citation guidelines for individual specimen

[jhpoelen]

Some datasets (e.g., Arctos) use urls to cite allow for citing their specimen (e.g., http://arctos.database.museum/guid/MSB:Para:3643) in their dwca references field:

...	references	institutionID	collectionID	institutionCode	collectionCode	basisOfRecord
...	http://arctos.database.museum/guid/MSB:Para:12837	MSB	27	MSB	Parasite specimens	PreservedSpecimen

However, other datasets do not provide an explicit references value.

@seltmann @zaspelj @juliema what is a traditional way to cite a specimen in literature? catalog number / collection code / institution code ? Or, how would you like others to cite your references?

[jhpoelen]

With specific examples, I can cobble together a citation string that can be applied across specimen without explicit reference string.

[neilcobb]

Some datasets (e.g., Arctos) use urls to cite allow for citing their specimen (e.g., http://arctos.database.museum/guid/MSB:Para:3643) in their dwca references field:

... references institutionID collectionID institutionCode collectionCode basisOfRecord
... http://arctos.database.museum/guid/MSB:Para:12837 MSB 27 MSB Parasite specimens PreservedSpecimen
However, other datasets do not provide an explicit references value.

@seltmann @zaspelj @juliema what is a traditional way to cite a specimen in literature? catalog number / collection code / institution code ? Or, how would you like others to cite your references?

Both catalogNumber and URLs are used

[jhpoelen]

Good to know - can you provide an example of a publication that did the specimen citation by the book ?

[jhpoelen]

@neilcobb thanks for chiming in btw!

[neilcobb]

Good to know - can you provide an example of a publication that did the specimen citation by the book ?

i missed "literature" I have never looked at records that did not use GBIF DOI, my guess is that they do not generally list individual records if they are citing SCAN or some other source besides GBIF

[jhpoelen]

Ah, interesting. Would you say that because it is hard to cite (and find cited) individual specimen, the link between a study on their underlying evidence established on the collection (e.g., Arctos MSB-PARA) or even network (e.g., SCAN) level?

[jhpoelen]

Or is it not valuable to know exactly what specimen were used in a study?

[neilcobb]

Or is it not valuable to know exactly what specimen were used in a study?

I think it varies greatly among researchers, some simply cite SCAN (or not), others go down to institution and some publish the records they use

[jhpoelen]

@neilcobb thanks for sharing your experience.

@seltmann @zaspelj @juliema katja, jen, julie, am curious to hear your thoughts on how we can best cite the parasite tracker specimen records that we include in our terrestrial parasite tracker indexed interactions and review reports.

[juliema]

this is a big question for sure. Lets discuss on Wednesday?

…

On Mon, Mar 2, 2020 at 11:26 AM Jorrit Poelen ***@***.***> wrote: @neilcobb <https://github.com/neilcobb> thanks for sharing your experience. @seltmann <https://github.com/seltmann> @zaspelj <https://github.com/zaspelj> @juliema <https://github.com/juliema> katja, jen, julie, am curious to hear your thoughts on how we can best cite the parasite tracker specimen records that we include in our terrestrial parasite tracker indexed interactions and review reports. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#12?email_source=notifications&email_token=AA2AZ3UNQINZGW4WIVAS6VLRFQB6VA5CNFSM4K72E5OKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENQTUJQ#issuecomment-593574438>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2AZ3VTNA6ORPMEZFGPBKDRFQB6VANCNFSM4K72E5OA> .

[jhpoelen]

Before we dive into a meeting, I would like to hear proposals for citing individual specimen and/or examples of existing best practices for citing individual specimen in literature. Then, if no consensus is reached, we can discuss the various proposals in a meeting.

[zaspelj]

Hi, I won’t be able to discuss until next week. Thanks! Jen

…

On Monday, March 2, 2020, Jorrit Poelen ***@***.***> wrote: Before we dive into a meeting, I would like to hear proposals for citing individual specimen and/or examples of best practices for individual specimen. Then, if no consensus is reached, we can discuss the various proposals in a meeting. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#12?email_source=notifications&email_token=AJ4HIMBWX723PCKRQVQWUNLRFRK2VA5CNFSM4K72E5OKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENRWBZQ#issuecomment-593715430>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJ4HIMGQCL6MW7UXFZRQI43RFRK2VANCNFSM4K72E5OA> .

-- *Jennifer M. Zaspel, PhD* Associate Curator and Head of Zoology Director of Puelicher Butterfly Wing Milwaukee Public Museum 800 West Wells Street, Milwaukee, WI <https://maps.google.com/?q=800+West+Wells+Street,+Milwaukee,+WI&entry=gmail&source=g> 414-278-6158| zaspelj@mpm.edu <youremail@mpm.edu> | www.mpm.edu

[neilcobb]

To add to my comment yesterday, catalogNumber is not unique for all collections (lots of legacy number-only catalogNumber records in use), I assume the URL specimen page is a GUID. But that GUID will be different for GBIF and SCAN. Some places use the triplet formula and include institution code. My guess is that institution code plus catalogNumber will work in most cases. I never knew the full function of the Symbiota GUID or anyone else’s GUID outside their respective software. I think occurrence ID works for a lot but not all records. Not sure if I am helping From: Jorrit Poelen <notifications@github.com> Sent: Monday, March 2, 2020 6:15 PM To: ParasiteTracker/tpt-reporting <tpt-reporting@noreply.github.com> Cc: Neil Stanley Cobb <Neil.Cobb@nau.edu>; Mention <mention@noreply.github.com> Subject: Re: [ParasiteTracker/tpt-reporting] citation guidelines for individual specimen (#12) Before we dive into a meeting, I would like to hear proposals for citing individual specimen and/or examples of best practices for individual specimen. Then, if no consensus is reached, we can discuss the various proposals in a meeting. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#12?email_source=notifications&email_token=ABNWKKSGZRN6Y4EKDESKDBTRFRK2VA5CNFSM4K72E5OKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENRWBZQ#issuecomment-593715430>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABNWKKTILOKI6C2D55QQP5LRFRK2VANCNFSM4K72E5OA>.

[jhpoelen]

@neilcobb thanks for sharing your insights -

So, what I hear you say is that a citation like:

[institutionCode] [collectionId] [collectionCode] [catalogNumber] [occurrenceId]

would provide the reader with various ways to identify the specimen record.

Should we add the other things too? Like scientific name, date and locality? Almost feels like we are reinventing the information present on a specimen label.

[neilcobb]

Those other variables may be annotated but [institutionCode] [collectionId] [collectionCode] [catalogNumber] [occurrenceId] should be constant and they should work in 99% or more of cases. Some institutions have multiple codes (legacy issues) and collection codes are still not widely used. From: Jorrit Poelen <notifications@github.com> Sent: Tuesday, March 3, 2020 8:00 AM To: ParasiteTracker/tpt-reporting <tpt-reporting@noreply.github.com> Cc: Neil Stanley Cobb <Neil.Cobb@nau.edu>; Mention <mention@noreply.github.com> Subject: Re: [ParasiteTracker/tpt-reporting] citation guidelines for individual specimen (#12) @neilcobb<https://github.com/neilcobb> thanks for sharing your insights - So, what I hear you say is that a citation like: [institutionCode] [collectionId] [collectionCode] [catalogNumber] [occurrenceId] would provide the reader with various ways to identify the specimen record. Should we add the other things too? Like scientific name, date and locality? Almost feel like we are reinventing the information present on a specimen label. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#12?email_source=notifications&email_token=ABNWKKWG2CBUCSS6EEHQT2DRFULPXA5CNFSM4K72E5OKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENT2GJA#issuecomment-593994532>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABNWKKRNK5E267R6BAIADC3RFULPXANCNFSM4K72E5OA>.