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ClinGen / clincoded

This GCI/VCI 1.0 platform has now been retired, and replaced with our new 2.0 platform:
https://github.com/ClinGen/gene-and-variant-curation-tools/issues
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Crediting data provenance (attribution/citation) in the VCI (e.g. myvariant.info and VEP) #800

Closed wrightmw closed 8 years ago

wrightmw commented 8 years ago

We need to think about how to credit resources we are using to download data into the variant curation interface.

Eventually we could create a source data page, until then I would suggest adding a link the tables, e.g. in the basic information tab for transcript tables put 'downloaded from VEP' and have a direct link the the VEP homepage, and in the 'Other predictors' tab have 'downloaded from myvariant.info' and a link to the myvariant.info homepage

@selinad Do you have a preferred way of crediting sources?

selinad commented 8 years ago

Hi @wrightmw. Thanks for making this ticket.

@kilodalton may have a preferred way, so I will let her weigh in.

My thought: how about at the bottom of the table (and outside of the table) - a text note in italics with the credit and link to the resource. I prefer not to put it in the table itself.

wrightmw commented 8 years ago

Matt to find out from VEP, how they want to be credited. @kilodalton to find out from myvariant.info how they want to be credited

kilodalton commented 8 years ago

How to cite MyVariant.info and MyGene.info from the info in the links below: http://myvariant.info/citation/ http://mygene.info/citation/

MyVariant.info

To reference MyVariant.info in your work, please cite this publication and also the "http://myvariant.info" URL:

Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C (2016) High-performance web services for querying gene and variant annotation. Genome Biology 17(1):1-7

MyGene.info

To reference MyGene.info in your work, please cite the following publications and also the "http://mygene.info" URL:

Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C (2016) High-performance web services for querying gene and variant annotation. Genome Biology 17(1):1-7 [link]

Wu C, MacLeod I, Su AI (2013) BioGPS and MyGene.info: organizing online, gene-centric information. Nucl. Acids Res. 41(D1): D561-D565. [link]

(see page for linkout URLs)

wrightmw commented 8 years ago

CFTR: A. Rychkova, M.C. Buu, C. Scharfe, M. Lefterova, J. Odegaard, I. Schrijver, C. Milla, C.D. Bustamante, "Developing gene-specific meta-predictor of variant pathogenicity" (in preparation) Anna will send actual link to the paper as soon as she has it.

VEP: The Ensembl Variant Effect Predictor. McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PMID: 27268795

wrightmw commented 8 years ago

Basic Info Tab:

'VEP' icon - These data in this table were retrieved using: The Ensembl Variant Effect Predictor (www.ensembl.org/Homo_sapiens/Tools/VEP) McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PMID: 27268795

wrightmw commented 8 years ago

Population Tab:

-put 'MVi' icon after 'ExAC' -put 'MVi' icon after 'Exome Sequencing Project (ESP)' -at bottom of page put: 'MVi' icon - These data in this table were retrieved using: MyVariant.info (http://myvariant.info) Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C (2016) High-performance web services for querying gene and variant annotation. Genome Biology 17(1):1-7

wrightmw commented 8 years ago

Predictors Tab:

-put 'MVi' icon after 'Other Predictors' -put 'MVi' icon after 'Conservation Analysis' -at bottom of page put: 'MVi' icon - These data in this table were retrieved using: MyVariant.info (http://myvariant.info) Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C (2016) High-performance web services for querying gene and variant annotation. Genome Biology 17(1):1-7

jimmyzhen commented 8 years ago

@wrightmw How does this look?

image

wrightmw commented 8 years ago

@jimmyzhen Great... I like the icons. Perhaps the text in the footer could be continuous, than than split into lines: 'MVi' icon - These data in this table were retrieved using: MyVariant.info (http://myvariant.info) Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C (2016) High-performance web services for querying gene and variant annotation. Genome Biology 17(1):1-7

wrightmw commented 8 years ago

'VEP' icon - These data in this table were retrieved using: The Ensembl Variant Effect Predictor (www.ensembl.org/Homo_sapiens/Tools/VEP); McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PMID: 27268795

jimmyzhen commented 8 years ago

@wrightmw Like this?

image

wrightmw commented 8 years ago

@selinad and I just debated the 'These data' (British English) to 'The data...' (American English)... since ClinGen is mostly American it seems fitting to change to 'The data...'. Thanks @jimmyzhen ... Looks great! 😸

jimmyzhen commented 8 years ago

No problem!

jimmyzhen commented 8 years ago

@wrightmw Please test this one: https://800-jz-data-credit-436b7fa-jzhen.demo.clinicalgenome.org

Thank you!

wrightmw commented 8 years ago

@jimmyzhen These look great to me, good work! The only changes I would make are omissions on my part, I think there should be links out to the articles and they should be the same set for both.

For VEP: PMID: 27268795 PMCID: PMC4893825 DOI: 10.1186/s13059-016-0974-4 http://www.ncbi.nlm.nih.gov/pubmed/27268795 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893825/ https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4

For MVI: PMID: 27154141 PMCID: PMC4858870 DOI: 10.1186/s13059-016-0953-9 http://www.ncbi.nlm.nih.gov/pubmed/27154141 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858870/ https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0953-9

wrightmw commented 8 years ago

@jimmyzhen MVI icon will need to be changed to MyVariant

wrightmw commented 8 years ago

VEP have now sent us an icon. Creating separate ticket for R7alpha3 to see whether their icon can be adapted for use in the interface, or not: see #906

wrightmw commented 8 years ago

Looks good to me

selinad commented 8 years ago

@wrightmw - sorry to just be seeing this but I noticed when there is no data in a table, it may look a bit like the resource is not doing its job since the icon is still there.

Would it make sense to say "When available, the data in this table..." or...."When available, data in this table..." ?

wrightmw commented 8 years ago

@selinad Oh, I see what you mean. Yes, I agree to the re-wording. I marginally prefer "When available, data in this table..." ...

selinad commented 8 years ago

that works - we owe you one ;-)

jimmyzhen commented 8 years ago

@selinad, @wrightmw, I have included this text change in #903.

selinad commented 8 years ago

👍 @jimmyzhen

kilodalton commented 8 years ago

Included in last release (R7alpha2). Nice job and thanks for your hard work.