insightsoftwareconsortium / insightjournal Goto Github PK

Hi @thewtex,

A question about ipfs, from the code above, that "path" of /articles/${pub_id}, from where is it coming?
It's because you uploaded the files with that structure?
Is there a way I can explore the ipfs layout? Just out of curiosity. Thanks!

I have to download the latest revision data, to parse the citations of each article, and not sure if doing it via ipfs, or https://data.kitware.com/#collection/5cb75e388d777f072b41e8db

Hi,

Thanks for the update to the journal website ! It is really welcome !

I know that the previous version comment section was polluted with spam bots...However, some codes samples age badly and I found some comments really helpful to update them.

Is there a way to make a safe comment section ? Maybe linked to discourse logins.
Another idea would be the mention of compatible ITK versions.

Cheers.

BibTex, etc.

For small screens, e.g. phones, make the GridItem's in the header wrap into multiple rows.

https://www.crossref.org/labs/citation-formatting-service/

Depends on #51 #52

A collection of information about the future of journals, publishers and the research ecosystem in the web 3.0.

Peer Review

• Journals outsourcing peer-review to communities: https://www.sciencemag.org/news/2021/04/fifteen-journals-outsource-peer-review-decisions
• Smart Contracts for peers to verify reproducibility, "review": 1 2

Hello,

I noticed that there is an issue with the order in which the authors appear. It's in alphabetical order (last name), not as on the paper or in the metadata. The author order is correct when browsing an issue.
Example:

• order correct: https://www.midasjournal.org/browse/issue/383
• order is alphabetical by last name: https://www.midasjournal.org/browse/publication/938

All publications in the above issue seem to be affected.

Thank you,
Matthias

https://www.gatsbyjs.com/docs/how-to/adding-common-features/creating-a-sitemap/

https://www.gatsbyjs.com/docs/how-to/adding-common-features/adding-search/

We could use Netlify CMS with GitHub integration and web3.storage API's.

New plan, greatly simplified and more capable: base on GitHub Actions, GitHub pull request forms! 🚀 ✨

Using the setup of @jcfr for the Project Week website. Refs:

• https://github.com/NA-MIC/ProjectWeek/issues/new/choose
• NA-MIC/ProjectWeek#667
• https://github.com/NA-MIC/ProjectWeek/blob/master/.github/workflows/project-page-pull-request.yml
• NA-MIC/ProjectWeek#668

We can likely avoid the issue creation and go forward directly with a PR from the form.

IJ publications cite other IJ publications.
Now that we have DOI's, we should rerun the query of the citation list in Crossref, to see if we can get a new score (a DOI match) for IJ articles. Right now, we have an unstructured citation with the parsed content from the publication pdf.

We do not need to parse the pdf again, it would be good to have an independent script to update the citation list from unstructured to doi match.

https://www.arweave.org/

Icon in footer

Will discuss with the ISC about sustainable generation.

citation_list is required by XML crossref for modern (<= 2 years) submissions.
It's a list of the references that the publication is citing.

• Crossref: References
• Crossref: citation and citation_list schema

We will extract it from either tex+bib file, or from PDF.

Resolving Citations (we don’t need no stinkin’ parser) - Crossref

From tex + bib:

• a) Parse the tex file for \cite{a_ref}, then extract a_ref from bib file.
  The only minor issue with this is that we might add \cite that have been commented out. A workaround would be to first remove all comments from the tex file, see arxiv-latex-cleaner.
• b) Remove unused (non-cited) articles from the bib file, and then just generate the citation list from the trimmed bib file. See https://tex.stackexchange.com/questions/43276/unused-bibliography-entries-how-to-check-which-entries-were-not-used, among others. Uses bibtool

From pdf:

This is hard.

GitHub - CeON/CERMINE: Content ExtRactor and MINEr is recommended by Crossref and used in production by OpenAIRE.

In Java, download .jar from github. (tested with 1.13), and put WaveletArticle.pdf in /tmp/pdfs (for example, the script recursively search all pdfs in input and below folders).

java -cp ~/Downloads/cermine-impl-1.13-jar-with-dependencies.jar \ 
pl.edu.icm.cermine.ContentExtractor -path /tmp/pdfs

This results in the file WaveletArticle.cermxml that honestly makes a better job than anystyle (a parser, see below). The article title is usually in the field article-title, and sometimes fails and ends in source.

The next step is to use the REST API from crossref. The API is public, so we can start working on it even before being Crossref members (on schedule).
With the output of the cermine parsing, we use a free-text query to the Crossref REST API. See GitHub - CrossRef/rest-api-doc: Documentation for Crossref's REST API

For a general query, use query.bibliographic under the work field.

Please notice that some characters need to be escaped in the url.
See HTML URL Encoding Reference for a reference.

Example:

<https://api.crossref.org/works?query.bibliographic=Carberry%2C+Josiah.+%E2%80%9CToward+a+Unified+Theory+of+High-Energy+Metaphysics%3A+Silly+String+Theory.%E2%80%9D+Journal+of+Psychoceramics+5.11+%282008%29%3A+1-3.#>

This will always give you results(!). Check the score value of each item.

See below a simplified response.

{
  "status": "ok",
  "message-type": "work-list",
  "message-version": "1.0.0",
  "message": {
    "facets": {},
    "total-results": 1903215,
    "items": [
      {
        "indexed": {
          "date-parts": [[2021, 5, 12]],
          "date-time": "2021-05-12T03:27:09Z",
          "timestamp": 1620790029774
        },
        "update-to": [
          {
            "updated": {
              "date-parts": [[2018, 1, 1]],
              "date-time": "2018-01-01T00:00:00Z",
              "timestamp": 1514764800000
            },
            "DOI": "10.5555/12345678",
            "type": "corrigendum",
            "label": "Corrigendum"
          }
        ],
        "reference-count": 1,
        "publisher": "Society of Psychoceramics",
        
        "score": 122.59374,
        "issued": { "date-parts": [[2008, 8, 13]] },
        "references-count": 1,
        "journal-issue": {
          "issue": "11",
          "published-online": { "date-parts": [[2008, 2, 29]] },
          "published-print": { "date-parts": [[2008, 2, 29]] }
        },
        "URL": "http://dx.doi.org/10.5555/12345678",
        "DOI": "10.5555/12345678",
        "type": "journal-article",
      },
      #More 
    ],
    "items-per-page": 20,
    "query": { "start-index": 0, "search-terms": null }
  }
}

Check status, check that top item, ordered by score, has a reasonable score value (TODO: which one?). The objective of this query is to get a DOI.

Then, use the the crossref DOI content negotiation to get that publication content in whatever format you want. See DOI Content Negotiation for options.

curl -LH "Accept: application/x-bibtex" http://dx.doi.org/10.5555/12345678  

@article{Carberry_2008,
        doi = {10.5555/12345678},
        url = {https://doi.org/10.5555%2F12345678},
        year = 2008,
        month = {aug},
        publisher = {Society of Psychoceramics},
        volume = {5},
        number = {11},
        pages = {1--3},
        author = {Josiah Carberry},
        title = {Toward a Unified Theory of High-Energy Metaphysics: Silly String Theory},
        journal = {Journal of Psychoceramics}
}% 

For XML crossref use: "Accept: application/vnd.crossref.unixref+xml"

Discarded solutions

anystyle (pdf parser)

From SO: Is it possible to extract the bibliography from a PDF file as a .bibtex? - TeX - LaTeX Stack Exchange
The anwers point to anystyle (ruby): GitHub - inukshuk/anystyle: Fast and smart citation reference parsing
gem install anystyle-cli rexml
gem find article.pdf returns a json.
It seems pretty bad when testing it with my own IJ article: GitHub - phcerdan/InsightJournal-IsotropicWavelets: Template of Technical Report to be submitted to the Insight Journal

• When the search box is empty, pressing the search button should not display that tiny floating rectangle. See gif.

Style suggestion: Maybe center the box and the button in the header row, instead of the button going off grid.

Greetings,

It appears that quite some publications went missing. I noticed that one of my own publications, which was part of the MICCAI 2014 Workshop on Image-Guided Adaptive Radiation Therapy (IGART) is not available anymore.

The handle and DOI links

http://hdl.handle.net/10380/3491
http://dx.doi.org/10.54294/lgcmkl

lead to the following error message:
ipfs resolve -r /ipfs/bafybeigcuragxgowyanltzo4t5wmzwdvlv5qxkyme3rdlfpb4nvdqp33pe/browse/publication/938: no link named "938" under Qme5S1jdJsrgd6GS3DSX41n1ZFbUeZhkUQa5kG6qQgnUqF

They are still listed/referenced in the file data/issues/383.json:

...
"issue": {
"date": "2014",
"issue_id": 383,
"name": "MICCAI 2014 Workshop: Image-Guided Adaptive Radiation Therapy (IGART)",
"publications": [925,937,938,939,940,941,942,945,946,947,948,958],
"short_description": "The workshop aims at presenting leading edge applications of medical image processing in the field of radiotherapy. The workshop provides an invaluable opportunity to present and discuss recent and preliminary research in this exciting field, in addition to providing a good forum to get constructive feedback from fellow researchers on more developed pieces of work."
...

They are also not listed on the website anymore, when I use, for instance, the search functionality or browse issues by year. Other workshop proceedings seem to be affected by this issue as well.

I hope this issue can get resolved somehow. Thank you,
Matthias

After #132

We would need to update the ISSN in Crossref for all the Midas Journal articles.

https://www.crossref.org/documentation/content-registration/descriptive-metadata/issns-isbns/

• Orcid IDS: This might require sending a google form to our submittors. Another option is to check if crossref itself has a way to query this after submission. I have been asked about authorship every know and then by multiple platforms.
• Text mining URL. See #75 . URL's for pdf's provided in #86 .
• Add Abstracts, PR incoming on this. (#85 )

Right now we have keywords (tags) but not categories.

Categories seem more consistent

https://material-ui.com/customization/palette/#user-preference

Using web form: https://apps.crossref.org/webDeposit/

ij_journals_doi = {
    3:  "10.54294/Insight", # insight
    31: "10.54294/MIDAS", # midas
    35: "10.54294/VTK" # vtk
}

Give it a DOI, providing all the associated benefits for their authors.

Also, it could be a good test case of publication with multiple revisions.

Just a proposal, looking forward to hearing your thoughts @thewtex

For example: https://www.midasjournal.org/browse/journal/48 is a workshop.
That should be an issue, under Midas Journal, not a journal itself.

Insight Journal: 2327-770X
VTK Journal: 2328-3459
Midas Journal: None

I think we need a ISSN for crossref registration, but not 100% sure if it is required.

Who is managing the ISSN account for the Insight Journal right now?
It would be interesting to check that ISSN account. https://portal.issn.org/faq8

@thewtex

Journal 11, is an open source workshop: https://www.insight-journal.org/browse/journal/11
where users uploaded their work.

For example, a journal 11 publication 186

Right now the ipfs node does not contain publication 186, probably because it had no pdf.

The article is not available: https://www.insight-journal.org/browse/publication/65

Could the old website be made available until the new website is working. Or is there a cache of the pdfs somewhere?

Could you add an estimated timeline for when the new site will be available?

Thanks,
Hans

Opening the Insight Journal through IPFS with brave. It's great, well done @thewtex!

How to Use IPFS With the Brave Browser

Currently provided at:

https://www.insight-journal.org/rire/index.php

We need folks to still able to access the provided articles, data, submission results.

@josephsnyder can you please run ScraPy on these pages? We will then host them and provide a redirect to the hosting location from the current location.

CC @aylward

On Home / About pages

I am building the XML that we are going to handle to Crossref for them to register.
There is a <resource> tag where we can directly link an url to the article.pdf or the source code associated to the publication.

I wonder if we have an exposed url to directly that file?

I see that when the user press the button Download PDF on the article tab it downloads it, but not sure if there is an url.

@thewtex

The PDF seems to load forever for this submission, even though the data exists.

BTW I am delighted to see Insight Journal making a comeback as a modern website! 🥲

Please bring back the Veggie MRIs - they were the best!!!

Old link: http://www.insight-journal.org/midas/collection/view/194

It seems to take > 10 sec for some publications until I can see that article, and several seconds until I get a download link for the source.
This seems a bit slow.

After reviewing the following, I suggest to evaluate adding the InsightJournal to https://www.theoj.org/

Ownership & Governance

Open Journals and each of its journals are community-organized and volunteer-led, with an editor-in-chief who leads each journal. Open Journals is fiscally sponsored by NumFOCUS, and has a documented governance structure.

Source: https://www.theoj.org/

References:

• https://www.theoj.org/
• https://github.com/openjournals/openjournals.github.io/blob/master/index.html

Last database dump was on 2017-09-08

Hi,

I am looking for the MRI informations or DICOM header of the MRA images from MIDAS. Unfortunately, it looks like the website is down. I think the old link was http://insight-journal.org/midas/handle/1926/597. Can someone help me with that ?

Thanks

Link from index, publication pages

Example: https://www.midasjournal.org/browse/journal/52

Separate sources and data.

https://github.com/ipfs/js-ipfs/tree/master/examples/browser-service-worker

@phcerdan is it possible to add the publication licenses to metadata.json (in the legacy journal, viewable with the View license link.?