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How to use github repo to host manuscript supplementary info? #10

Open shellywanamaker opened 4 years ago

shellywanamaker commented 4 years ago

Continuing this slack conversation here:

can anyone link a paper that uses a github repo to host all their supplementary info? I'm having a hard time finding a good example of what this looks like, and reconciling my paper repo with the journal requirements for including additional information https://www.biomedcentral.com/getpublished/writing-resources/additional-files

kubu4: What are you having problems with? Looks like they want you to upload any/all "additional" files to their servers.Are you battling file size limits?

I have been making a clean paper repo like we normally do, but I was looking for examples of how people reference supplementary tables or figures that are in a github repo. BMC does ask for the 'additional' files to be uploaded and it seems they publish the additional info on figshare. But I see there is also an option to link mini-website which seems like could be a github repo. I just haven't found an example of this anywhere. I guess I'm wondering if people normally include supplementary tables and figures in a paper repo, and if so how they reference them in the manuscript

kubu4: Usually, you'll need to generate a DOI (can use Zenoto for GitHub repos) and reference as indicated by the journal. BMC has a section on this in their list of recommended repositories for data larger than 20MB. You could probably just go this route, for all of your additional files, regardless of size.Of course, you could always contact an editor at BMC, too.

sr320: You can cite just like any other paper / product once you have the DOI. We should have several examples!

github-actions[bot] commented 4 years ago

Thanks so much for posting your first issue in this repo!

shellywanamaker commented 4 years ago

@sr320 how would you cite a table that is in your repo?

Traditional way would be something like: "proteins identified by... (Supplementary Table X)" Would you do something like: "proteins identified by ... (ASCA_TempAffectedProteins.csv10)" where the 10 refers to my paper repo DOI listed in my reference section.

I'm just looking for some examples of how this is best done.

sr320 commented 4 years ago

Would love to hear other opinions... but I think something to strive for is https://research-compendium.science/

but to more directly address one question, in my opinion you would cite table as (Trigg et al 2019) and in the references, you would have your DOI'd the product with your Readme clearly denoting what is in the repo.

Here is some examples from years ago https://faculty.washington.edu/sr320/?p=11381

but I am hoping someone can provide a more ideal example.

laurahspencer commented 4 years ago

In my recent paper I created a traditional supplementary file (word doc), which I submitted to the journal. Additionally, I created a cleaned up github repo (which also housed a copy of the supp.), which I then published to Figshare, and which I reference in the MS.

I wouldn't consider this the gold standard, though. Main thing I'm seeing now is that I haven't yet created a readme file to describe what the files are, and how they connect to the tables and figures in the manuscript and in the supplementary file.

shellywanamaker commented 4 years ago

Jay's repo is probably the closest to what I have now. And he references the output tables from his analysis in his manuscript as "Data files generated for these analyses are available in a repository at doi:10.5061/dryad.pq827, and the analysis workflow is available at https://github.com/jldimond/Coral-CpG" rather than calling out individual tables he generated. I think this makes sense in his case since he generated similar tables for many species. In my case, where I'm trying to reference specific lists of proteins found to be significantly affected by experimental factors, I'm concerned citing these lists like Jay did may be too ambiguous for the reader. The reader would have to search through my readme and hopefully find the correct file I'm citing in my paper.

I'm really interested in what others think!

yaaminiv commented 4 years ago

@shellytrigg I did something similar to Jay with this paper repo (ex. R Scripts are available in the supplementary Github repository (Venkataraman et al. 2018).)

The reader would have to go through my READMEs to find things, but I also wonder if there's a better way to do this.

mdscheuerell commented 4 years ago

@shellytrigg: I'm late to the party, but here's a repo for a paper currently in review at J Appl Ecol.

https://github.com/mdscheuerell/steelhead_IPM

The manuscript mentions the 3 different appendices, and the data are also available on Figshare.