Assigning papers to more than one group (aliases)

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vinschger
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Assigning papers to more than one group (aliases)

Post by vinschger »

Wouldn't it be great if bookends would allow to assign papers to more than one (static) group or instead of duplicates create aliases? as far as I have understood, it's not possible to assign one publication to more than one group. Let say if I am researching for a new project, I do a pubmed search within bookends and download all relevant papers for this topic into bookends. Some results might be existing already in my bookends library (in another group) and might be yellow in the bookends pubmed search. If I do not download them to the new group, I will miss them when going through the group that contains all relevant papers for this topic, if I i download them, duplicates will be generated, which will be a problem when citing them, as during floating citation process it's not clear in which group a duplicate is, so I might select the wrong. It would be great that while importing it would be possible that already existing papers are not downloaded again as a duplicate, but that the already existing item is assigned to this additional group. Do you think this might be useful? Or do you have another workflow to solve this?
Jon
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Re: Assigning papers to more than one group (aliases)

Post by Jon »

I'm not sure exactly what you want that doesn't already exist. You can have one reference in as many static groups as you want -- it won't be duplicated in the database when you add it to another group. Furthermore, if you're using Online Search in Bookends, as you are, and you see you already have a reference (it's yellow), don't download it again -- right-click on the yellow reference and Bookends will take you to the corresponding reference in your library, where you can assign it to any group you want.

Jon
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vinschger
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Re: Assigning papers to more than one group (aliases)

Post by vinschger »

Thanks, Jonathan,Indeed, I didn't know that it's possible to have a reference in more than one static group. Would it be possible when doing a pubmed search and dragging all selected search results into a group, that existing (yellow) references will not be added as duplicates but just assigned to the group, where they are imported to? so it would not be necessary to go to each (already) existing reference manually and assign it to the wanted group?
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Re: Assigning papers to more than one group (aliases)

Post by Jon »

That's a very high level of intrusion (meaning Bookends deciding what you want and doing it behind your back). I'll offer another, generalizable, solution.

Open the PubMed filter and click on the Misc tab. There you can tell Bookends to add text you want to a particular field. Let's say you tell Bookends to add words that describe the project, such as "CD45 paper" to User 20.

In your library create a smart group that searches for references where User 20 contains "CD45 paper".

Now all papers you import for this project will be dynamically collected for you.

You can change the text in Misc when you want to work on another project, or turn off this feature and assign nothing, whenever you want.

Jon
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vinschger
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Re: Assigning papers to more than one group (aliases)

Post by vinschger »

Would this really be an intrusion if user select files to import to a group in a bookends pubmed search, and bookends adds the already existing item to the selected group instead of creating a duplicate? I do not think that any user wants to create on purpose a duplicate by importing a reference that already exists in the library. The program could also ask for the first time when importing already existing references in a pubmed search "You are importing some references that already exist in your library. Do you want to create them a) as duplicates in the selected group b) assign the already existing reference to the selected group without creating duplicates").

However, I am open for alternative ways or other workflows. I tried to reproduce your recommendation. MacOS Bookends > Online Search: Pubmed is selected. I search for search terms. Some are already in my library (yellow), some not. There is no no Misc Tab in the search window. I assume I have not understood your approach. Could you provide a screenshot.

Maybe I was not able to explain my situation:
I do a pubmed search for "searchterm1" and "searchterm2". I get 100 results, about 30 of them exist already in other static groups1, groups2 and groups3 of my library. I select all 100 items and want to add them to the new_project group. If I do so, I will have 30 duplicates in my library. If I cite them with floating citation, I risk to cite not always the same reference of a duplicate. Therefore I am looking for a way to import all 100 references to the new_project, without creating duplicates and without deleting the already existing references, just by assigning the existing references to the newproject group. Doing this manually for each "yellow" (=already existing) reference is quite time consuming. Therefore I am really interested in your suggested approach.

Thanks so much for your help in advance! I would really appreciate to be able to reproduce your suggested workflow.
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Re: Assigning papers to more than one group (aliases)

Post by Jon »

This Misc tab is in the import filter PubMed.fltr. You open it in the Import Filter Manager.

With the workflow I suggested all references downloaded would automatically populated the smart group you created. Once set up it's transparent to you.

I'm not keen on your suggestion. But what I think would work just as well is this -- in Online Search, right-click and Select References You Have (which will be the ones in yellow), then right-click and select "Show In Library". Now only the first one will be selected and shown, but I could have Bookends select all of them in the library. Finally, in the library, drag and drop them into the static group you want (all will be dragged at once), or use the menu or right-click contextual menu to add them to an existing static group. So the whole process would be two clicks and a drag.

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vinschger
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Re: Assigning papers to more than one group (aliases)

Post by vinschger »

interesting approach. but if I have 300 results in a search, with some of them already in the database, then I would have to select each yellow one manually? this would be really a lot of work. or selecting all (yellow and notyellow ones) and right-click "import sll to selected group without creating duplicates". I am just brainstorming...
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Re: Assigning papers to more than one group (aliases)

Post by Jon »

Please see the previous post --
in Online Search, right-click and Select References You Have (which will be the ones in yellow)
It's a single action.

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vinschger
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Re: Assigning papers to more than one group (aliases)

Post by vinschger »

would this also work, if the yellow references are in different groups of the library? so when I look the yellow ones up in the library, although only the first one is shown, I could move all of them to my new project group? could work for me, but maybe is not really intuitive for other users (?) for me drag and drop from the search window of all references to a group - or by clicking import - is the most intuitive way. bookends could then just ask "How do you want to handle references, that already exist in your library?" and then allow to answer, if duplicates should be created (if there are really users that want such a behaviour, difficult to believe for me); option2: existing references would just be assigned to the group of import option3: cancel". But I am still open for your solution, as this might at least allow me to have a workflow that avoids duplicates and allows me to have all references in the new project group. thanks so much for listening and for thinking about to handle this.I absolutely understand, that different users have different workflows.
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Re: Assigning papers to more than one group (aliases)

Post by Jon »

I've already told you what I'm going to do, there is nothing more to discuss.

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vinschger
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Re: Assigning papers to more than one group (aliases)

Post by vinschger »

Okay. No problem. I had an open question regarding your suggested workflow ("would this also work, if the yellow references are in different groups of the library?). Furthermore, as you have written "But what I think would work" and "I could have bookends select" it was not clear for me that you have already made a final decision. I had the (wrong) impression that you suggested a potential solution/feature to improve the import of already existing references, therefore I clearly stated that your suggested workflow would already be fine for me, but might not be the most intuitive workflow for others. If you prefer to stop the discussion here, this is fine for me. I appreciate that you have been listening and also making the final decision for potential future features.
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