CSV export

[ChristianGerloff]

Hey @LeonDLotter & @kashyapm94 , To enable a feasible integration with rayyan, we want to add a csv export. :smiley: Therefore, we can utilize the rayyan example csv. The column Notes contains several rayyan specific fields. Before we integrate all the fields, I would like to ask you for your thoughts on that. What do you think we really need, what can we leave out?

suggestion

column	comment
key	required --> id
authors	required
journal	for preprints it corresponds to the db see also publication obj
issn	publication obj
volume	publication obj
issue	publication obj
pages	publication obj -- check! @ChristianGerloff
day	publication_date
month	publication_date
year	publication_date
publisher	publication obj
pmc_id	check @ChristianGerloff
pubmed_id	check @ChristianGerloff
url
abstract	@LeonDLotter required?
notes	see sec. table

notes field	comment
Accession Number	no ?
Language	available? required?
Entry Date	?
Revision Date	?
Publication Type	publication obj
Journal Subset:	publication.category
Country:	?
Double Blind Peer Reviewed; Editorial Board Reviewed; Expert Peer Reviewed; Peer Reviewed	-
Grant Information	-
Grant Information	-
RAYYAN-INCLUSION: {"Ifah"=>"Included"}	possible, could contain result form set-you-free
RAYYAN-LABELS	? @LeonDLotter

Example

key	title	authors	journal	issn	volume	issue	pages	day	month	year	publisher	pmc_id	pubmed_id	url	abstract	notes
1	what a paper	really important senior author, f.	Fancy Journal		25	6	519-522		6	2030	Taylor and Francis		24215475		Please read this paper its awesome	Accession Number: 109849757. Language: French. Entry Date: 20080815. Revision Date: 20150923. Publication Type: Journal Article; research; tables/charts. Journal Subset: Biomedical; Blind Peer Reviewed; Canada; Double Blind Peer Reviewed; Editorial Board Reviewed; Expert Peer Reviewed; Peer Reviewed. Grant Information: Societe Alzheimer du Canada. NLM UID: 8406631. RAYYAN-INCLUSION: {"Ifah"=>"Included"} RAYYAN-INCLUSION: {"Fadhil"=>"Excluded"} | RAYYAN-LABELS: somelabel

[LeonDLotter]

Hi @ChristianGerloff, nice idea! Regarding your tags:

1. I think the abstract is actually one of the most important things when it comes to integration into Rayyan as the initial screening should usually be based on the abstract. Otherwise, you would have to use the DOI/URL/pubmed-id (whatever is available) to get it. So I think the abstract would best be included.

2. I am not sure, if I understand the "RAYYAN-INCLUSION" and "-LABEL" categories correctly. If I do, these are the user-defined labels and include/exclude/maybe decisions which are printed into the csv when it is exported from Rayyan after the screening process in Rayyan is completed? This would mean that we do not need to define content for the "INCLUSION" and "LABEL" variables if it is about creating a csv for import into Rayyan.

However, before, we also discussed the possibility to include a function that collects all the reference lists of a given subset of papers (i.e., papes, screened positively in Rayyan) and uses this a input for a "second-level" literature search. To generate a list of this subset of papers, one would either have to export only the references from Rayyan that are labelled as "include" to csv, or export all papers to csv with the labels included in the "RAYYAN-LABEL" column and select the included references afterwards. In the second case, the "LABEL" variable would make sense. However, I think the first way is actually possible - so no need for that.

Is there possibly another use for the RAYYAN-NOTES variable that I am not aware of? Otherwise I actually think one could drop it entirely.

ADDITION: Would it be possibly to include the DOI (or URL if DOI not available) in the "URL" field? This would provide direct access to a potential source of the full text, figures, etc during the Rayyan Screening process. Also, is there an actual need for the Pubmed and PMC IDs? Maybe for a function, as referred to above, to search each papers reference list as pubmed stores a full list of references with each paper? If the latter is not needed, we could maybe also drop pubmed/pmc IDs.

[ChristianGerloff]

Hey @LeonDLotter, thank you - yes, let's drop the "RAYYAN" fields for now. We don't really need the Pubmed and PMC IDs, but it's a default from rayyan, but I think it's fine if the field is empty. The notes will include the doi/url. For cross-refs, I would suggest to open a new issue.