Lens.org

[sdspieg]

Any plans to also enable us to load exported lens.org files into bibliometrix? It's a great bibliometric resource, because it allows us to download as many documents as we want - admittedly 'only' with Lens IDs, but those should still suffice to even build co-citation networks... And its coverage is also quite a bit bigger than Dimensions - which you already support (thanks!). Pretty please/per favore, caro Massimo ? :)

[massimoaria]

Dear Stephan, I promise I will try to do it asap.

[sdspieg]

Grazie mille! :)

[HCSS-StratBase]

Any progress on this?

[massimoaria]

We are working on it. Please don't ask for ETA.

[massimoaria]

Just added support to lens.org CSV files.

Let me know any issues and bugs.

to import a lens.org file using convert2df: M <- convert2df(file="mylensfile.csv", dbsource="lens", format="csv)

using biblioshiny, you have just to choose"lens.org" when selecting the database in the "import raw file" menu.

[sdspieg]

Great! Thanks much. A few comments.

• the conversion seems to work partially. My biggest Lens csv file has 49,687 scholarly docs, and the conversion results show only 15,381 (RStudio shows an error message: "Warning: In sliderInput(): value should be greater than or equal to min (value = 1, min = 3)."
• annual scientific production, sources, works (for those 15k)
• authors works for most fields that are in the csv (e.g. affiliations are not in there, so that does not work), but for. Also Author local impact took 45' to compute [to be continued...]

[massimoaria]

Great! Thanks much. A few comments.

• the conversion seems to work partially. My biggest Lens CSV file has 49,687 scholarly docs, and the conversion results show only 15,381 (RStudio shows an error message: "Warning: In sliderInput(): value should be greater than or equal to min (value = 1, min = 3)."
• annual scientific production, sources, works (for those 15k)
• authors works for most fields that are in the CSV (e.g. affiliations are not in there, so that does not work), but for. Also, the Author local impact took 45' to compute [to be continued...]

convert2df works fine with your CSV file (you sent me it in a previous message)

Moreover, biblioshiny works well too (using the same CSV file)

Please provide more info about errors you are facing.

Regarding the high computational time of some functions (i.e. author local impact), that's normal when analyzing a such big collection.

[massimoaria]

I have completely rewritten the function Hindex that performs author and source impact analysis. Now, with your collection of quite 50.000 rows, author impact calculation takes just 30 seconds (on my MacBook air i5) instead of 45 minutes!!

[mlagisz]

sadly, lens it crashes for me with a message: "Error in strsplit(DATA$AU, split = "; ") : non-character argument" It may need some additional cleaning step?

[massimoaria]

sadly, lens it crashes for me with a message: "Error in strsplit(DATA$AU, split = "; ") : non-character argument" It may need some additional cleaning step?

I need more info about your issue. Please, provide your code and CSV lens file.

[mlagisz]

Hi, I am attaching a file (had to save it as .xlsx as it was not possible to upload .csv here) - it was originally downloaded from Lens.org as a .csv export, as recommended earlier in this issue. Unfortunately, exporting to .csv messes up encoding of special characters, e.g.: "Neal R. Haddaway; Colin D. Brown; Sönke Eggers; Jonas Josefsson; Brian Kronvang; Nicola P. Randall; Jaana Uusi-Kämppä" .

Working with .bib exports has no such problem (but does not work for importing data into bibliometrix). However, it looks like not all fields get exported. For example, the field with references gets lost, which makes any bibliometric analyses basing on lists of citations impossible.

bib_lens <- convert2df("lens-export.csv", dbsource = "lens", format = "csv") #using a recent version of the function from GitHub, not CRAN
dim(bib_lens) #crashes with error message: Error in strsplit(DATA$AU, split = "; ") : non-character argument

lens-export.xlsx

[massimoaria]

Hi, I am attaching a file (had to save it as .xlsx as it was not possible to upload .csv here) - it was originally downloaded from Lens.org as a .csv export, as recommended earlier in this issue. Unfortunately, exporting to .csv messes up encoding of special characters, e.g.: "Neal R. Haddaway; Colin D. Brown; Sönke Eggers; Jonas Josefsson; Brian Kronvang; Nicola P. Randall; Jaana Uusi-Kämppä" .

Working with .bib exports has no such problem (but does not work for importing data into bibliometrix). However, it looks like not all fields get exported. For example, the field with references gets lost, which makes any bibliometric analyses basing on lists of citations impossible.

bib_lens <- convert2df("lens-export.csv", dbsource = "lens", format = "csv") #using a recent version of the function from GitHub, not CRAN
dim(bib_lens) #crashes with error message: Error in strsplit(DATA$AU, split = "; ") : non-character argument

lens-export.xlsx

You raised two points: Differences among Lens export file formats and an importing issue with CSV. Focusing on the first point, Lens allows exporting collections using three different file formats: RIS, CSV, and BibTeX. Currently, none of the three formats allow you to export the entire set of metadata (i.e no format provides author's affiliation info). Comparing the three files (CSV, RIS, and BibTeX), CSV appears to be more complete. That's why we choose to include it in bibliometrix.

Regarding the importing issue, I need the original CSV you downloaded from Lens. Please zip and upload it on GitHub. I cannot identify the issue through the XLSX file.

[mlagisz]

lens-export.csv.zip thank you for your reply - here is the zipped file

[massimoaria]

I just tried to import your lens file and all works fine on my pc. Maybe it could depend on your R enconding setting that returns an error when trying to import foreign characters. Please execute the following code in R console and let me know what is your encoding:

getOption("encoding")

lens-export.csv.zip thank you for your reply - here is the zipped file

[mlagisz]

Hi, thanks a lot - it looks like it might have something to do with encoding on my computer. I would appreciate any suggestions on how to get around this issue.

Here is my encoding and session info:

getOption("encoding") [1] "native.enc"

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base ...

[massimoaria]

Hi, thanks a lot - it looks like it might have something to do with encoding on my computer. I would appreciate any suggestions on how to get around this issue.

Here is my encoding and session info:

getOption("encoding") [1] "native.enc"

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base ...

I am trying to fix your issue. Please try if now lens importing works fine.

[lercari]

Hello and thank you for your work. I have a problem importing from lens.org to biblioshiny. Everything seems fine, no errors but in the Most Global Cited Documents analysis, all the documents appear with 0 citations. The same happens in Average citations per documents. How can I fix it? thanks

[massimoaria]

This is not an issue. Lens.org database does not export citation counts. So the bibliometrix importing routine set TC column to 0 for all documents.

[lercari]

This is not an issue. Lens.org database does not export citation counts. So the bibliometrix importing routine set TC column to 0 for all documents.

Thanks!

[gavieira]

Hi, I am attaching a file (had to save it as .xlsx as it was not possible to upload .csv here) - it was originally downloaded from Lens.org as a .csv export, as recommended earlier in this issue. Unfortunately, exporting to .csv messes up encoding of special characters, e.g.: "Neal R. Haddaway; Colin D. Brown; Sönke Eggers; Jonas Josefsson; Brian Kronvang; Nicola P. Randall; Jaana Uusi-Kämppä" . Working with .bib exports has no such problem (but does not work for importing data into bibliometrix). However, it looks like not all fields get exported. For example, the field with references gets lost, which makes any bibliometric analyses basing on lists of citations impossible.

bib_lens <- convert2df("lens-export.csv", dbsource = "lens", format = "csv") #using a recent version of the function from GitHub, not CRAN
dim(bib_lens) #crashes with error message: Error in strsplit(DATA$AU, split = "; ") : non-character argument

lens-export.xlsx

You raised two points: Differences among Lens export file formats and an importing issue with CSV. Focusing on the first point, Lens allows exporting collections using three different file formats: RIS, CSV, and BibTeX. Currently, none of the three formats allow you to export the entire set of metadata (i.e no format provides author's affiliation info). Comparing the three files (CSV, RIS, and BibTeX), CSV appears to be more complete. That's why we choose to include it in bibliometrix.

Regarding the importing issue, I need the original CSV you downloaded from Lens. Please zip and upload it on GitHub. I cannot identify the issue through the XLSX file.

Hi!

I'm not sure when this was implemented, but currently Lens allows to export data in .json and .jsonl formats, both of which provide author affiliation data. Are there any plans to include options for parsing these files in future releases of bibliometrix?

Thanks for this amazing software!

[HCSS-StratBase]

Did something break or change? When I try to import an exported csv-file through the gui I first see this `Converting your lens collection into a bibliographic dataframe

Rows: 17309 Columns: 32
── Column specification ────────────────────────────────────────── Delimiter: "," chr (26): Lens ID, Title, Publication Type, Source Title, ISS... dbl (4): Publication Year, PMID, Citing Patents Count, Citin... lgl (1): Is Open Access date (1): Date Published

ℹ Use spec() to retrieve the full column specification for this data. ℹ Specify the column types or set show_col_types = FALSE to quiet this message.`

But then it just keeps spinning and spinning... Could you please take a look? https://drive.google.com/open?id=1G6uZEijKJ94sJxmXOneFXGjF5DqLtFNH&usp=drive_fs

[HCSS-StratBase]

Update - it just took very long. But it DID complete successfully