41c63e4b0795abf47b9fcbaf7554da7f50741ad5 lrnassar Fri Jul 19 16:29:55 2024 -0700 Sprucing up the cite.html page with general improvements and organization, refs #31996 diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index c6a0913..9f0359e 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,203 +1,212 @@

Citing the UCSC Browser in a Publication or Web Page

-You are free to use all graphics produced by this website in your published work or on other websites, there -is no need to contact us to request permission, see the license page for details. -

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-But the UCSC Genome Browser is exclusively funded by NIH and if research articles do -not cite or mention us, we cannot report the citations and it is harder for NIH to justify funding one of the -few stable resources in genomics that you can rely on. -

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-At the moment, the most recent UCSC Genome Browser paper has the PMID 36420891, - DOI 10.1093/nar/gkac1072. In addition, you can include a reference to the Genome -Browser website in your manuscript: http://genome.ucsc.edu or mention in the text that you used the "UCSC Genome Browser". -To cite just one of our computational tools, see the reference section below. -

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While doing this, you can check if the genome coordinates in your paper are -clear to the readers and if you specified the genome assembly that you used. -One cannot mention the genome assembly too often. Computational -biologists will appreciate if your supplemental files with genome annotations -include the genome assembly identifier directly in the file name. We keep these -identifiers short, currently they are "hg19" and "hg38" for the most common -human assemblies. In a similar vein, references to nucleotides ideally have the -full chromosome position in your publication text somewhere or in a -supplemental table, and not only the position on the transcript and or coding -sequence, as transcript models can change a lot. -

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To make this even easier, when refering to a gene or genomic location, you can -use the menu "My Data > My Sessions", to -generate a short, stable link to your current genome browser view for your -publication. In this way, readers can jump from your publication to this -genome location and get their view configured for your particular message. -You can even add your own annotations to the UCSC Genome Browser, either as -very simple text labels, by pasting a line like "chr1 1 1000 my_annotation" -into the box found under "My Data > Custom - Tracks" or by loading all your genomics results into the browser with -Track Hubs. -

+You are free to use all graphics produced by this website in your published work or on other websites, +there is no need to contact us to request permission. See the license page for details.

+ +

How to cite the UCSC Genome Browser

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+The UCSC Genome Browser is exclusively funded by the NIH, please consider citing us properly +so that we may report usage and continue to develop this resource.

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What manuscript to cite?

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+Please cite our latest paper, currently PMID 36420891, +DOI 10.1093/nar/gkac1072. In addition, you can reference the Genome Browser website +in your manuscript: http://genome.ucsc.edu or +mention in the text that you used the "UCSC Genome Browser". To cite one of our +computational tools, see the reference section below.

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General best practices for publications

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+The following are recommendations to improve communication in your +scientific manuscript and ensure readers in 10 years can still find the +DNA sequence that you analyzed. This requires mention of the assembly, +chromosome position, any transcripts, and ideally also a +Genome Browser stable link:

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  1. Assembly: Provide a clear mention of which genome assembly you are working with, e.g. +"hg19" or "hg38". It is often helpful to place the assembly name directly on +any supplemental file names if they contain annotations. E.g. "promoters.hg38.bed".
    2. +
  2. Chromosome Position: References to nucleotides should have full chromosome positions in the +publication text or a supplemental table, whenever possible. Including only the position on the +transcript or coding sequence can be confusing later as transcript models change. +E.g. mention "NC_000023.11:g.32389644G>A", in addition to the transcript-based +description "NM_004006.2:c.4375C>T". Or, in the manuscript, you can add the chromosome +location in brackets, such as "(hg38,chr11:32389644)", when nucleotide 4375 of +NM_004006.2 is discussed.
    3. +
  3. Transcript: Transcripts change. Always mention the accession of a transcript, not only the gene name. E.g "NM_004006.2", not just +"the longest transcript of the gene DMD". Gene symbols and transcripts change over time, so any sort of accession is helpful. +
  4. Stable links: A UCSC Genome Browser link is a great way to +share results or regions of +interest in a way readers and reviewers can explore. It includes the assembly, position, all transcripts, +any tracks visible, all filter settings that you made and any other settings in the browser. +If you would like to include +a link, do not copy the URL directly from the address bar, the one with +"hgsid=xxx". These links are long and expire after a few days. +Instead, use the menu option "My Data > My +Sessions", to generate a short, +stable link to your current genome browser view. For more information on how to add your +own annotations to share this way see Custom Tracks +and Track Hubs.
    5. +

Genome Browser software and website references

Genome Browser screenshots:
Journal-quality screenshots of the Genome Browser can be produced by using the View -> PDF utility in the top navigation bar from the tracks page. When including a screenshot in your manuscript, reference http://genome.ucsc.edu in the caption and cite the most recent Genome Browser paper in the manuscript. As mentioned above, we recommend including a My Data > My Sesssion URL of your screenshot to allow readers to interact with your data and get more information.

Most recent UCSC Genome Browser publication:
Nassar et al. The UCSC Genome Browser database: 2023 update. Nucleic Acids Research 2023 PMID: 36420891, DOI: 10.1093/nar/gkac1072

Original UCSC Genome Browser publication:
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.

All present and past UCSC Genome Browser updates sorted by date can be shown with this PubMed search.

BLAT:
Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

LiftOver:
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8.

UCSC Table Browser:
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.

UCSC Data Integrator and Variant Annotation Integrator:
Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D et al. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 May 1;32(9):1430-2.

BigWig and BigBed tools:
Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics. 2010 Sep 1;26(17):2204-7.

RESTful API:
Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC et al. UCSC Genome Browser enters 20th year. Nucleic Acids Res. 2020 Jan 8;48(D1):D756-D761.

Track Data Hubs:
Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13.

Genome Browser in a Box (GBiB):
Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics. 2015 Mar 1;31(5):764-6.

UCSC Gene Sorter:
Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 2005 May;15(5):737-41.

UCSC SARS-CoV-2 Genome Browser:
Fernandes JD, Hinrichs AS, Clawson H, et al. The UCSC SARS-CoV-2 Genome Browser. Nat Genet. 2020 Sept 9; 52:991-998.

GenArk: UCSC Genome Archive:
Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM et al. GenArk: Towards a million UCSC Genome Browsers. Res Sq. 2023 Apr 3;.

Other genome assemblies:
Manuscripts that include the use of Genome Browser assembly data from organisms other than human should, e.g. one of the thousands of GenArk assemblies that we provide, should cite the relevant sequencing paper. Usually this information can be found on the assembly description that appears when the genome is selected on our gateway page or on the NCBI GenBank BioProject page of the assembly.