Ensure that the prefixes used for x-refs are in bioregistry

[sabrinatoro]

If we refer to other databases, we need to use a unique prefix for the x-ref (e.g. OMIM:xx, OMIA:xx, VENOM:xx). These unique prefixes should be requested at the bioregistry: https://bioregistry.io/

So for every x-ref we have (in Mondo and in VBO), we need to make sure the prefix we use are in the bioregistry. There are 2 things to do:

1) figure out whether we can use the OMIA: prefix. Currently, this prefix is “deprecated” in the bioregistry. https://bioregistry.io/registry/omia This should be resolved. This is also be done via their GH repository (which is probably somewhere on their website, I haven't look for it). 2) we need a prefix for VENOM. I didn’t see any prefix available for them. This probably needs to be done working with VeNom.

Note: more investigation is needed to figure out what type of information is required (this is probably on their website). Their GH repository is: https://github.com/biopragmatics/bioregistry/issues

[katiermullen]

1. It appears that OMIA has been deprecated in the bioregistry due to "website is down as of 2021-10-04" and missing contact information. The website link is currently to http://omia.angis.org.au/ and needs to be updated. A Contributor name, GitHub username and ORCiD need to be added. This information can be updated here: https://github.com/biopragmatics/bioregistry/issues/new?assignees=cthoyt&labels=Update&template=update-misc.yml
2. For databases that do not have a prefix, for example Venom and iDog, the contributor can request a new prefix here: https://github.com/biopragmatics/bioregistry/issues/new?assignees=biopragmatics%2Fbioregistry-reviewers&labels=New%2CPrefix&template=new-prefix.yml&title=Add+prefix+%5BX%5D

[katiermullen]

@ImkeTammen @franknic

[franknic]

Dear Katie, Frank and I made the Github request: https://github.com/biopragmatics/bioregistry/issues/719 Do we need to request any changes to ‘Pattern for Local Unique Identifiers’ and to ‘Pattern for CURIES’ Kind regards, Imke PS from Frank: I've copied and pasted the above text from Imke's email sent earlier today Katie: would you please add Marius to this? His GitHub id is mmat6620

[cthoyt]

Hi all, I’m happy to help facilitate anything related to the Bioregistry. Ideally we can chat on the issue tracker there, but please ping me on GitHub or slack with any questions!

Wrt iDOG, I found their "breeds" vocabulary has links like https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=4, meaning that it has a pattern of ^\d+$ and an example local identifier of 4.

[cthoyt]

we need a prefix for VENOM. I didn’t see any prefix available for them. This probably needs to be done working with VeNom.

Note that Bioregistry prefix requests explicitly do not need the advice/consent of the resources that they point to. This kind of red tape slows down efforts massively, and the goal of the Bioregistry is to describe the world the best that the community can. If you can clarify what the VeNom database is by linking to it, I can also take a look.

[sabrinatoro]

Thank you for offering your assistance, @cthoyt! We will definitely reach out.

[katiermullen]

Thank you for your assistance @cthoyt!

Regarding VeNom (Veterinary Nomenclature), the source is here: https://venomcoding.org/. @sabrinatoro and I met with Prof. Dave Brodbelt who is the chair of the VeNom Coding Group, and he is aware of our efforts to include VeNom codes related to breeds in VBO (and VeNom codes related to diseases in Mondo in the future). His contact information is here: https://venomcoding.org/contact-us/. I am happy to reach out to him as well. Just let me know what you prefer.

WRT iDog, we do not have a contact there. We came across that source via an online search. I am happy to have your help in facilitating registration of the prefix with Bioregistry in possible. Just a quick question, at https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=4, I fine the "iDog Breed Number: CB4." Is the correct identifier for use in VBO "iDog:4" or "iDog:CB4", in this example example?

[cthoyt]

Regarding VeNom (Veterinary Nomenclature), the source is here: https://venomcoding.org/. @sabrinatoro and I met with Prof. Dave Brodbelt who is the chair of the VeNom Coding Group, and he is aware of our efforts to include VeNom codes related to breeds in VBO (and VeNom codes related to diseases in Mondo in the future). His contact information is here: https://venomcoding.org/contact-us/. I am happy to reach out to him as well. Just let me know what you prefer.

Can you send me the excel sheet? Apparently this resource thinks that it's valuable to password protect it. If I were you, I would avoid including references to this resource on principle.

WRT iDog, we do not have a contact there. We came across that source via an online search. I am happy to have your help in facilitating registration of the prefix with Bioregistry in possible. Just a quick question, at https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=4, I fine the "iDog Breed Number: CB4." Is the correct identifier for use in VBO "iDog:4" or "iDog:CB4", in this example example?

The way I think about this is by looking at the URI and finding the part that changes for each page. It seems that https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId= is the URI prefix, and 4 by itself is the identifier. Therefore, I would say that it should be iDog:4. This phenomena of adding extra stuff in front of the local unique identifier (which has been dubbed the banana) is usually a phenomena that occurs within groups that have not thought about identification carefully and do not use CURIEs.

Luckily, this is such a widespread problem that we engineered a solution into the Bioregistry to help people who are unaware of these kinds of mistakes :)

[katiermullen]

Please let me check into sending you the VeNom excel sheet.

Thank you for the information on the iDog local unique identifiers. I understand now and will update the iDog identifiers in VBO.

[franknic]

Thank you very much for your help, @cthoyt. The VeNom team comprises academics and others at the Royal Veterinary College in London. They have put an enormous effort into creating their resource, which is incorporated into commercial case-load databases used in many veterinary practices. My understanding is that this is at least part of the reason why the codes are password protected. As Katie will know, they are happy to register and hence provide password access to not-for-profit collaborators.