Papers allows you to import or export a library as a .csv (comma-separated values) file. This format will allow you to make batch edits to your information using a spreadsheet (with software such as Excel).
What is a CSV file?
A CSV file has a fairly simple structure. It’s a list of data separated by commas. For example, if you have a few contacts in a contact manager and you export them as a CSV file, you would get a file that looks like this:
Name,Email,Phone Number,Address
Bob Smith,[email protected],123-456-7890,123 Fake Street
Mike Jones,[email protected],098-765-4321,321 Fake Avenue
Essentially, this is all a CSV file is. They can be far more complicated with thousands of lines, a large number of entries for each line and/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 however this is the basic format.
What kind of CSV's can I import?
There are many different types of CSV files and while most should work with Papers, there will be some that may not. However, most CSV's should work if they have at least one of the following fields that are 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 or some titles of references. Note that if there is no identifier (such as DOI, PMID, etc.) we won't be able to fill in any more metadata information for you (as the app requires identifiers to search for and locate metadata information of a reference).
For instance, the following CSV will allow you to import these DOIs and get information on them. If any of the articles are open access ones the app will automatically import the PDFs for them (from this particular example, the last article is an open access one). 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 changing the format to 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 file support?
Any of the fields that are part of our 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.
