Tasks to do for completing project

lwjohnst86 commented 2 years ago

Whatever task we work on, we should follow scoping review guidelines (e.g. #10). Everything is at this point in rough draft stage, but we should be working as much as possible to fill out the doc/review.md and doc/protocol.md file (and other supporting documents).

Team-wide general collaboration tasks

[x] Contributing document to guide how we will contribute to the work
[ ] Workflow and process strategy for working collaboratively on the search strategy, briefly in the Methods section of doc/protocol.md and more detailed in the Methods of the doc/papers.md and in the CONTRIBUTING.md document
[x] Update README with more relevant information about the project
[x] Fill in the GitHub repo "description" details

Protocol tasks (in `doc/protocol.md`)

(Inspired from manual)

[x] Draft of title
[x] Draft of objectives/research questions/aims (see #11, #10)
[x] Draft of overview/introduction, with basic terms and definitions (e.g. what is open, what is science)
[x] Draft of inclusion criteria and exclusion criteria (in Methods)
[x] Draft of search strategy in Methods (search terms used, databases used)
- [x] Including how data is extracted and saved (which folder, file naming, etc)
[x] Draft of post-search source selection, like how we decided to keep sources for further inclusion (in Methods)
[x] Draft of data extraction details in Methods
- [x] Including how we decide who does it, how the data is saved (which folder, file naming, etc)
[x] Draft of how we will "analyze"/"synthesize" the data
- [x] Draft "charting form" (for data extraction)
[x] Review protocol by at least two people
[x] Upload protocol to OSF

Code and data extracted from sources

[x] #32

Paper (in `doc/paper.md`)

[ ] #14

(More will be added here as we go on).

danielibsen commented 2 years ago

Hi @lwjohnst86 @hchats @MarioGuCBMR I have made some edits to the protocol document including: updated aims, suggested search terms and included a definition of open collaboration systems.

Note that I found some paper last week that may be of interest when building the search and looking at similar project here: https://github.com/science-collective/scoping-review/issues/10

hchats commented 2 years ago

Hi @lwjohnst86 @hchats @MarioGuCBMR I have made some edits to the protocol document including: updated aims, suggested search terms and included a definition of open collaboration systems.

Note that I found some paper last week that may be of interest when building the search and looking at similar project here: #10

Thanks, @danielibsen! I have added some further information regarding how, exactly, we would go about the database searches and hand searches. I have also proposed some details for how we would analyze the data. I have noted some TODO points throughout, though I'm wondering if I should create separate issues for them on GitHub (@lwjohnst86).

I am now going to move on to trialing some searches (e.g., in EMBASE/MEDLINE) to see what sorts of results we are likely to find.

MarioGuCBMR commented 2 years ago

Hi all, I started doing some test queries, focus on the book part since we did not agree on anything specific. I opened an issue regarding the book selection specifically, since the search might be a bit different.

Finally, @lwjohnst86, I have been doing some tests with code for rscopus and easyPubMed. How are we approaching test code? I will open another issue to discuss how to organize testing code and examples.

danielibsen commented 2 years ago

05-08-2022:

1) I started working with easypubmed but did retrieve the same number of papers using the same search in R and on pubmed website.

=> I will continue looking into this, try to write the code so we can extract a dataset with all the articles from pubmed and be able to merge this with the other databases.

2) I tested out the search on Pubmed and looking at the first 250 papers there was very few relevant ones. A caveat is that pubmed may not be the most relevant database for this topic.

=> I will test whether we could limit some of the terms to have to be present in the title. Hopefully we can have our final search strategy in place soon and submit the protocol.

hchats commented 2 years ago

05-08-2022:

I spent most of the session refining the protocol and getting a better sense of what our outputs may look like. I think that we are almost ready to finalize the protocol, pending the search strategy. I then spent some time playing around with easyPubMed, rscopus, and medrxivr. I didn't get very far with any of them, but I will come back to this next week.

science-collective / scoping-review