Papers allows you to export or import a library as a .csv(comma-separated values) file. This format will allow you to make batch edits to your information using the power and robustness of excel. Please note this feature is only available in the desktop app.
What is a CSV file?
A CSV file has a fairly simple structure. It’s a list of data separated by commas. For example, let’s say you have a few contacts in a contact manager, and you export them as a CSV file. You’d get a file containing text like this:
Name,Email,Phone Number,Address
Bob Smith,bob@example.com,123-456-7890,123 Fake Street
Mike Jones,mike@example.com,098-765-4321,321 Fake Avenue
That’s all a CSV file really is. They can be more complicated than that and can contain thousands of lines, more entries on each line, or long strings of text. Some CSV files may not even have the headers at the top, and some may use quotation marks to surround each bit of data, but that’s the basic format.
What kind of CSV's can I import?
CSV's come in many different shapes and sizes so not all of them will work with Papers but we have been testing this to make sure it's as seamless as possible. Most CSV's should work if they have at least one of the following fields is required when you import a CSV:
| Title | The title of the reference you are importing |
| DOI | DOI of reference |
| PMID | PMID of reference |
| PMCID | PMCID of the reference |
| ArXiv | ArXiv id of the reference |
Only one of the above fields is required. This allows you to import a list full of DOI's if you want or import some titles of references. Note that if there is no identifying identifier (DOI, PMID, etc.) we won't be able to fill in any more information for you. For instance, the following CSV will allow you to import these DOI's and get information on them. Also if any of the articles are deemed open access we will import the PDF for you automatically (The last DOI in this list). You can get a copy of this file at the bottom of the page (DOIExample.csv).
doi
10.1038/s41409-021-01219-8
10.1038/s41409-021-01237-6
10.1038/s41409-021-01248-3
10.1038/s41409-021-01217-w
10.1038/s41409-020-01198-2
10.1038/s41368-021-00111-x
Another common CSV you might want to import is a PubMed search result. You can find this option under "Save" and by selecting the format of CSV. Results will be formatted like:
PMID,Title,Authors,Citation,First Author,Journal/Book,Publication Year,Create Date,PMCID,NIHMS ID,DOI
"28580133","The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates","Peat JR, Ortega-Recalde O, Kardailsky O, Hore TA.","F1000Res. 2017 Apr 20;6:526. doi: 10.12688/f1000research.11281.1. eCollection 2017.","Peat JR","F1000Res","2017","2017/06/06","PMC5437953","","10.12688/f1000research.11281.1"
"31164478","Transcriptional activation of elephant shark mineralocorticoid receptor by corticosteroids, progesterone, and spironolactone","Katsu Y, Kohno S, Oka K, Lin X, Otake S, Pillai NE, Takagi W, Hyodo S, Venkatesh B, Baker ME.","Sci Signal. 2019 Jun 4;12(584):eaar2668. doi: 10.1126/scisignal.aar2668.","Katsu Y","Sci Signal","2019","2019/06/06","","","10.1126/scisignal.aar2668"
"30468718","Elephant shark melanocortin receptors: Novel interactions with MRAP1 and implication for the HPI axis","Barney E, Dores MR, McAvoy D, Davis P, Racareanu RC, Iki A, Hyodo S, Dores RM.","Gen Comp Endocrinol. 2019 Feb 1;272:42-51. doi: 10.1016/j.ygcen.2018.11.009. Epub 2018 Nov 20.","Barney E","Gen Comp Endocrinol","2019","2018/11/24","","","10.1016/j.ygcen.2018.11.009"
"33214712","Author Correction: Elephant shark genome provides unique insights into gnathostome evolution","Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC.","Nature. 2020 Dec;588(7837):E15. doi: 10.1038/s41586-020-2967-4.","Venkatesh B","Nature","2020","2020/11/20","","","10.1038/s41586-020-2967-4"
"30782839","White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability","Marra NJ, Stanhope MJ, Jue NK, Wang M, Sun Q, Pavinski Bitar P, Richards VP, Komissarov A, Rayko M, Kliver S, Stanhope BJ, Winkler C, O'Brien SJ, Antunes A, Jorgensen S, Shivji MS.","Proc Natl Acad Sci U S A. 2019 Mar 5;116(10):4446-4455. doi: 10.1073/pnas.1819778116. Epub 2019 Feb 19.","Marra NJ","Proc Natl Acad Sci U S A","2019","2019/02/21","PMC6410855","","10.1073/pnas.1819778116"
"31112680","Elephantfish","Rizzari JR, Finucci B.","Curr Biol. 2019 May 20;29(10):R352-R353. doi: 10.1016/j.cub.2019.03.021.","Rizzari JR","Curr Biol","2019","2019/05/22","","","10.1016/j.cub.2019.03.021"
"18319338","Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster","Yu WP, Rajasegaran V, Yew K, Loh WL, Tay BH, Amemiya CT, Brenner S, Venkatesh B.","Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3819-24. doi: 10.1073/pnas.0800398105. Epub 2008 Mar 4.","Yu WP","Proc Natl Acad Sci U S A","2008","2008/03/06","PMC2268768","","10.1073/pnas.0800398105"
"19805301","Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes","Ravi V, Lam K, Tay BH, Tay A, Brenner S, Venkatesh B.","Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16327-32. doi: 10.1073/pnas.0907914106. Epub 2009 Sep 3.","Ravi V","Proc Natl Acad Sci U S A","2009","2009/10/07","PMC2752591","","10.1073/pnas.0907914106"
"24402279","Elephant shark genome provides unique insights into gnathostome evolution","Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC.","Nature. 2014 Jan 9;505(7482):174-9. doi: 10.1038/nature12826.","Venkatesh B","Nature","2014","2014/01/10","PMC3964593","NIHMS559768","10.1038/nature12826"
"21208605","The early origin of melanocortin receptors, agouti-related peptide, agouti signalling peptide, and melanocortin receptor-accessory proteins, with emphasis on pufferfishes, elephant shark, lampreys, and amphioxus","Västermark A, Schiöth HB.","Eur J Pharmacol. 2011 Jun 11;660(1):61-9. doi: 10.1016/j.ejphar.2010.10.106. Epub 2011 Jan 3.","Västermark A","Eur J Pharmacol","2011","2011/01/07","","","10.1016/j.ejphar.2010.10.106"
These have a lot more information and will import automatically into your library. To get an example of this file see below(csv-ElephantSh-set.csv)
What kind of fields does the CSV support?
Any of the fields that are part of Advanced Search Syntax article can be imported. The length of these items can only be 256 characters long. Importing other fields will work but we currently hide these fields in the app. We will be adding a way to visualize these fields in the future.
Can I import a TSV(Or another file that has different delimiters)?
Currently, we don't support TSV but the easiest way to fix this is to open the TSV in a program like Excel and then save it as a CSV file. This will allow you to use other file formats that use different delimiters to separate fields. If you can't import the file in excel you can always use the Data tab and import from file or database:
Exporting CSV from Papers
To export from Papers all you need to do is hit the gear next to a library and click export as "Comma-separated Values". This will open up a dialog box that allows you to save the CSV to your computer and default to the library's name. Once saved you can edit the file in excel or any other program to edit the CSV. You can then import this file back into the app to bulk update any of the items you had updated.
