Integrate Plos Collection Data Dump in sources

[solstag]

Two perspectives:

1. ensure we'got all articles in this collection covered
2. together with the other sources, produce a larger collection for https://github.com/amchagas/open-source-toolkit

In doing this I may be tempted to refactor data loading a little bit.

[amchagas]

I worked on the original file that lives in https://github.com/amchagas/open-source-toolkit. Namely classified all entries as hardware, software or both... Now it should be easy to filter out only the hardware ones.

Sorry I am only seeing that you working on the data now.. would you mind giving a little bit more detail on what you have done so far?

[solstag]

ACK, since it's such a small file, I'll update the code to download it from that repository instead of keeping a copy. We'll talk details on Monday (:

[solstag]

Ni! André (@amchagas), when you find the time, can you work a bit more on the plos-items.csv? Specifically:

• Most addresses in the DOI field are already DOIs or very close to a DOI (like plos URLs that contain the DOI), only 46 are not. Can you check if those 46 have DOIs on the page in the URLs, and in that case replace them by the DOIs?

• As you do that, can you take note of whether our search query would match those articles (title+abstract+keywords)?

• Also, here's a sample of 10 pone dois from the collection, can you also check if they'd get picked by our search query?

index  doi
350    10.1371/journal.pone.0187219
405    10.1371/journal.pone.0059840
407    10.1371/journal.pone.0030837
393    10.1371/journal.pone.0118545
310    10.1371/journal.pone.0206678
388    10.1371/journal.pone.0143547
295    10.1371/journal.pone.0220751
398    10.1371/journal.pone.0107216
281    10.1371/journal.pone.0226761
338    10.1371/journal.pone.0193744

PS: I think I've explained the situation in DM, but if you wanna see what I'm seeing check out b2cab27
.~´

[amchagas]

Hi @solstag !

just worked a bit more on the csv file, it is uploaded to the repo.

• Most addresses in the DOI field are already DOIs or very close to a DOI (like plos URLs that contain the DOI), only 46 are not. Can you check if those 46 have DOIs on the page in the URLs, and in that case replace them by the DOIs?

to keep track of which entries were missing DOIs, I added a new column "missing DOIs" and added the missing information there. I managed to get 32 DOIs, but in the process of doing so, noticed that there was some missclassified entries. For instance, some things that should have been classified as "web articles" were classified as "research articles" (the page showing the GOSH manifesto was one of them). counted 14 of these missclassifications (but note that in this number are also things that were the other way around > research articles classified as web articles). From what I remember, this classification came from PLoS people, so I am not sure if there are more of these cases in there.

For the cases that have a new DOI, I found that some of them do not get found by our query, some are found and some are not found because of hyphen.. So the papers spell "open-hardware" and not "open hardware" or "open-source hardware" etc. Maybe we would gain from adding these instances to the query.

The same is true for the DOIs from PLoS one you listed above. (also these DOIs, in their current format, do not lead to the article webpage when I past them to the address bar on my navigator).

[solstag]

Ni! Cool, excellent, thanks!

Hm, I would be surprised if Scopus or WOS would not find "open-hardware" from "open hardware", I was assuming they treat hyphens as spaces. Did you confirm that?

[amchagas]

ok, so you are correct, both databases manage differences between "open hardware" and "open-hardware" and so does Scielo

[amchagas]

I forgot to follow up on my comment:
If hyphenation is not the issue for some of them getting found and some not, then what could be the issue? I could not think of anything obvious...

(Could be that the ones that are not found are not indexed in those databases somehow?)

I guess the question is, do we want to do a deep dive in this issue, or do we acknowledge it exists and move on?

[solstag]

The issue is that these open hardware papers may not use any terms to designate open hardware in their title+abstracts+keywords, or we might not have the good terms.

A ideia seria para os 10 fazer uma tabela com:

1. quais dos nossos termos tão presentes
2. se ele seria achado pela nossa query ou não
3. quais outros termos usa para referir que trata de OH

[amchagas]

some results are in :P
from the ten papers I found some keywords that we might want to test:
3 papers use Open source design ~100 hits at WOS
1 paper uses open source method 50 hits at WOS
1 paper uses open source tool 1201 hits at WOS (and quite some software papers)
1 paper uses open source electronics 62 hits at WOS
1 paper uses inexpensive hardware (using this could lead to a lot of papers that describe affordable solutions but not necessarily open source)

Other than that, one of the papers does not actually shares the needed data for replication and is more focused on a biological question, rather than the description of a tool method.

Other two papers mention likely keywords only in the introduction, they are open hardware design and open source hardware

One paper has no mentions to open source whatsoever, even though code and design files are nicely placed in GH.

All of these do not have our terms in the title and/or abstract

I have saved a table with this info under the /data folder

---

[amchagas]

A quick look at WOS shows that "open source design" puts out about ~100 entries. Some are not hardware, but there are also some hardware articles we did not find before

a possible keyword combination is open source 3D printed which outputs 20 articles in WOS and all of them are about hardware.

[solstag]

Ni! Ok, I've checked the table. It answers question 3 (quais outros termos usa para referir que trata de OH), but it doesn't answer questions 1 and 2 (quais dos nossos termos tão presentes / se ele seria achado pela nossa query ou não). So we still don't know whether our current search would catch those. Or am I missing something? Cheeeers

[amchagas]

you are not missing something. I missed to write down specifically:
On the ods file there is an "observations" column where I made comments to some of the papers, things like "our keywords are only present in the introduction" - so not in abstract, title or keywords. The rows where no observations are made, our keywords were not found on the paper. This is because the plos collection was made by people either submitting things to it (so the authors knew their paper matched the collection requirements, even though they did not use the keywords we are now looking for), or by us finding papers "by chance"...