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TaxoDros / TaxoDros.github.io

TaxoDros - The database on Taxonomy of Drosophilidae. Compiled by Gerhard Bächli, Universität Zürich-Irchel, Institut für Evolutionsbiologie und Umweltforschung, Zürich, Switzerland. https://orcid.org/0000-0002-8402-176X
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boesiger, 1974c listed as article in DROS5, but source points to a book chapter #19

Open jhpoelen opened 7 months ago

jhpoelen commented 7 months ago

https://sandbox.zenodo.org/records/31753 uis a book chapter but in Bächlis' list it is a journal article? leave as is?

Originally posted by @myrmoteras in https://github.com/bio-guoda/preston/issues/275#issuecomment-1969980923

Associated DROS5 record retrieved via https://linker.bio/line:hash://md5/ff86b940567d278e50fa00672cf96629!/L17005-L17014 on 2024-02-29 - 

.TEXT;
boesiger, 1974c
.A Boesiger, E.,
.J 1974
.S The role of sexual selection in the maintenance
of the genetical heterogeneity of Drosophila
populations and its genetic basis.
.Z Front. Biol., 38:167-184.
.K ocr / part / p 813882 / 1974c
.P Boesiger, 1974c.pdf

indicates that the book chapter is archived as a article instead of a book. Expected a DROS5 record with 

.Z. Front. Biol., 38:167-184.

instead (note the period following (e.g., .Z.))

myrmoteras commented 7 months ago

following our strategy to get Bächli data into Zenodo with minimal correction, besides data cleaning needed for successful upload, and the option for later improvements, I would go ahead

jhpoelen commented 7 months ago

@myrmoteras thanks for taking the time to review. The Zenodo records related to the TaxoDros literature can be traced by their LSIDs. These LSIDs can be used to update the Zenodo records with TaxoDros updates.

Just to make sure - Would you like me to go ahead and upload all TaxoDros records to Zenodo (production not sandbox)?

myrmoteras commented 7 months ago

Yes, I would upload a couple to production and see what's happening d

From: Jorrit Poelen @.> Sent: Thursday, February 29, 2024 6:23 PM To: TaxoDros/TaxoDros.github.io @.> Cc: Donat Agosti @.>; Mention @.> Subject: Re: [TaxoDros/TaxoDros.github.io] boesiger, 1974c listed as article in DROS5, but source points to a book chapter (Issue #19)

EXTERNAL SENDER

@myrmoterashttps://github.com/myrmoteras thanks for taking the time to review. The Zenodo records related to the TaxoDros literature can be traced by their LSIDs. These LSIDs can be used to update the Zenodo records with TaxoDros updates.

Just to make sure - Would you like me to go ahead and upload all TaxoDros records to Zenodo (production not sandbox)?

- Reply to this email directly, view it on GitHubhttps://github.com/TaxoDros/TaxoDros.github.io/issues/19#issuecomment-1971610366, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABDFPJHZANSTCL7KWIISFKLYV5RW5AVCNFSM6AAAAABEAF3LMOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZRGYYTAMZWGY. You are receiving this because you were mentioned.Message ID: @.***>

jhpoelen commented 7 months ago

Ok, I've uploaded two records - one existing one, and one new one. Please see #28 and #27 or https://zenodo.org/records/10728948 and https://zenodo.org/records/10728911

myrmoteras commented 7 months ago

Looks good.

Your idea to add "terrestrial" as keyword would be good.

In this https://zenodo.org/records/10728911, you added a new version. Did you do it because the files are different and because it has now its own DOI?

I add Terry, in case he has a moment to look at it. @Terry @.***> these are the first two uploads to the BLR and taxodros and start of uploading all the rest. Any observations, comments or is it ok?

Cheers donat

From: Jorrit Poelen @.> Sent: Thursday, February 29, 2024 10:10:43 PM To: TaxoDros/TaxoDros.github.io @.> Cc: Donat Agosti @.>; Mention @.> Subject: Re: [TaxoDros/TaxoDros.github.io] boesiger, 1974c listed as article in DROS5, but source points to a book chapter (Issue #19)

EXTERNAL SENDER

Ok, I've uploaded two records - one existing one, and one new one. Please see #28https://github.com/TaxoDros/TaxoDros.github.io/issues/28 and #27https://github.com/TaxoDros/TaxoDros.github.io/issues/27 or https://zenodo.org/records/10728948 and https://zenodo.org/records/10728911

- Reply to this email directly, view it on GitHubhttps://github.com/TaxoDros/TaxoDros.github.io/issues/19#issuecomment-1971967350, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABDFPJFGNDO746DETDRXEM3YV6MNHAVCNFSM6AAAAABEAF3LMOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZRHE3DOMZVGA. You are receiving this because you were mentioned.Message ID: @.***>

jhpoelen commented 7 months ago

In this https://zenodo.org/records/10728911, you added a new version. Did you do it because the files are different and because it has now its own DOI?

Not that fancy yet. The bot noticed an older version, and created a new one.

myrmoteras commented 7 months ago

How does the bot decide? What are the criteria?

jhpoelen commented 7 months ago

Each TaxoDros record has a lsid that marks a Zenodo record.

When updating a TaxoDros into Zenodo, the bot queries Zenodo for records with that lsid. If the lsid is not found, a new records is created, if a record with the lsid is found, a new version is created. If more than one record with the lsid are found, this is logged and no action is taken.

An example of such lsid is: urn:lsid:taxodros.uzh.ch:id:abd%20el-halim%20et%20al.%2C%202005

as currently found in https://zenodo.org/records/10728948

with associated record: 

.TEXT;
abd el-halim et al., 2005
.A Abd El-Halim, A.S., Mostafa, A.A.,
& Allam, K.A.M.a.,
.J 2005
.S Dipterous flies species and their densities in
fourteen Egyptian governorates.
.Z J. Egypt. Soc. Parasitol., 35:351-362.
.K ocr
.P Abd El-Halim et al., 2005.pdf

Note how the lsid is derived from the id that Bächli used in the DROS5 records (i.e., 'abd el-halim et al., 2005').

So, the lsid builds a bridge from the Zenodo universe to the TaxoDros universe.

I hope this answers your question.

myrmoteras commented 7 months ago

Ok tx

From: Jorrit Poelen @.> Sent: Friday, March 1, 2024 1:09 PM To: TaxoDros/TaxoDros.github.io @.> Cc: Donat Agosti @.>; Mention @.> Subject: Re: [TaxoDros/TaxoDros.github.io] boesiger, 1974c listed as article in DROS5, but source points to a book chapter (Issue #19)

EXTERNAL SENDER

Each TaxoDros record has a lsid that marks a Zenodo record.

When updating a TaxoDros into Zenodo, the bot queries Zenodo for records with that lsid. If the lsid is not found, a new records is created, if a record with the lsid is found, a new version is created. If more than one record with the lsid are found, this is logged and no action is taken.

An example of such lsid is: urn:lsid:taxodros.uzh.ch:id:abd%20el-halim%20et%20al.%2C%202005

with associated record:

.TEXT;

abd el-halim et al., 2005

.A Abd El-Halim, A.S., Mostafa, A.A.,

& Allam, K.A.M.a.,

.J 2005

.S Dipterous flies species and their densities in

fourteen Egyptian governorates.

.Z J. Egypt. Soc. Parasitol., 35:351-362.

.K ocr

.P Abd El-Halim et al., 2005.pdf

Note how the lsid is derived from the id that Bächli used in the DROS5 records (i.e., 'abd el-halim et al., 2005').

So, the lsid builds a bridge from the Zenodo universe to the TaxoDros universe.

I hope this answers your question.

- Reply to this email directly, view it on GitHubhttps://github.com/TaxoDros/TaxoDros.github.io/issues/19#issuecomment-1973075028, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABDFPJD777WKF5MDTGOVJ73YWBVU5AVCNFSM6AAAAABEAF3LMOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZTGA3TKMBSHA. You are receiving this because you were mentioned.Message ID: @.***>

jhpoelen commented 7 months ago

@myrmoteras would you like me to proceed uploading the entire corpus? Or would you rather wait until others have reviewed the test records? Please advise.

myrmoteras commented 7 months ago

one question concerns the 160 articles that we at TreatmentBank have already processed covering Asteiidae Aulacigastridae Camillidae Cryptochaetidae Curtonotidae Diastatidae Periscelididae Xenasteiidae Drosophilidae included in taxodros and might overlap. For this one, we should not replace the PDF and especially the metadata which includes all the links to figures, treatments etc.

how can we assure that the remain intact?

html

csv

or do you want to create a new version? Ideally we could add the link to Taxodros etc. into the existing deposits?

jhpoelen commented 7 months ago

The bot only touches records with taxodros lsids. Assuming that treatmentbank does not include TaxoDros lsids, the 160 fruit fly pubs in Treatment Bank will not be messed with by the bot.

jhpoelen commented 7 months ago

I see treatment bank and the TaxoDros corpus as separate corpora. Their records may be linked at some point, and this requires some curatorial decisions/workflows/work to the put in place.

myrmoteras commented 7 months ago

But then we create duplicates which is against the rule. d

From: Jorrit Poelen @.> Sent: Friday, March 1, 2024 5:02 PM To: TaxoDros/TaxoDros.github.io @.> Cc: Donat Agosti @.>; Mention @.> Subject: Re: [TaxoDros/TaxoDros.github.io] boesiger, 1974c listed as article in DROS5, but source points to a book chapter (Issue #19)

EXTERNAL SENDER

The bot only touches records with taxodros lsids. Assuming that treatmentbank does not include TaxoDros lsids, the 160 fruit fly pubs in Treatment Bank will not be messed with by the bot.

- Reply to this email directly, view it on GitHubhttps://github.com/TaxoDros/TaxoDros.github.io/issues/19#issuecomment-1973447923, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABDFPJDF7FH3MEEMT6UW5JTYWCQ6PAVCNFSM6AAAAABEAF3LMOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZTGQ2DOOJSGM. You are receiving this because you were mentioned.Message ID: @.***>

myrmoteras commented 7 months ago

I see treatment bank and the TaxoDros corpus as separate corpora. Their records may be linked at some point, and this requires some curatorial decisions/workflows/work to the put in place.

then we need to get the TaxoDros lsids into the existing records.

jhpoelen commented 7 months ago

Perhaps best to have a video chat on how to proceed. Let me know your availability.

myrmoteras commented 7 months ago

Now?

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: Jorrit Poelen @.> Sent: Friday, March 1, 2024 5:15:07 PM To: TaxoDros/TaxoDros.github.io @.> Cc: Donat Agosti @.>; Mention @.> Subject: Re: [TaxoDros/TaxoDros.github.io] boesiger, 1974c listed as article in DROS5, but source points to a book chapter (Issue #19)

EXTERNAL SENDER

Perhaps best to have a video chat on how to proceed. Let me know your availability.

— Reply to this email directly, view it on GitHubhttps://github.com/TaxoDros/TaxoDros.github.io/issues/19#issuecomment-1973471359, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABDFPJEWQT347AY5ALK24UDYWCSQXAVCNFSM6AAAAABEAF3LMOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZTGQ3TCMZVHE. You are receiving this because you were mentioned.Message ID: @.***>

jhpoelen commented 7 months ago

@myrmoteras thanks for the chat. As discussed, I'll schedule a first round of uploading the TaxoDros corpus.