Harold W. Manter Laboratory of Parasitology Collection (HWML) missing from Vertnet RSS

[jhpoelen]

Hi!

GloBI uses the Vertnet RSS IPT feed to track all DwC-A that Arctos makes available for their related collections.

Today, I noticed that a parasite of reference from https://arctos.database.museum/guid/MSB:Mamm:232346 to specimen http://arctos.database.museum/guid/HWML:Para:66271 could not be resolved by GloBI. The bidirectional link works as expected in the Arctos specimen web pages.

After checking the Vernet RSS IPT , using:

curl "http://ipt.vertnet.org:8080/ipt/rss.do" | grep HWML

, I noticed that the Arctos managed HWML collection does not appear to be listed.

Is these a reason why the HWML collection is not included in vertnet RSS feed? I am looking in the wrong place?

Thanks in advance for your response. -jorrit

PS If there's a better way to track all Arctos records than using the Vertnet RSS feed , please let me know.

[campmlc]

Yes, we were discussing this in November - should be one of the backlogged collections in progress, @dbloom All arctos data for all collections are publicly available through the main Arctos portal https://arctos.database.museum/. But we publish to external resources and aggregators via the VertNet IPT.

[campmlc]

@dustymc

[jhpoelen]

ok @campmlc thanks for confirming that HWML is waiting to be added to VertNet . Would you like to keep this issue open until the addition to VertNet is complete?

[tucotuco]

Yes, please.

On Wed, Oct 28, 2020 at 10:05 PM Jorrit Poelen notifications@github.com wrote:

ok @campmlc https://github.com/campmlc thanks for confirming that HWML is waiting to be added to VertNet . Would you like to keep this issue open until the addition to VertNet is complete?

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[tucotuco]

Yes. This process is pending work that Mariel is doing with that collection. We're ready to make it public via the VertNet IPT as soon as all of the collection issues have been resolved. Wherever that is.

David Bloom VertNet Coordinator

Phone: +01 510 859 7773 Email: dbloom@vertnet.org Skype: dabblepop Hangouts: dbloom@vertnet.org

On Wed, Oct 28, 2020 at 6:41 PM John Wieczorek tuco@berkeley.edu wrote:

Yes, please.

On Wed, Oct 28, 2020 at 10:05 PM Jorrit Poelen notifications@github.com wrote:

ok @campmlc https://github.com/campmlc thanks for confirming that HWML is waiting to be added to VertNet . Would you like to keep this issue open until the addition to VertNet is complete?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/3176#issuecomment-718295018, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADQ725JXPC2UDSXNVKSOYTSNC5VVANCNFSM4TCWR7BA .

[campmlc]

This collection should be ready to publish to the IPT. I'll check the metadata.

On Thu, Oct 29, 2020, 10:07 AM John Wieczorek notifications@github.com wrote:

• [EXTERNAL]*

Yes. This process is pending work that Mariel is doing with that collection. We're ready to make it public via the VertNet IPT as soon as all of the collection issues have been resolved. Wherever that is.

David Bloom VertNet Coordinator

Phone: +01 510 859 7773 Email: dbloom@vertnet.org Skype: dabblepop Hangouts: dbloom@vertnet.org

On Wed, Oct 28, 2020 at 6:41 PM John Wieczorek tuco@berkeley.edu wrote:

Yes, please.

On Wed, Oct 28, 2020 at 10:05 PM Jorrit Poelen <notifications@github.com

wrote:

ok @campmlc https://github.com/campmlc thanks for confirming that HWML is waiting to be added to VertNet . Would you like to keep this issue open until the addition to VertNet is complete?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/ArctosDB/arctos/issues/3176#issuecomment-718295018 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AADQ725JXPC2UDSXNVKSOYTSNC5VVANCNFSM4TCWR7BA

.

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[campmlc]

Here is the EML metadata. OK to publish @tucotuco @dbloom

HWML EML for VertNet IPT.docx

[jhpoelen]

Just stumbled across this issue and confirmed that HWML is still waiting to be added to vertnet by running

$ curl "http://ipt.vertnet.org:8080/ipt/rss.do" | grep HWML

and finding 0 hits.

Am assuming that y'all are pretty busy and that adding Harold W. Manter Laboratory of Parasitology Collection (HWML) to vertnet is pending. Thanks for all your hard work!

[campmlc]

Yes, my understanding is that it is in the cue. @dbloom @tucotuco Thanks for checking!

[seltmann]

@tucotuco @campmlc @jhpoelen Checking back about the HWML collection on vertnet. I am still not seeing it in the RSS feed. We are hoping to include this collection in the next Terrestrial Parasite Tracker indexed biotic interactions and review summary data publication

Thanks again for your help, Katja

[campmlc]

I'm not sure why this collection has not been published. There is no holdup on the Arctos end.

On Sat, May 29, 2021, 10:33 AM Katja Seltmann @.***> wrote:

• [EXTERNAL]*

@tucotuco https://github.com/tucotuco @campmlc https://github.com/campmlc @jhpoelen https://github.com/jhpoelen Checking back about the HWML collection on vertnet. I am still not seeing it in the RSS feed. We are hoping to include this collection in the next Terrestrial Parasite Tracker indexed biotic interactions and review summary data publication http://doi.org/10.5281/zenodo.4070039

Thanks again for your help, Katja

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[dbloom]

@seltmann @campmlc The loose end is my pending question to Arctos: Who is the publishing organization? As far as I can tell HWML is not a registered publisher with GBIF. Univ or Nebraska is in SciCol but not a registered publisher. The U of Neb State Museum is a publisher (https://www.gbif.org/publisher/9b049850-d958-11da-9047-b8a03c50a862), but nobody has confirmed that this is the correct entity to which I should register this collection.

Clarification is needed - and possibly the registration of a new publisher to GBIF. I can do that, I just need to know where this collection belongs. Otherwise, the collection is ready to go.

[campmlc]

I will confirm with the Manter lab right away. To my knowledge they are part of U N State Museum.

On Mon, May 31, 2021, 9:30 AM David Bloom @.***> wrote:

• [EXTERNAL]*

@seltmann https://github.com/seltmann @campmlc https://github.com/campmlc The loose end is my pending question to Arctos: Who is the publishing organization? As far as I can tell HWML is not a registered publisher with GBIF. Univ or Nebraska is in SciCol but not a registered publisher. The U of Neb State Museum is a publisher ( https://www.gbif.org/publisher/9b049850-d958-11da-9047-b8a03c50a862), but nobody has confirmed that this is the correct entity to which I should register this collection.

Clarification is needed - and possibly the registration of a new publisher to GBIF. I can do that, I just need to know where this collection belongs. Otherwise, the collection is ready to go.

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[dbloom]

@campmlc Before this fades from memory again, have you heard anything from Manter? This is what happened last time - we asked and then moved on without an answer. Would be good to get this finished. Let me know if I need to deplay an iNag (tm) and I will.

[dustymc]

Do we need to add something to the model, and/or pass it on with the EML?

[dbloom]

@dustymc No need to change the model. This is a one-off residual of conversations that stems from parasite collection consolidations and uncertainty about whether or not this particular collection wanted to its own "organization" on GBIF because it's acronym is not the expected UNSM that the other collections at Neb use, inkages to Smithsonian, etc... You know, people, politics, blah. Just trying to be certain that how they want to be represented so we don't have to undo and redo a bunch of crap.

If someone wants to make an executive dcn about UNSM I can have them up in a few minutes and that would make @seltmann super happy.

[campmlc]

Yes, I heard back via email. @gracz-UNL was going to try to email you, but in the meantime, the answer is yes, we need to move forward with publishing.
There are currently University of Nebraska State Museum records for other collections, and also some older Manter lab records at GBIF. The older Manter lab resource should be deprecated in favor of the Arctos data via the VertNet IPT. But this needs to be associated with the other material from the UNSM - possible? Here is reply from @gracz-UNL:

Hi David,

As you mentioned: "University of Nebraska State Museum" the official name of our institution is a publisher at GBIF. https://www.gbif.org/publisher/9b049850-d958-11da-9047-b8a03c50a862

According the the short description:

Administrative contact Thomas Labedz ---> still CORRECT (email: tlabedz1@unl.edu) Description http://www-museum.unl.edu/ (OUT OF DATE) update to -->https://museum.unl.edu/ At this point, GBIF stores 4 collections under Univ. Nebr. State Museum: Mammal, Bird, Herp, and Fish Collection.

As a fifth one, you can add "Parasite Collection - Harold W. Manter Laboratory of Parasitology" and add my name as contact person (Gabor Racz - gracz2@unl.edu). I can be an alternate contact person next to Tom Labedz, our offices are just a few doors apart in the same building.

Here is info on populating the specific page: Description The Harold W. Manter Laboratory of Parasitology (HWML) was established 29 March 1971 at the University of Nebraska - Lincoln as a new division in the University of Nebraska State Museum (UNSM). The founding core of the collection was based on Dr. Manter's research collection of parasitic trematodes of oceanic fishes. In 1981 the HWML was designated as one of three National Resource Centers for Parasitology and many students associated with the lab have been trained in systematics as well as other aspects of parasitology. Three Henry Baldwin Ward Medalists (the highest annual award that is given by the American Society of Parasitologists) were students in Parasitology and in the lab while Professor Mary Hanson Pritchard directed the laboratory (Professor Pritchard is now Curator Emeritus). In the past 5 years, more than 150 publications have resulted from research both in the HWML and from specimens loaned from, or deposited into, the HWML as types or vouchers. On an annual basis we process more than 20 outgoing loans per year and we receive thousands of specimens into the collection from researchers world-wide for archiving and safe storage of valuable voucher specimens.

Temporal scope January 1, 1909 - present Geographic scope Worldwide with approximately 80% of the specimens from North America.

Taxonomic scope Phylum Platyhelminthes - flatworms Class: Cestoda, Trematoda, Monogenea Phylum Nematoda, Phylum Nematomorpha, Phylum Acanthocephala Phylum Arthropoda including Acari (mites and ticks), Siphonaptera (fleas), Phthiraptera (lice). plus some minor parasitic specialized taxonomic groups: Myxospora, "Protozoa", Pentastomida, etc.

Additional info http://vertnet.org/resources/norms.html

Contacts Gabor R. Racz Originator Metadata author Administrative point of contact Collection Manager Harold W. Manter Laboratory of Parasitology, University of Nebraska State Museum W529 Nebraska Hall Lincoln 68588-0314 NE United States of America gracz2@unl.edu +01 402-472-3334 http://hwml.unl.edu/

Scott L. Gardner Administrative point of contact Curator Harold W. Manter Laboratory of Parasitology, University of Nebraska State Museum W529 Nebraska Hall Lincoln 68588-0314 NE United States of America gracz2@unl.edu +01 402-472-3334 http://hwml.unl.edu/

Data description Metadata language English Data language English GBIF registration

hosted by Arctos (https://arctos.database.museum/SpecimenSearch.cfm?guid_prefix=HWML%3APara)

Citation Scott L. Gardner and Gabor R. Racz (2021). University of Nebraska State Museum - Parasitology. Harold W. Manter Laboratory of Parasitology. University of Nebraska State Museum.

David: let me know what other information you will need or what needs to be tweaked.

[campmlc]

My understanding is that the reason that USNM wasn't used for Manter has to do with misunderstandings during portal creation some many years ago now, so now all the Arctos records have guids as HWML:Para.

[campmlc]

And we should be able to use the Arctos generated EML file.

[dbloom]

Thanks @gracz-UNL @campmlc et al.

So, as I understand it I need to:

1. update the metadata in the new resource to reflect the changes provided above (I've already used the EML generator for this, but I will confirm that the metadata is correct and update as necessary).
2. notify GBIF that the old "orphaned" dataset (https://www.gbif.org/dataset/8117733e-f762-11e1-a439-00145eb45e9a) can be removed from the index.
3. When cleared by GBIF publish the new Manter collection as a part of UNSM.

Am I missing anything?

[campmlc]

Sounds correct to me!

On Wed, Jun 2, 2021, 1:17 PM David Bloom @.***> wrote:

• [EXTERNAL]*

Thanks @gracz-UNL https://github.com/gracz-UNL @campmlc https://github.com/campmlc et al.

So, as I understand it I need to:

1. update the metadata in the new resource to reflect the changes provided above (I've already used the EML generator for this, but I will confirm that the metadata is correct and update as necessary).
2. notify GBIF that the old "orphaned" dataset ( https://www.gbif.org/dataset/8117733e-f762-11e1-a439-00145eb45e9a) can be removed from the index.
3. When cleared by GBIF publish the new Manter collection as a part of UNSM.

Am I missing anything?

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[dbloom]

Published. https://www.gbif.org/dataset/c43384a9-8d9d-40c0-8cda-40ad47d2d69d 60+k records and images indexed.

Updates should occur on the 2nd of each month. @seltmann

I will let @campmlc or @gracz-UNL confirm the publication and resolve this issue.

[seltmann]

@dbloom @campmlc @gracz-UNL Thank you for making this happen!

What lovely flea photographs. Awesome!

[campmlc]

Yes, more host para linkages pending to this collection!

On Wed, Jun 2, 2021, 5:32 PM Katja Seltmann @.***> wrote:

• [EXTERNAL]*

@dbloom https://github.com/dbloom @campmlc https://github.com/campmlc @gracz-UNL https://github.com/gracz-UNL Thank you for making this happen!

What lovely flea photographs. Awesome!

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[jhpoelen]

@campmlc @dbloom @seltmann @tucotuco @dustymc @gracz-UNL thanks for helping to make Harold W. Manter Laboratory of Parasitology Collection easier to access!

[jhpoelen]

I was able to confirm that Manter lab interaction are now being read by GloBI. I've attached a list of interactions to this issue generated by:

$ elton update globalbioticinteractions/unl-nsm && elton interactions 

So far a little shy of 900 interaction records, and, as @campmlc intuited, these interaction records are linking specimen to specimen into the msb mamm records. Very cool to see this rich data coming out of your collections!

globi-indexed-manter-interactions-2021-06-02.tsv.txt

[jhpoelen]

And via https://travis-ci.com/github/globalbioticinteractions/unl-nsm/jobs/510571696#L247

   _____ _       ____ _____   _____            _                
  / ____| |     |  _ \_   _| |  __ \          (_)               
 | |  __| | ___ | |_) || |   | |__) |_____   ___  _____      __ 
 | | |_ | |/ _ \|  _ < | |   |  _  // _ \ \ / / |/ _ \ \ /\ / / 
 | |__| | | (_) | |_) || |_  | | \ \  __/\ V /| |  __/\ V  V /  
  \_____|_|\___/|____/_____| |_|  \_\___| \_/ |_|\___| \_/\_/   
 | |           |  ____| | |                                     
 | |__  _   _  | |__  | | |_ ___  _ __                          
 | '_ \| | | | |  __| | | __/ _ \| '_ \                         
 | |_) | |_| | | |____| | || (_) | | | |                        
 |_.__/ \__, | |______|_|\__\___/|_| |_|                        
         __/ |                                                  
        |___/                       
Review of [local] started at [2021-06-03T00:05:53+00:00].

updating [local]... done.
creating review [local]... done.
listing interactions [local]... done.
listing taxa [local]... done.
listing nanopubs [local]... done.

Review of [globalbioticinteractions/unl-nsm] included:
  - 861 interaction(s)
  - 0 note(s)
  - 2 info(s)
Hurray! [globalbioticinteractions/unl-nsm] passed the GloBI review.

[gracz-UNL]

Published. https://www.gbif.org/dataset/c43384a9-8d9d-40c0-8cda-40ad47d2d69d 60+k records and images indexed.

Updates should occur on the 2nd of each month. @seltmann

I will let @campmlc or @gracz-UNL confirm the publication and resolve this issue.

Hi, I spotted one mistake that I made: the zip code for Scott Gardner and me (Gabor Racz) has a typo. The correct zip code is 68588-0514 NE

Thank you, Gabor

[dbloom]

corrected and republished