@tcatapano here is an article published in 2006. It is open access, but in fact be closed access. Do you have a policy for this? https://doi.org/10.5281/zenodo.805052

Dont understand why uploads are failing. Maybe a problem with the syntax of requested URI?

using curl:

Terrys-MacBook-Air:zenodo_uploads terry$ curl -i -H "Content-Type: application/json" -X POST -d @uploads/abdullah_et_al._2009.json https://zenodo.org/api/deposit/depositions?access_token=igt9FdYKYr2sKuK4AxdnIR5J6Pkw0py558eqVQs6ks2RmTVzHZhK4NgcDNFT
HTTP/1.1 100 Continue

HTTP/1.1 400 BAD REQUEST
Server: nginx/1.10.2
Date: Fri, 09 Jun 2017 12:32:16 GMT
Content-Type: application/json
Content-Length: 114
Access-Control-Allow-Origin: *
Access-Control-Expose-Headers: Content-Type, ETag, Link, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset
X-RateLimit-Limit: 5000
X-RateLimit-Remaining: 4999
X-RateLimit-Reset: 1497015135
Retry-After: 3598
X-Sentry-ID: None

{
  "message": "The browser (or proxy) sent a request that this server could not understand.", 
  "status": 400
}

json data is:

{
    "metadata": {
    "title": "Progeny Estimation of Different Entomopathogenic Nematodes in Full Fed Larvae of Fruit Flies Drosophila Sp. (Drosophilidae: Diptera).",
    "upload_type": "publication",
    "description": "uploaded by Plazi from Taxodros",
    "access_right": "open",
    "journal_pages": "981-985",
    "journal_title": "Life Sci. Int. J.",
    "journal_volume": "3",
    "publication_type": "article",
    "publication_date": "2009-12-31",
    "keywords": [
      "Biodiversity",
      "Taxonomy",
      "Animalia",
      "Arthropoda",
      "Insecta",
      "Diptera",
      "Drosophilidae",
      "flies",
      "fruit flies",
      "terrestrial"
    ],
    "license": "cc-by",
    "creators": [
      {
        "name": "Abdallah, K."
      },
      {
        "name": "Khan, S.M."
      },
      {
        "name": "Yasmin, S."
      },
      {
        "name": "Gowen, S."
      },
      {
        "name": "Khattak, M.K."
      },
      {
        "name": "Kiani, A.R."
      },
      {
        "name": "Ukeh, D.A."
      }
    ],
    "communities": [
      {
        "identifier": "biosyslit"
      }
    ]
  }
}  

@tcatapano could you please produce a list of the taxodros deposits that have abbreviated journal names so that I can fix them, unless there is a way to fix this using the API

Change from cc-by to "no known license"

https://docs.google.com/document/d/1rFYk4MpFMLDjQaXxzq3uuINQP1Eazls0bAsT8q9O5Ek/edit#heading=h.7ae6692xg3sa has the explanation to the abbreviated / extended version of journal names

e.g.

*s Studies Neotrop. Fauna Environ.
*u Studies on Neotropical Fauna and Environment

Data includes invalid dates such as

adams_1899.json : 1899-04-31
adams_1905b.json: 1905-04-31
adell_+_botella_1986.json: 1986-06-31

will make fixes in source data eventually, but will just capture and set aside problem files for now.

I have seen your efforts in preparing keywords. May I suggest to add some of the keywords presented on the publications.
(bächli)

I am not sure how to make use of these keywords as they seem to be linked to species rather publications?!
https://docs.google.com/document/d/1rFYk4MpFMLDjQaXxzq3uuINQP1Eazls0bAsT8q9O5Ek/edit#heading=h.n4emxdl7lxkc

II've asked Bächli for advice - will add the response here

https://github.com/plazi/drosophilid-data/journalOrPublisher_values.txt

would facilitate tracking and updating later

Probably most related to issue #10

achumi_et_al__2011
adams_1899
adams_1905b
adell_+_botella_1986
adrianov_et_al__2008
al-taweel_1986
alahiotis_+_goulielmos_1986
alahiotis_1980
alatossava_+_lakovaara_1981
alberola_+_frutos_1993b
albers_+_bijlsma_1986
albuquerque_+_napp_1980
alcorta_et_al__1986
alcorta_et_al__1987
aldrich_1915

would be some work, but ideally would be part of the process

perhaps a curl problem. Fixed now in pdfs and corrected article xml and downstream files

@myrmoteras: Ive created this private repo for the prep of the Drosophilid data. The first step is to define the target metadata fields and what cleaning needs to be done. Take a look at https://raw.githubusercontent.com/plazi/drosophilid-data/master/BibData-Drosophila.corrected.tab.csv and let me know what you think needs to be done.

Right now the fields are:

ID-taxodros|author|year|title|pagination|volume|journalOrPublisher|formatAndMeta|pubDate|libNumber|issue|editor|volumeTitle

Lieber Lukas
Ich hab mit Gerhard Bächli gesprochen und ich werd einen letzten Anlauf machen, all die PDFs auf Biodiversity Literature Repository in Zenodo hochzuladen. Gemäss Bächli wird es eine neue Version von Taxodros anfangs Januar geben.

Die Fragen sind

• gbit es eine Möglichkeit für eine finanzielle Unterstützung für den upload?
• was passiert mit Taxodros datenbank mittlefristig?
• was ist Euer Interesse in diese doch sehr wichtigen Resource?

Mit herzlichen Grüssen und Dank im Voraus für eine kurze Antwort

Donat

Lieber Donat

Du scheinst hellseherische Fähigkeiten zu haben: mein Kalender hat am kommenden Montag einen Eintrag "Donat wegen Taxodros schreiben". Du bist mir also 72 Stunden zuvorgekommen :)

Ja, Michael Greef von der Entomologischen Sammlung der ETH und ich haben ein Projekt, bei dem wir alle Typen der Drosophila, die wir haben, hochauflösend einzuscannen. Teil dieses SwissCollNet Projekts ist es auch, die Taxodros Datenbank von Bächli zukunftsfähig zu machen. Dabei ist die Verlinkung mit den Papern auch ein grosses Thema.

Wollen wir uns mal treffen, um Möglichkeiten auszuloten, da etwas zusammen zu machen?

Mit herzlichen Grüssen nach Berlin,

Lukas

On 15.12.23 15:46, Donat Agosti wrote:

Lieber Lukas

Nach langem wieder einmal ein Lebenszeichen meinerseits, seit einem guten Monat von Berlin.

Wir versuchen einmal mehr all die PDFs, welche Bächli für Taxodros gesammelt hat, online via die Biodiversity Literature Repository zugänglich zu machen. Du hast erwähnt, dass Ihr plant die drosophilien Typen bei Euch am Museum zu digitalisieren. Was sind da Eure Pläne? Gäbe es da Möglichkeiten, etwas zusammen zu machen?

Wir werden unser swissuniversities open science project eBioDiv im März offizell abschliessen. Eine wichtiger Teil ist ein matching service (https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprod.ebiodiv.org%2F&data=05%7C02%7Cagosti%40amnh.org%7C89eb3e72042249cce14408dbfd9bc963%7Cbe0003e8c6b9496883aeb34586974b76%7C0%7C0%7C638382617764045807%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IuDuYAfuIEQGaI1Pjxfx3rFoBpFWskh6Q4jOMVtZGBw%3D&reserved=0), welcher es erlaubt, in der Literatur zitierte specimens mit den digitalisierten specimens zu verlinken. Falls Ihr die Typen digitalisiert, könnte man ja auch die Literatur aufarbeiten, damit wir die Typen damit verlinken könnt.

Mit herzlichen Grüssen und Dank zum Voraus für eine kurze Antwort

Donat

done. see files in plazi_sources

Phone call with Gerhard Bächli:

• he is still active, using the same old infrastructure at UNIZ to twice a year upload the newest version of taxodros
• he added all the DOI to the arcticles
• adding ca 200 new articles per year
• is interested to get a Zenodo deposit link to include in this extended catalogue
• UNIZH not interested to deal with PDFs
• will contact me when a new version is ready in the second week of January 2024

uploadType | publication
PublicationType | Journal article
Description | uploaded by Plazi from Taxodros
AccessRight | open access
License | either CC BY or licence not specified
Communities | Biodiversity Literature Repository

taxonomic hierarchy (use wikipedia; diptera)
biodiversity
taxonomy
flies
fruit flies
terrestrial

• book: Book
• section: Book section
• conferencepaper: Conference paper
• article: Journal article
• patent: Patent
• preprint: Preprint
• report: Report
• softwaredocumentation: Software documentation
• thesis: Thesis
• technicalnote: Technical note
• workingpaper: Working paper
• other: Other

when creating deposition, script needed to get id from returned json. Was being passed to jq via a tail -1. Fixed now by turning off curls -i swith (no header response) and passing response to jq:

curl -H "Content-Type: application/json" -X POST -d @"$PUB" https://zenodo.org/api/deposit/depositions?access_token="$ACCESS_TOKEN" | tee -a deposition_logs/"$NUM"_deposition.log | jq '.id' >> zenodo_id.txt

These are the articles we already uploaded to BLR

https://zenodo.org/communities/biosyslit/search?page=1&size=20&q=taxodros

This is an article, where we discovered that there is also an existing DOI:
https://doi.org/10.5281/zenodo.805071 (see the link to related identifiers)