly, then using org=human will work as long the ucID is
for the current assembly version. Unfortunately you may also run into
problems with this approach if your ucID is for an old assembly, like
hg19.

We do not provide a mapping service like you ask about, but we have
created a feature request ticket to add ucID's to hgLinkIn so you
could generate the correct links with only a ucID. I cannot say
when/if this feature will be implemented, but we will notify you
when/if the feature gets released.

Another method, if you knew the assembly for your ucID's and had less
than 1000 of them, is to paste your ID's into the paste identifiers
box on the Table Browser and select the "hyperlinks to Genome Browser"
output method. This method probably won't work for you since you don't
know the assembly and it is a manual method, but it may still be of
interest.

Thank you again for your inquiry and using the UCSC Genome Browser. If

you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a

publicly-accessible forum. If your question includes sensitive data,

you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/4f4a320b-1f87-492d-22d4-58f5303e4b62%40oicr.on.ca.