Add "Mason's world encyclopedia of livestock breeds" source in VBO

[sabrinatoro]

from the VBO meeting on 2023-10-05:

"Mason's world encyclopedia of livestock breeds" has a wealth of information about livestock breeds and has been a reference for livestock breed for a long time.

We want to add a reference to this encyclopedia in VBO.

TO DO:

• @franknic will review the VBO list, and add a column for the book reference.
  - book reference should be ISBN:978-1-84593-466-8 (Sabrina checked for a similar example in Mondo and confirmed the format)
  - Spreadsheets to use are here:
  - copy of DADIS livestock (there are 2 tabs: transboundary and country breed)
  - copy of livestock
  - Add the ISBN number in the column called "Mason source" (Col E) for each VBO term that needs to get this reference

• After Frank is done, Sabrina and/or Katie will update the master spreadsheet

[sabrinatoro]

@franknic, please find the spreadsheet for your review in the issue description. Let me know if you have any questions.

Once you are done, please assign this issue to katie or myself, and we will update the master spreadsheet.

Thank you!

[franknic]

Thank you, Sabrina.
I've worked through manually all 21 of the Ass transboundaries and the first 10 Cattle transboundaries. If they are mentioned in the Mason Dictionary, I have entered its ISBN in column E. If that breed is also mentioned in Mason's Encyclopedia, I have entered its ISBN in column F. Of the 21 Ass transboundaries, 19 are mentioned in the dictionary and 18 in the encyclopedia. For the first 10 cattle transboundaries, all 10 are in the dictionary and 8 are in the encyclopedia.
I haven't done any breed-country entries, because the only relevant ones are those that have species as a parent (i.e. exist in only one country); and we probably need a separate list of such breeds to facilitate the matching.
Overall, we can conclude that Mason's Dictionary and Encyclopedia should be citable for a high proportion of VBO transboundaries.
Having tested the system, there is no real point in me doing any more manual matching. So you and Katie could proceed with the ones I've just done. Imke and I will chat with Marius about automating the matching. And Stephen Hall has given me a contact in CABI to whom I shall soon write, enquiring whether there is a feasible way for us to link to an online version of the Dictionary/Encylopedia.

[franknic]

Greetings, all
I have just assigned Imke, Marius and Katie to this issue.
Katie: as mentioned in the previous comment, I have now done some manual matching of Mason's Dictionary and Mason's Encyclopedia to VBO in the sheets provided by Sabrina.
Imke and I will discuss the automation of this process with Marius.
In the meantime, since this task will have to be placed in the Marius queue, it might be worth while to incorporate the manually-assigned matches now, as a test for this strategy.

[katiermullen]

@franknic can you share the spreadsheet that you are working on to add the manually assigned matches?

[franknic]

Thank you, Katie
I was away yesterday but am back in action now. The Mason ISBNs mentioned above were added to the transboundary page of copy of DADIS livestock
I should have mentioned this in my previous message!

[franknic]

Back again, Katie
I also forgot to ask if every occurrence of an ISBN could point to its URL, i.e.
Each occurrence of ISBN:978-1-78924-153-2 points to:
https://www.cabidigitallibrary.org/doi/book/10.1079/9781789241532.0000
Each occurrence of ISBN:978-1-84593-466-8 points to:
https://www.cabidigitallibrary.org/doi/book/10.1079/9781845934668.0000
This would enable us to show the Mason team how we can cite their books in VBO.

[katiermullen]

@franknic Thank you for performing the trial mappings of the Mason terms to the VBO terms! I have included your manual mappings in the master spreadsheet and they will appear in VBO at the next release for you to share with the Mason team. If approved, we can proceed with programmatically adding the Mason annotations.

[franknic]

Thank you very much, Katie. An important step along an important road.

[katiermullen]

@sabrinatoro please update QC checks so we can use the "isbn:" prefix. Thank you!!!!!

[sabrinatoro]

@katiermullen I could not find a QC check related to unacceptable prefixes (similar to qc-illegal-prefix-on-zref-annotation.sparql in Mondo). So you should be able to use ISBN:
(though I guess the final word will be from the QC checks themselves)

[franknic]

I have realised that it is a trivial task for me to provide page numbers in the Mason Dictionary 6th edn for the small number of Ass breeds for which ISBNs have already been incorporated into VBO. The relevant page numbers are included in the table below, in a new column alongside existing columns. I appreciate that the last thing you need now is another task before launching the new release. But I am hoping it would be a simple matter to include the page number alongside the URL linking to the book on the publisher's website. This would provide powerful evidence to the Mason authors and publisher.

<style> </style>

	VBO transboundary breed	Mason dictionary 6th edn	Page number in Mason’s Dictionary 6th edn	Mason Encyclopedia
VBO:0000042	Andaluza	ISBN:978-1-78924-153-2	2	ISBN:978-1-84593-466-8
VBO:0000043	Balearic donkey breed	ISBN:978-1-78924-153-2	2	ISBN:978-1-84593-466-8
VBO:0000044	Burro Criollo
VBO:0000045	Burro Kentucky	ISBN:978-1-78924-153-2	3
VBO:0000046	Cyprus	ISBN:978-1-78924-153-2	3	ISBN:978-1-84593-466-8
VBO:0000047	Damascus	ISBN:978-1-78924-153-2	4	ISBN:978-1-84593-466-8
VBO:0000048	Dongolawi	ISBN:978-1-78924-153-2	4	ISBN:978-1-84593-466-8
VBO:0000049	Hamadan	ISBN:978-1-78924-153-2	5	ISBN:978-1-84593-466-8
VBO:0000050	Khulan	ISBN:978-1-78924-153-2	6	ISBN:978-1-84593-466-8
VBO:0000051	l’Ane Africain
VBO:0000052	Majorero	ISBN:978-1-78924-153-2	7	ISBN:978-1-84593-466-8
VBO:0000053	Mammoth Jack Stock	ISBN:978-1-78924-153-2	7	ISBN:978-1-84593-466-8
VBO:0000054	Masai	ISBN:978-1-78924-153-2	7	ISBN:978-1-84593-466-8
VBO:0000055	Meskhet-Javakhet	ISBN:978-1-78924-153-2	7	ISBN:978-1-84593-466-8
VBO:0000056	Native of North Africa	ISBN:978-1-78924-153-2		ISBN:978-1-84593-466-8
VBO:0000057	Pega	ISBN:978-1-78924-153-2	8	ISBN:978-1-84593-466-8
VBO:0000058	Poitou	ISBN:978-1-78924-153-2	9	ISBN:978-1-84593-466-8
VBO:0000059	Somali	ISBN:978-1-78924-153-2	10	ISBN:978-1-84593-466-8
VBO:0000060	Somali Wild Ass	ISBN:978-1-78924-153-2	10	ISBN:978-1-84593-466-8
VBO:0000061	Syrian	ISBN:978-1-78924-153-2	10	ISBN:978-1-84593-466-8
VBO:0000062	Tibetan	ISBN:978-1-78924-153-2	11	ISBN:978-1-84593-466-8

[sabrinatoro]

@franknic Because of how the cross-references are formatted, we cannot add the page number to the cross-reference. However, if you believe the page number is important, we could add it in a comment.

My personal opinion is that this information can easily get out of date. For example, if there is a new edition, this page number might become incorrect.

[franknic]

Thank you very much, Sabrina. I agree about page numbers getting out of date, although that's an unlikely problem for Mason's dictionary. In any case, the aim was simply to enable us to show the Mason editors and publishers that we can link to their information, and this is (I hope) just an interim strategy. I look forward to showing the editors and publisher the links (without page numbers) in the new release, and I hope that we can use those links to enable us to establish am fruitful collaboration with the Mason enterprise.

[franknic]

Greetings, Sabrina and Katie
The new release looks very good!
To get a feel for the Mason links in the new release, I have looked at Andaluza (Ass).
Thank you for including the ISBNs. Since there is a hyperlink in the same section ("Source"), I assume that it would be feasible to include the hyperlink to the ISBNs in this section. However, since the Mason books are not yet a source, we probably should think about including them elsewhere. Is it feasible to include the hyperlink to the books in a comment with a title something like "Further information"?

[katiermullen]

As discussed in the VBO call on 2024-02-01, it would be best to include the ISBN in Bioregistry format. Updating the ISBN's provided to this format. See https://bioregistry.io/registry/isbn.

[franknic]

Thank you very much, Katie. We are very grateful for your efficient solution to this challenge.

[franknic]

Greetings, Katie
Would it be possible for you to list a few VBO entries that include a comment, so that we can contemplate how best to incorporate Mason information in a comment?
With thanks
Frank

[katiermullen]

Hi Frank,

I think that if we can avoid using the comment to incorporate the Mason information, it would be best. There is only one comment allowed per VBO ID and it gets a bit cumbersome to manage a variety of information in a comment. I think that if the hyperlink for the Mason's ISBN from OLS takes the user directly to the Mason ISBN URL will be most efficient and still provide attribution to the Mason reference.

@matentzn is it possible to refresh VBO_DEV so I can see if this the Mason db-xrefs are working as expected?

[matentzn]

Yes, but you will have to check if Trish can review https://github.com/monarch-initiative/ontotools-docker/pull/18/files, because else the redeploy pipeline will fail.

[franknic]

Thank you, Katie and Nico
I accept your point about the comment field. Since the Mason links will now remain in the Source field, is it possible for this field to contain text such as "Mason’s World Dictionary of Livestock Breeds, Types and Varieties, 6th Edition" hyperlinked to https://www.cabidigitallibrary.org/doi/book/10.1079/9781789241532.0000 ?

[katiermullen]

Unfortunately, we cannot add the hyperlink to the website or text field with source name because the standard format for this source in the ontology is ISBN:123. This is similar to how we use PMID:123 for sources. Using the ISBN will ensure that that there is a permanent link to the source. If the URL changed, then users would not be able to access the source from VBO. Standards for metadata like sources are important to make sure VBO is interoperable with other ontologies and for providing full and permanent attribution and provenance for breed sources.

[franknic]

Thank you very much. Katie. Your explanation is very helpful.
I'm on a steep learning curve! And I'm trying to understand the possibilities when we (hopefully) have reached agreement with the Mason team to refer directly to an online source of their information.
At present, the source section includes the URL https://www.fao.org/dad-is. Does this mean that if we were given access to a web-based version of the Mason information, we could also include in the source section a URL that points to their information?

[katiermullen]

Frank, I am right there with you on the steep learning curve :) Yes, if Mason's had an online database like FAO DAD-IS, we could include the URL as a source. Please let us know if you think it would be helpful to arrange a meeting with the Mason's team, OMIA and the VBO team.

[sabrinatoro]

It is not entirely correct.

What we want to use in the ontology is an identifier that is unique and permanent (ie that will never change). PMID, ISB ids are unique and permanent and therefore are the best to use when referring to something, for instance, a source.
If Mason had an online presence, we would not refer to their website, we would still refer to their book ID OR to the ID corresponding to the specific breed records, we would use the (the same way that we refer to OMIA:1234, and not omia.org in Mondo).

The reason why we have a website address for FAO DAD-IS (and for most international societies) is that they do not have unique and permanent IDs that are publically available and that we can refer to. They also don't have a publication that we can refer to in order to indicate that "the information from this breed came from this specific publication/record". Therefore, in the case of FAO, a link to the website is not ideal, but is the best thing we can use to refer to the source.

Another example to look at is the iDog source for which we use the iDog ID, and not website.
I hope that helps.

[franknic]

Thank you Katie and Sabrina
So, the order of preference for hyperlinks in the Source field is:

1. hyperlink to an unchanging and specific site for information on that particular entry
2. hyperlink to a book containing that information but (if I recall correctly) it is not possible to provide a page number for information directly relevant for that entry
3. hyperlink to a generic website

For the has_dbxref field, I can certainly see the utility of the hyperlink to iDog ID. I also see that it is possible in that field to have specific information that is not hyperlinked, but for which a generic hyperlink is provided under the i symbol, e.g. VeNom:14631 for Labrador Retriever (Dog). Does this suggest we could include in this field, for example, something like Mason Dictionary, page xxx, and then provide a hyperlink to the book under the i symbol?