WoRMS deleted aphia ids

[pcrjoana]

Hello!

While dealing with submitting the VME DwC dataset to EDMODnet biology, it came to that two aphia IDs have been deleted and new ones created: 286418 became 125314 347758 became 128495

[MariaMakri]

@pcrjoana to contact WoRMs cc BODC regarding the deletion of AphiaIDs, since it is happening on large scale. Also deprecate the two old AphiaIDs, create the new ones and link them.

[pcrjoana]

The replacement aphia IDs are actually for higher taxonomic levels, and are already in RECO.

[pcrjoana]

Email sent.

[pcrjoana]

There is been a lot of back and forth with Bart from WoRMS. He requested that we provide a list of the deleted aphia ids, and also of the edited aphia ids. I requested @HansMJ to make an extraction with these. @Osanna123 wants to discuss this before replying to Bart again, so my/our reply is on hold until the next RMG.

[Osanna123]

From: World Register of Marine Species (WoRMS) info@marinespecies.org Sent: 10 September 2024 15:03 Subject: RE: WoRMS codes with status 'Deleted"

Hi Joana,

You are right. This taxon was added in 2009 and changed in 2014

In 2014, we were not yet so strict on this, like nowadays… I’m afraid we can’t do much about this, i.e. reverting this would be worse …

Regards,

Bart Vanhoorne WoRMS Data Management Team Flanders Marine Institute (VLIZ) - Ostend, Belgium http://www.marinespecies.org info@marinespecies.org

From: Joana Ribeiro [joana.ribeiro@ices.dk](mailto:joana.ribeiro@ices.dk) Sent: Tuesday, September 10, 2024 14:37 To: Bart Vanhoorne [bart.vanhoorne@vliz.be](mailto:bart.vanhoorne@vliz.be) Cc: Anna Osypchuk [anna.osypchuk@ices.dk](mailto:anna.osypchuk@ices.dk); neilh@ices.dk; Hebden, Mark [mahe@noc.ac.uk](mailto:mahe@noc.ac.uk) Subject: Re: WoRMS codes with status 'Deleted"

Dear Bart,

We found one example of an edited/reused, but never deleted, Aphia ID, where data management did not follow best practices. Aphia ID 430189 used to be assigned to species Conus magus, but it became Cucullus magus (we can see this in our local copy of WoRMS).

[Osanna123]

From: World Register of Marine Species (WoRMS) info@marinespecies.org Sent: 10 September 2024 14:45 Subject: RE: Deleted aphia IDs from WoRmS database

Hi Joana,

I think your email is an over-reaction on only 3 cases out of the 1M names in Aphia/WoRMS, so I think this is a minor issue. If we leave the names visible, we will lose (the trust of) our editors, so we must hide them for the general public.

In both cases, just ask us, and we will tell you the name it was attached to, so you can move on.

So here we go:

1. AphiaID 286418 = Swiftia miniata (Valenciennes, 1855) – this is a non-existing name, an invention of data manager (see the delete reason at https://www.marinespecies.org/aphia.php?p=taxdetails&id=286418)
2. AphiaID 347758 = Pennatula Linnaeus, 1758 – exact copy of its replacement AphiaID 128495

If the names have been used in the literature, or we can make more sense out of them, we can certainly make the AphiaIDs available again, and document this properly. We’ll discuss the 1st case with our editors.

Regards, Bart

From: Joana Ribeiro [joana.ribeiro@ices.dk](mailto:joana.ribeiro@ices.dk) Sent: Tuesday, September 10, 2024 14:19 Subject: Re: Deleted aphia IDs from WoRmS database

Hello again Bart,

1. Unfortunately, we cannot find the AphiaID that was reused, but we found one earlier this year.

2. What we mean by deleted is when you cannot see which species corresponds to the aphia ID. I'm sorry if I did not explain myself correctly. If the identifier is available, but we have no way to know which species was reported, that is not useful to us. For example see AphiaID 286418 or Aphia ID 347758. At least one of these used to refer to a species, and now the suggested AphiaIDs link to genuses. To keep our data integrity, we really need to be able to link the AphiaID to what was originally assigned to it. With your current system, there is no way of doing it in certain cases. We have even been contacted by our submitters regarding this. I will forward you an email between my colleague and one of her submitters regarding this. The system where you assign the status "unaccepted" is much more useful to us, and it is also the one we think is most correct from a data management perspective.

If I can find the example for 1, I will send it to you.

Kind regards,

Joana Ribeiro Data Officer – Cross Discipline International Council for the Exploration of the Sea (ICES)

Email: joana.ribeiro@ices.dk Web: www.ices.dk

H.C. Andersens Boulevard 44-46 1553 Copenhagen V, Denmark

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From: World Register of Marine Species (WoRMS) [info@marinespecies.org](mailto:info@marinespecies.org) Sent: Tuesday, September 10, 2024 1:50 PM Subject: RE: Deleted aphia IDs from WoRmS database

Hi Joana,

I must totally disagree with your statements

1. WoRMS NEVER re-uses existing AphiaIDs for other names or concepts. At least that is what we explain to our editors, and we try to enforce that. But we can obviously not control that the full 100%
2. Deleted AphiaIDs are NEVER actually deleted or orphaned, they get a tombstone page, that redirects you to the replacement AphiaID

In conclusion: the WoRMS AphiaID & LSIDS are PERSISTENT identifiers, we make that VERY, VERY clear: https://www.marinespecies.org/aphia.php?p=webservice

Life Science Identifier (LSID) LSIDs are persistent, location-independent, resource identifiers for uniquely naming biologically significant resources.

So please, can you come up with examples, where you think that this is not the case?

Regards,

Bart Vanhoorne WoRMS Data Management Team Flanders Marine Institute (VLIZ) - Ostend, Belgium http://www.marinespecies.org info@marinespecies.org

From: Joana Ribeiro [joana.ribeiro@ices.dk](mailto:joana.ribeiro@ices.dk) Sent: Tuesday, September 10, 2024 11:47 To: Bart Vanhoorne [bart.vanhoorne@vliz.be](mailto:bart.vanhoorne@vliz.be); info@marinespecies.org Cc: Anna Osypchuk [anna.osypchuk@ices.dk](mailto:anna.osypchuk@ices.dk); neilh@ices.dk Subject: Deleted aphia IDs from WoRmS database

Dear WoRMS staff, Your database is an extremely important tool for the global marine biology community, where many national and international databases and datasets are dependent on WoRMS names and references. At ICES, we use WoRMS references for the majority of our databases. We’ve had good cooperation with your colleagues over time, where your fast and diligent work helped our scientists to deliver their data to us. However, we have noticed a sad tendency by some WoRMS taxonomists to delete some Aphia IDs. When your references are exposed to the external users, they are implemented for use immediately. But when your codes get deleted from your database, it creates orphan, anonymous records in all external dependencies. In addition, it looks like you have allowed re-use of the deleted codes for new species references, which alters data recorded in external databases. Therefore, we would like to highlight the fact that your use of the option to delete the existing references is against any reasonable data management practices that has negative adverse effect on all databases and datasets referring to WoRMS. This is why we would strongly advise you to revise your use of the delete option and prohibit it for the codes that have been published and can be replicated in the external resources. As we are closely acquainted with work on variety of reference lists, we can suggest that use of the existing option for assigning the ‘unaccepted’ status, or perhaps a new status ‘deprecated’ that would leave the entry in your database, would be more optimal and transparent way to manage your invaluable collection of species references.

Kind regards,

Joana Ribeiro Data Officer – Cross Discipline