Citation
Slabicki, Mikolaj
Dear all,
I would like to cite properly in my paper the fact that there exist a binding cite for Transcription Factor ChIP-Seq from ENCODE with Factor Motifs in front of the gene of my interest. I found it by browsing Genome Browser. What is the correct way of citation – I might be limited to one or two citation. Should I refer to web portal or to the original paper? If yes, which one?
Thanks a lot in advance,
Mikolaj
Brian Lee
Dear Mikolaj,
Thank you for using ENCODE data and your question about how to correctly create a citation.
The ENCODE project portal has the following link about data usage, https://www.encodeproject.org/about/data-use-policy, where the policy is to cite the consortium's most recent integrative publication (PMID: 22955616; PMC: PMC3439153):http://www.ncbi.nlm.nih.gov/pubmed/22955616
When referencing the UCSC Genome Browser, please also see this citation page, http://genome.ucsc.edu/cite.html. When including a Browser screen shot in your manuscript, please reference http://genome.ucsc.edu in the caption and cite the 2002 Genome Browser paper. Please note to remove any hgsid reference in any URLs, for example, to directly reference the Transcription Factor ChIP-seq from ENCODE with Factorbook Motifs tracks you could use this URL with in your paper: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3
You may also wish to reference the Factorbook paper noted at the bottom of the above Track Description page (PMID: 23203885; PMC: PMC3531197): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531197/
Thank you again for using ENCODE data in your research and for citing the project in your paper!
All the best,
Brian Lee
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Slabicki, Mikolaj
Dear Brian,
Is it possible to include the link to “My Session” to scientific publication? Is it possible to make it active for long period of time?
Thanks a lot in advance,
Mikolaj
Matthew Speir
Thank you for your questions about sharing sessions. Yes, it is possible to include a link to a session in your publication. You can find information on sharing your sessions with others in the Session user guide, under the section titled "Sharing a Session": http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html#Share. You can also find information about how long your saved sessions persist under the "Lifespan of a Session" section: http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html#Lifespan.
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.
Matthew Speir
UCSC Genome Bioinformatics Group
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Slabicki, Mikolaj
Dear Matthew,
Thank you very much for the information. Is there a way to prolong the life spam of the session above the default settings? Otherwise it will be difficult for me to make sure that the session is active for years.
Cheers,
Mikolaj
Matthew Speir
There are a few steps you can take to preserve the life of a session or display data from a paper in the UCSC Genome Browser.
If you only want to share a specific configuration of tracks, you can save your session to a local file and then place this file in a publicly accessible URL. From that URL, users can load it using the "Restore Settings" section at the bottom of the Session management page. Or, they can build a URL to the Genome Browser that will load the session; you can find information on loading sessions via URL under "Share a web URL" here: http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html#Share. Again, any custom data saved as part of these sessions are subject to the limits described under the "Lifespan of a Session" section.
If you only have custom data that you would like to share and be able to display using the Genome Browser, you can create a track hub: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html. Similar to sessions, you can create a URL to the UCSC Genome Browser that will load a track hub. You can find information on sharing your track hub via URL in the"Displaying Track Hubs by URL and in Sessions" section here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Session.
You can also combine these two methods. You can save your current track visibilities in a session, place your data in a track hub, and then create a URL that will load both the track and session at the same time. Information for loading both of these in the same URL can be found in the "Displaying Track Hubs by URL and in Sessions" section linked above.
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.
Matthew Speir
UCSC Genome Bioinformatics Group