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Request for new ontology GallOnt #2522

Closed adeans closed 7 months ago

adeans commented 9 months ago

Title

Gall Ontology

Short Description

Ontology of plant gall phenotypes

Description

Galls are novel plant structures that are induced by other organisms - i.e., parasites of the plants. These parasites can be insects, nematodes, fungi, or other organisms, and there is a large corpus of research on their interactions with plants. Despite this research, however, the phenomenon of gall induction remains only poorly understood. An ontology of gall terms could serve as a controlled vocabulary for gall phenotype descriptions but also as a means to connect gall research to what is understood from studies involving model plants (e.g., Arabidopsis). A draft version of this ontology was developed by mapping concepts from the plant gall literature to relevant classes in PATO, PO, and related OBO ontologies. Any concept/term that did not map to existing classes (e.g., "plant gall") was given a genus differentia definition and related to other classes using properties from RO. I used ODK as my development environment, with some help from Jim Balhoff.

Identifier Space

GALLONT

License

CC0

Domain

phenotype

Source Code Repository

https://github.com/adeans/gallont/tree/main

Homepage

https://github.com/adeans/gallont/tree/main

Issue Tracker

https://github.com/adeans/gallont/issues

Contribution Guidelines

https://github.com/adeans/gallont/blob/main/CONTRIBUTING.md

Ontology Download Link

https://raw.githubusercontent.com/adeans/gallont/main/gallont.owl

Contact Name

Andy Deans

Contact Email

adeans@psu.edu

Contact GitHub Username

adeans

Contact ORCID Identifier

0000-0002-2119-4663

Formats

Dependencies

Related

https://obofoundry.org/ontology/po.html https://obofoundry.org/ontology/pato.html

Usages

- user: https://orcid.org/0000-0002-2119-4663
  description: Andy Deans am using it to annotate the phenotypes of galls that are found on white oaks
  examples:
    - url: https://pennstateoffice365-my.sharepoint.com/:x:/g/personal/ard19_psu_edu/Ed0euAwwkiBJsSaYic4qjEwBhQF4Jlq-eHC2MU1sAoVJhA?e=HBEu8a
      description: "spreadsheet of phenotype descriptors from the literature which will be turned into a proof of concept for GALLONT"

Intended Use Cases and/or Related Projects

Annotate gall phenotypes described in publications, in order to build a data set to reason over and to make discoveries. Also, to possibly connect these phenotypes to knowledge derived from model plant systems. The ontology could also be used as a controlled vocabulary or even a relatively flat glossary for users of the Gall Formers website.

Data Sources

The terms were initially harvested from the gall description literature, using resources like the Biodiversity Heritage Library. The initial list of terms, roughly categorized into higher classes -- like texture, color, and shape -- was then shared with the community of plant gall researchers who subscribe to the gall listerserv (gal-l@lists.psu.edu). We took suggestions and iterated on this initial term set.

Additional comments or remarks

We have plans to further forge connections to the Plant Ontology developers, through a workshop planned in late February 2024. Until then, and when our ontology has been tested a bit more, we won't have much of an online presence.

OBO Foundry Pre-registration Checklist

pfabry commented 9 months ago

Dear @adeans,

Thank you for your submission. The review will be executed as a two stage process.

First, you will have to pass the new ontology precheck, including the OBO NOR Dashboard. Pass means that no check apart from Users and Versioning may be red. After you have successfully passed these verfications, you will be assigned an OBO Operations committee member to review the ontology.

Usually, the review will result in an opportunity for you to improve the ontology. When the reviewer believes the ontology is ready for presentation to the OBO Operations Committee, they will present your ontology during an OBO Operations Call. This gives other members of the committee the opportunity to assess your work.

When a decision is reached by the committee you will be informed here on the issue tracker. The process can take any number of weeks or months, depending on the case at hand. Please inform us about any reasons you might have for increased urgency. You will be informed once your ontology is loaded in the OBO NOR Dashboard.

Good luck!

pfabry commented 9 months ago

Meanwhile, you should consider changing the name of the ontology to avoid confusion with other meanings of "gall".

adeans commented 9 months ago

It's important to keep the term "gall" in there, but maybe we could change the title to "Plant Gall Ontology" ... ?

mbrochhausen commented 9 months ago

I think, Plant Gall Ontology would be ok. Just my 2cents.

On Thu, Feb 1, 2024 at 3:52 PM Andy Deans @.***> wrote:

It's important to keep the term "gall" in there, but maybe we could change the title to "Plant Gall Ontology" ... ?

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2522#issuecomment-1922222982, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACF6DLS34OIWEZO4PF6UTMTYRP6AFAVCNFSM6AAAAABCVNJHG6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRSGIZDEOJYGI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

pfabry commented 9 months ago

Your ontology has been added to the OBO NOR Dashboard. Could you specify which license are you using? The license actually mentioned in the owl file is https://creativecommons.org/licenses/unspecified

adeans commented 9 months ago

Oh sorry. The license I specified here - https://github.com/adeans/gallont - is CC0-1.0. I'll have to fix that!

adeans commented 9 months ago

I updated the gallont-edit.owl file to address the concerns above (i.e., the name and the license): Annotation(dcterms:license https://creativecommons.org/publicdomain/zero/1.0/) Annotation(dcterms:title "Plant Gall Ontology")

pfabry commented 9 months ago

Thanks for the update. A reviewer will be assigned soon.

pfabry commented 9 months ago

@adeans

After updating the gallont-edit,owl file, you should create the release version with make prepare_release or make prepare_release_fast to propagate your modifications to the gallont.owl file, which is the "public" version of your ontology. Additionally, that's the file that the dashboard is based on.

adeans commented 9 months ago

@pfabry Got it. I think it should be good to go now?

pfabry commented 9 months ago

@adeans @nicolevasilevsky has been assigned to review your ontology. In addition, a new check is currently implemented: it consists in a lexical match of your original terms with those already existing in OBO Foundry published ontologies. The goal is to prevent the duplication of terms with similar meanings (cf. Review SOP). A list of terms that are potential duplicates will be provided soon.

cmungall commented 8 months ago

Have you coordinated with PO? cc @jaiswalp @cooperl09

adeans commented 8 months ago

@cmungall I will be at their workshop next week :-)

cmungall commented 8 months ago

Awesome! And I meant to link to this ticket https://github.com/Planteome/plant-ontology/issues/641, which I will update

nicolevasilevsky commented 8 months ago

Manual review of GallOnt

  1. Ontology scope ✅
    • The terms fall within the ontology’s stated target domain of knowledge and appropriately import terms from other OBO ontologies such as PO and GO.
    • The Gall Ontology was developed for the plant gall research community to provide a controlled vocabulary for describing plant galls in model plant systems.
  2. Terms with the new ontology prefix ✅
    • Do the terms follow the OBO identifier scheme? yes
    • Are there terms with the same meaning available in another OBO Foundry ontology? no, I spot checked about 10 terms in GALLONT and did not find any overlap with existing OBO terms. There are a few terms that are subclasses of GALLONT:0000007 'internal quality' that have the same label as PATO terms (eg GALLONT:0000008 filamentous and PATO:0001360 filamentous, but the meaning is different.
    • Is there another OBO Foundry ontology whose scope covers any of the new terms? no, and this ontology reuses existing terms where appropriate.
  3. Correct use of imported terms ✅
    • If the ontology reuses terms from other OBO ontologies, are they used accurately? yes
    • Are imported terms in appropriate hierarchies, and do they preserve the term’s upper-level alignment? yes, I spot checked several terms/hierarchies and everything looks correct
    • Are any additional axioms used for these terms correct in both a technical (e.g. passes reasoning) and substantive sense? N/A, it does not appear that additional axioms were added, the terms are imported without modification from the external ontologies.
  4. Basic review of axiomatic patterns ✅ (see one question below)
    • Are axioms generally stated simply or are they highly complex? (Highly complex axioms will require extra scrutiny.) The axioms are simply and appropriately constructed and are consistent with patterns used in other OBO ontologies. One question is about the relation GALLONT:0000000 'has associate'. This is used to associate an NCBITaxon term with an anatomical entity, but I wonder if there is an existing RO term that could be used here?
    • Are existential restrictions used correctly? yes, as far as I can tell.
  5. Appropriate use of object properties ✅
    • Are object properties used in a manner consistent with their definitions, domain, and range? yes, I spot checked a few of the properties that are used ('has quality' and 'develops from' and they are properly being used.
  6. Responsiveness to suggested changes: ✅ yes. As evidenced above, the ontology developer has been very responsive to requests for changes and other queries.

Additional Questions/Suggestions

  1. Above it is suggested to rename this ontology to Plant Gall Ontology, will this suggestion be implemented?
  2. You may want to consider requesting felt-like as subclass of PATO hairy and replacing GALLONT:0000029 felt-like
adeans commented 8 months ago

Thanks! I will indeed change the name to "Plant Gall Ontology". And I do have some other candidate classes I will submit to PATO, along with felt-like (e.g., filamentous GALLONT:0000008, cupuliform GALLONT:0000015 plus a few others)

nicolevasilevsky commented 8 months ago

@adeans could you also please comment on how this ontology is different from the Plant Ontology and why it is needed, versus adding gall terms to PO? Thank you!

adeans commented 8 months ago

@nicolevasilevsky I am at a workshop right now hosted by the Planteome group, and this is one of the topics we'll cover. I like GALLONT as a compact set of classes that are specific to galls, including plant parts (PO), phenotype descriptors (PATO), and even arthropod classes (e.g., HAO). It's easy for an annotator to navigate while staying connected to relevant ontologies. Maybe there are other ways to handle this? A slim within PO? I am open to suggestions.

nicolevasilevsky commented 8 months ago

Sounds good @adeans, please update us here on your conversation with the Planteome group. Your justification for a separate Plant Gall Ontology makes sense to me.

Upon discussion with the OBO Operations committee, we should leave this ticket open for another 2 weeks to allow for others in the community an opportunity to comment.

Thanks for your quick responses!

pfabry commented 8 months ago

@adeans @nicolevasilevsky Below are the result of the lexical match for original terms from the Plant gall ontology:

Lexical matching returned results

Full results are attached: GALLONT lexmatch 20240229.txt

adeans commented 8 months ago

Interesting! These results will be very helpful as we move forward with gall-relevant terms.

nicolevasilevsky commented 8 months ago

@adeans Thank you again for your ontology submission to the OBO Foundry. We are happy to inform you that your ontology (GALLONT) has been accepted following discussion in the OBO Operations Committee meeting, 2024-03-05. Before we can add it to the OBO ontology registry you need to complete the following steps.

Create a metadata record for your ontology to be included in the registry:

  1. Create a new file in https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology, called GALLONT.md (there is an “Add file” button in the top right).
  2. Obtain the already curated metadata that relates to your ontology from https://github.com/OBOFoundry/obo-nor.github.io/blob/master/dashboard-config.yml (you’ll need to scroll down to locate yours; it will have your prefix in the “ - id:” field.)
  3. Create a pull request to add the metadata record. This pull request should include a link to this issue (the New Ontology Request issue).

Here is an example record for the PATO ontology: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/ontology/pato.md?plain=1

Your metadata will be reviewed and merged by a member of the OBO Foundry Operations Committee. Permissible content for fields is being documented here.

To create a PURL registry entry for your ontology:

  1. Go to https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config, click “Add file” and add a file named YOURID.yml.
  2. Add the desired configuration.
  3. Make a pull request with a link to this issue See here for an example of a PURL yml file: https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/pato.yml “
nicolevasilevsky commented 8 months ago

⬆️ this information will also be shared by email.

adeans commented 7 months ago

Got it! Just met with my Planteome collaborator, after a short delay, to finalize a path forward. I will made some edits and follow the steps outlined above. Thanks!

nicolevasilevsky commented 7 months ago

Thank you @adeans! We'll report this new ontology in our upcoming OBO Newsletter, which I think will be finalized on March 18. If it is at all possible to get these last steps done before that date, it would be greatly appreciated.

matentzn commented 7 months ago

Gallont is public, thank you @nicolevasilevsky for managing the review and @adeans for patiently addressing all concerns!

https://obofoundry.org/ontology/gallont.html