Convert RIS or NBIB or JSON to bibtex?

Question

This article is not in Google Scholar, and they offer citations in RIS, NBIB, and JSON.

So the big question is, how can I convert this to bibtex?

Here is how it looks in JSON:

{"source":"PMC","accessed":{"date-parts":[[2015,9,29]]},"id":"aiid:181008","title":"The Genome Sequence of <i>Yersinia pestis</i> Bacteriophage φA1122 Reveals an Intimate History with the Coliphage T3 and T7 Genomes","author":[{"family":"Garcia","given":"Emilio"},{"family":"Elliott","given":"Jeffrey M."},{"family":"Ramanculov","given":"Erlan"},{"family":"Chain","given":"Patrick S. G."},{"family":"Chu","given":"May C."},{"family":"Molineux","given":"Ian J."}],"container-title-short":"J Bacteriol","container-title":"Journal of Bacteriology","publisher":"American Society for Microbiology","ISSN":"0021-9193","issued":{"date-parts":[[2003,9]]},"page":"5248-5262","volume":"185","issue":"17","PMID":"12923098","PMCID":"PMC181008","DOI":"10.1128/JB.185.17.5248-5262.2003","type":"article-journal"}

or in pretty print:

{
"DOI": "10.1128/JB.185.17.5248-5262.2003",
"ISSN": "0021-9193",
"PMCID": "PMC181008",
"PMID": "12923098",
"accessed": {
    "date-parts": [
        [
            2015,
            9,
            29
        ]
    ]
},
"author": [
    {
        "family": "Garcia",
        "given": "Emilio"
    },
    {
        "family": "Elliott",
        "given": "Jeffrey M."
    },
    {
        "family": "Ramanculov",
        "given": "Erlan"
    },
    {
        "family": "Chain",
        "given": "Patrick S. G."
    },
    {
        "family": "Chu",
        "given": "May C."
    },
    {
        "family": "Molineux",
        "given": "Ian J."
    }
],
"container-title": "Journal of Bacteriology",
"container-title-short": "J Bacteriol",
"id": "aiid:181008",
"issue": "17",
"issued": {
    "date-parts": [
        [
            2003,
            9
        ]
    ]
},
"page": "5248-5262",
"publisher": "American Society for Microbiology",
"source": "PMC",
"title": "The Genome Sequence of <i>Yersinia pestis</i> Bacteriophage \u03c6A1122 Reveals an Intimate History with the Coliphage T3 and T7 Genomes",
"type": "article-journal",
"volume": "185"
}

If it isn't in Google Scholar, why does it matter what they offer? Presumably 'they` does not refer to 'Google Scholar', but that's the obvious interpretation. — cfr, Jul 06 '17 at 01:25
Keep in mind that these software-generated data sometimes have their pitfalls https://tex.stackexchange.com/q/386053/35864 — moewe, Jul 18 '20 at 15:49

score 18 · Answer 1 · answered Sep 30 '15 at 00:27

18

To convert from RIS to BibTeX, I use this as part of a shell script:

ris2xml <filename>.ris | xml2bib -b > <filename>.bib

RIS is therefore my second choice of download format and quite handy since several places don't provide BibTeX but do provide RIS export.

Both ris2xml and xml2bib are provided by bibutils.

If you use a GNU/Linux distro, check for a package before resorting to a direct CTAN download as that will be easier to maintain in most cases.

For Arch Linux, there's a PKGBUILD in AUR, for example, and I think Fedora provides a package, as well.

answered Sep 30 '15 at 00:27

cfr

198,882

'If you use a frequently-updated GNU/Linux distro' -- if you run on Ubuntu LTS versions or some other stable builds everything TeX-related get hopelessly out of date. – Chris H Sep 30 '15 at 08:24
@ChrisH Well, LTS is aimed at stability. Besides, bibutils has not changed in quite some time, so it is extremely unlikely that using an LTS distro's package will get you anything different from a direct download. (But should there be an update, of course you wouldn't then get it for some time.) – cfr Sep 30 '15 at 12:56
1

Yes, I like stability in my OS. Not necessarily in the application software though. And I did a lot of work last year under Ubuntu 12.04 LTS (not wanting to update in the middle of writing my thesis). It had TeX live 2009. – Chris H Sep 30 '15 at 13:27
3

@ChrisH bibutils hasn't been touched on CTAN since 2008. – cfr Sep 30 '15 at 21:34

score 8 · Answer 2 · answered Jul 18 '20 at 15:34

8

Tool doi2bib has moto "give us a DOI and we will do our best to get you the BibTeX entry" and it works for DOI specified in given json.

answered Jul 18 '20 at 15:34

Jan Holčák

81

This is amazing! – user2561747 Dec 18 '21 at 01:47

score 3 · Accepted Answer · answered Sep 29 '15 at 23:02

3

You sure about that?

@article{garcia2003genome,
  title={The genome sequence of Yersinia pestis bacteriophage $\varphi$A1122 reveals an intimate history with the coliphage T3 and T7 genomes},
  author={Garcia, Emilio and Elliott, Jeffrey M and Ramanculov, Erlan and Chain, Patrick SG and Chu, May C and Molineux, Ian J},
  journal={Journal of bacteriology},
  volume={185},
  number={17},
  pages={5248--5262},
  year={2003},
  publisher={Am Soc Microbiol}
}

answered Sep 29 '15 at 23:02

Nicholas Hamilton

13,173

Can I ask what you searched for? I have really spend a lot of time on this. – Jasmine Lognnes Sep 29 '15 at 23:04
2

I put the full title of the article into google scholar search box – Nicholas Hamilton Sep 29 '15 at 23:05
5

On another note, don't overcomplicate things, if something cannot be found, just write the entry by hand, either in a notepad, or using Jabref or some other Bibtex Manager -- you don't need a converter unless you had like 100+ in a particular format and it would save time over doing it manually... – Nicholas Hamilton Sep 29 '15 at 23:07
1

Ok, I feel really stupid now. I have really tried this... Anyway thanks a lot =) – Jasmine Lognnes Sep 29 '15 at 23:07
1

No worries, all good. – Nicholas Hamilton Sep 29 '15 at 23:08

Tony · Answer 4 · 2017-07-06T06:58:01.930

2

To complement the other answers, there are also some online tools to do that. If you don't intend to convert many references it's probably a good option.

From a Google search, this "Online ris2bib" and that "Online Web of Science to bibTeX" seem quite popular.

For more than a few conversions, I find Jabref very useful.

EDIT

With the first tool, it is actually possible to input text that is a concatenation of several RIS entries. So it might be good for bulk conversion after all...

edited Jul 06 '17 at 06:58

answered Jul 06 '17 at 00:45

Tony

171

Welcome! Please label your links more informatively. If those links die, searching the internet for 'this one' or 'that one' is unlikely to return much of use. – cfr Jul 06 '17 at 01:29
JabRef is indeed a life saver! – Hosein Rahnama Jul 21 '23 at 13:35

score 1 · Answer 5 · edited May 22 '22 at 09:48

For the sake of completeness you can of course write a converter to convert from JSON to BibTeX. The following snippet (based on code from stackoverflow) shows, that just a few lines of e.g. Python code are required to get to information from this JSON object.

# http://stackoverflow.com/questions/20199126/reading-a-json-file-using-python
import json
import codecs
with codecs.open("bibtex.json", "r", "utf-8") as jsonfile:
    py_object = json.load(jsonfile)
    jsonfile.close()
    print(py_object['publisher'])

score 1 · Answer 6 · edited May 22 '22 at 09:48

1

A R answer:

# system terminal
pip install citepy
citepy pandas > pandas.json #(not in python)

# R
library(jsonlite)
#install.packages("RefManageR")
library(RefManageR)
pan<-fromJSON("pandas.json")
pan$bibtype<-"Misc"
rownames(pan)<-"pandas2021"
panbib<-as.BibEntry(pan)
WriteBib(panbib,"pandas.bib")

edited May 22 '22 at 09:48

Marijn

37,699

answered Sep 03 '21 at 21:41

Ferroao

111

score 0 · Answer 7 · answered Oct 24 '20 at 04:12

0

You can download medley desktop, import your format source and then select studies and export to .bib format. Simple and useful.

answered Oct 24 '20 at 04:12

Marcelo

1

Convert RIS or NBIB or JSON to bibtex?

7 Answers7