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Request for new ontology [Occupation Ontology] #2428

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11 of 13 tasks
zhengj2007 opened this issue Sep 1, 2023 · 33 comments
Closed
11 of 13 tasks

Request for new ontology [Occupation Ontology] #2428

zhengj2007 opened this issue Sep 1, 2023 · 33 comments
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@balhoff
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new ontology - accepted The ontology has been accepted, but the metadata has not yet been entirely processed. new ontology Use for new ontology registration requests

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@zhengj2007
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Title

Occupation Ontology

Short Description

Occupation Ontology The Occupation Ontology (OccO) is an ontology in the domain of human occupations.

Description

OccO is an initial ontological presentation of information taken from a standardized occupation taxonomy, the US Standard Occupational Classification (SOC) as enhanced by the O*Net system. These systems have been developed by the following US Federal agencies:

  • Department of Labor
  • Bureau of Labor Statistics
  • The O*NET Program, the United States' primary source of occupational information.

OccO reflects the data content of the O*Net-SOC 2019 taxonomy, which is based on the 2018 SOC, and it is developed by following OBO Foundry principles. The data used is from O*Net data by the U.S. Department of Labor, Employment and Training Administration (USDOL/EGA). It is used under the CC BY 4.0 license.

Identifier Space

OCCO

License

CC-BY 4.0

Domain

information

Source Code Repository

https://github.com/Occupation-Ontology/OccO

Homepage

https://github.com/Occupation-Ontology/OccO

Issue Tracker

https://github.com/Occupation-Ontology/OccO/issues

Contribution Guidelines

https://github.com/Occupation-Ontology/OccO/blob/main/CONTRIBUTING.md

Ontology Download Link

https://raw.githubusercontent.com/Occupation-Ontology/OccO/main/occo.owl

Contact Name

Jie Zheng

Contact Email

zhengj2007@gmail.com

Contact GitHub Username

zhengj2007

Contact ORCID Identifier

0000-0002-2999-0103

Formats

  • OWL RDF/XML (.owl)
  • OBO (.obo)
  • OBO Graph JSON (.json)

Dependencies

  • BFO
  • OMO
  • IAO
  • NCBITaxon
  • RO

Related

  • OMRSE

Usages

- user: Alabama government
  description: Alabama government employee related data integration and management
- user: https://www.hegroup.org
  description: Wikidata occupation data analysis

Intended Use Cases and/or Related Projects

  • Occupation classification data integration.
  • Alabama government employee related data integration and management

Data Sources

The primary data source used for current OccO ontology developer is the US SOC and O*Net occupation classification. The future, we will incorporate more data sources such as the ESCO data source.

Additional comments or remarks

References:
Foundational Development of an Occupation Ontology. https://ceur-ws.org/Vol-3249/paper6-OSS.pdf

Toward an Occupation Ontology, OccO. https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_5061.pdf

OBO Foundry Pre-registration Checklist

  • I have read and understood the registration process instructions and the registration checklist.
  • There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.
  • My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
  • My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy
  • I understand that term definitions, while not mandatory, are key to understanding the intentions of a term especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology have definitions, using the IAO:0000115 property.
  • For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
  • For all relationship properties (Object and Data Property), I checked whether the Relation Ontology (RO) includes an appropriate one. I understand that aligning with RO is an essential part of the overall alignment between OBO ontologies!
  • For the selection of appropriate annotation properties, I looked at OMO first. I understand that aligning ontology metadata and term-level metadata is essential for cross-integration of OBO ontologies.
  • If I was not sure about the meaning of any of the checkboxes above, I have consulted with a member of the OBO Foundry for advice, e.g., through the obo-discuss Google Group.
  • The requested ID space does not conflict with another ID space found in other registries such as the Bioregistry and BioPortal, see here for a complete list.
@zhengj2007 zhengj2007 added the new ontology Use for new ontology registration requests label Sep 1, 2023
@hoganwr
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hoganwr commented Sep 4, 2023 via email •
edited

@mbrochhausen
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mbrochhausen commented Sep 4, 2023 via email

@yongqunh
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yongqunh commented Sep 5, 2023

As I remember, we have been discussing and working with Bill Hogan, Matt Diller (Bill's PhD student), Bill Duncan, John Beverley, etc. on the occupation ontology (OccO) related collaborations since last year's ICBO 2022 conference. Sam Smith presented an OccO poster in ICBO 2022, and I introduced the work to Bill H., informed some possible overlapping with OMRSE, and initiated our discussions, negotiations, and collaborations. Matt has regularly attended our OccO working group meetings, and Bill has sometimes attended as well. Both Matt and Bill are OccO occupation ontology developers, and they are also co-authors of our recent OccO conference paper, which was presented by John Beverley in the the International Workshop on Ontologies for Social Services (OSS2023), July 2023, in Canada.

The main overlapping exists in that OMRSE represents medically related social entities and OccO represents all occupations. OccO has ontologized all the occupations represented by the US Standard Occupational Classification (SOC), released by the US Bureau of Labor. Later we plan to integrate and incorporate occupation related terms from other occupational classification systems including the ESCO from European Union, etc.

Both OMRSE and OccO follow the BFO upper level ontology. The high level terms and structural design have been well discussed since ICBO 2022 and have achieved agreement by our working group members including Matt and Bill H.

We have also discussed the submission of OccO to OBO Foundry (or another foundry such as IOF) for a long time. In the last few months we have basically achieved an agreement to submit it to OBO library.

One major difference between OccO and OMRSE is that OccO represents all specific occupations under the branch of 'occupation holder' (a subclass of human), and OMRSE puts them under 'role'. So in OccO, we treat each occupation type (e.g. pharmacist) as a human being and OMRSE treats it as a job role. Both approaches appear to work well. Considering both ontologies following the same BFO design, the different representation emphases unde the same BFO can be the basis of the interoperabilty between the two ontologies.

@hoganwr
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hoganwr commented Sep 5, 2023 via email

@yongqunh
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yongqunh commented Sep 5, 2023

Thanks, Bill, for your confirmation and clarification. I would also like to clarify two things:

First, our work of developing an occupation focused ontology has lasted for a long time (about 10 years), initially with the name RoleO (Role Ontology), which was submitted to BioPortal: https://bioportal.bioontology.org/ontologies/ROLEO. I also presented a RoleO related poster presentation with a Wikidata use case demonstration in the BioCuration 2018 conference. The OccO is an updated version of RoleO with a new name and focus. Sam Smith, a primary developer of RoleO and later OccO, has been leading the technical development since the beginning.

Second, I agree that initially we had no intention to submitting the OccO to OBO. We thought it might be sufficient to submit it to BioPortal. We discussed different options over the time. Recently Chris Mungall submitted an issue ticket to OccO GitHub:
Occupation-Ontology/OccO#3
To address the issue of making ontology IRI resolvable, we have followed Chris's suggestion, and Jie submitted the OccO to OBO for consideration.

Also, I agree with Bill that the dispute is not very large and can be solved. Bill, let's find time to discuss and negotiate on this. Thanks.

@pfabry
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pfabry commented Sep 12, 2023

OccO has been integrated in the NOR dashboard. The main issues are the following:

  • Lack of definition for > 500 c;lasses: these are mainly classes that overlap with the Standard Occupational Classification: this is not a red flag.
  • Duplicate alternative label, that is the same alternative label is used in different classes: this is not a red flag.
  • Versioning red flag: the version IRI is well formed, so this is more a problem with the dashboard IMHO.

On the whole, the ontology passes the dashboard

@cthoyt
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cthoyt commented Sep 13, 2023 •
edited

OccO has been integrated in the NOR dashboard. The main issues are the following:

* Lack of definition for > 500 c;lasses: these are mainly classes that overlap with the Standard Occupational Classification: this is not a red flag.

* Duplicate alternative label, that is the same alternative label is used in different classes: this is not a red flag.

* Versioning red flag: the version IRI is well formed, so this is more a problem with the dashboard IMHO.

On the whole, the ontology passes the dashboard

@pfabry it's more than the version IRI being well-formed, it actually has to point to the correct artifact

also, the alternative label problem is very worrysome, can we make this an explicit requirement that we don't add ontologies that have internal consistency issues like this?

@mbrochhausen
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mbrochhausen commented Sep 13, 2023 via email

@zhengj2007
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I noticed the issues when I ran Robot report. The issue is not only shown in OccO. I pointed out the issue before and was told it is useful in NLP.

For OccO, I am not clear where the alternative coming from and their usage.

@hoganwr
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hoganwr commented Sep 13, 2023 via email

@shawntanzk shawntanzk added the new ontology - reviewer required Indicates that an ontology is ready for review label Sep 19, 2023
@pfabry
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pfabry commented Sep 25, 2023

@dosumis
According to the OBO operation Duty Rotation list, the reviewer for this ontology is David Osumi-Sutherland.
Could you please let us know your availability for this review?

@dosumis
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dosumis commented Sep 25, 2023

What's the timeline?

@pfabry
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pfabry commented Sep 27, 2023

What's the timeline?

There is no deadline set, but a reasonable (few weeks) timeframe is expected.
However, this ontology is also the subject of ongoing discussions concerning orthogonality issues with OMRSE (cf. this issue). It seems relevant to wait for the conclusion of these discussions before going ahead with the review.

@yongqunh
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We (OccO team) have discussed with Bill Hogan @hoganwr at OMRSE, and have basically achieved an agreement on the harmonization.

@pfabry
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pfabry commented Sep 28, 2023 •
edited

We (OccO team) have discussed with Bill Hogan @hoganwr at OMRSE, and have basically achieved an agreement on the harmonization.

Great! Does it have a direct impact on the current release of OccO ? Should @dosumis wait for a new release before starting the review process ?

@hoganwr
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hoganwr commented Sep 28, 2023 via email

@zhengj2007
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Based on the discussion, OccO will import the OMRSE and replace the OccO terms with OMRSE ones, see: Occupation-Ontology/OccO#20

@matentzn
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matentzn commented Oct 2, 2023

@dosumis has been contacted again to provide this review as part of the general OFOC membership duties. "Remember you dont have to deal with this in Person. But you are responsible that this ontology gets reviewed by someone, by the next OFOC call (Oct 17th)."

@pfabry pfabry added new ontology - reviewer response required Reviewer of this ontology needs to respond to an update or question. and removed new ontology - reviewer required Indicates that an ontology is ready for review labels Oct 3, 2023
@nlharris
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@dosumis did you find someone else to hand this off to? Please let us know.

@pfabry
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pfabry commented Oct 30, 2023

Hello @dosumis and @nlharris,

@balhoff has been assigned to review this ontology as he is the next in line in the OBO operations Duty Rotation list.

In fact, @zhengj2007 was the next in line, but as she is directly involved in this ontology, I moved on to the next person.

@wdduncan
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@hoganwr will report back about whether he can do this.

@yongqunh
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It would be great to have @hoganwr do this. Thanks for consideration!

@hoganwr
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hoganwr commented Nov 30, 2023 via email

@yongqunh
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Thanks, @hoganwr !

@balhoff
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balhoff commented Nov 30, 2023

I have reviewed according to the criteria here: https://obofoundry.org/docs/RegistrationChecklist.html and don't see any issues to be corrected. There are a number of terms without textual definitions, although these seem mainly to be groupings, and most leaf terms I checked do have definitions. @zhengj2007 is there a plan to add further definitions?

I think it looks good, and we can discuss in the next operations committee meeting.

@balhoff balhoff added attn: OFOC call Issue to discuss on fortnightly OBO Operations meeting and removed new ontology - reviewer response required Reviewer of this ontology needs to respond to an update or question. labels Nov 30, 2023
@balhoff
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balhoff commented Dec 1, 2023

@zhengj2007 I also meant to suggest that you add has ontology root term annotations to your ontology.

@zhengj2007
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@balhoff Thanks for reviewing the OccO and for your valuable comments and suggestions.

  • We are planning to add the missing definitions, with a particular focus on high-level organizational terms.
  • We will add has ontology root term annotations in OccO ontology.

@yongqunh
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yongqunh commented Dec 1, 2023

That's great. Thanks, Jim @balhoff !

This was referenced Dec 10, 2023
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@zhengj2007
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Discussed on 2023-12-12 call, it is accepted.

@nlharris nlharris added new ontology - accepted The ontology has been accepted, but the metadata has not yet been entirely processed. and removed attn: OFOC call Issue to discuss on fortnightly OBO Operations meeting labels Dec 12, 2023
@balhoff
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balhoff commented Dec 12, 2023

I've sent the acceptance email to @zhengj2007 and copied the OBO-discuss and OBO-operations mailing lists.

@zhengj2007
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@balhoff Thanks a lot!

What are the next steps? Do I need to create occo.md and OCCO.yml?

@balhoff
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balhoff commented Dec 12, 2023

Here is the email sent to the list:

@zhengj2007,

Thank you again for your ontology submission to the OBO Foundry. We are happy to inform you that your ontology (OccO) has been accepted following discussion in the OBO Operations Committee meeting, 2023-12-12. 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:

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: https://obofoundry.org/faq/permissible-metadata-content.html

To create a PURL registry entry for your ontology:

Best regards,
Jim
on behalf of the OBO Operations Committee

@yongqunh
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That's great news. Thanks, Jim and the OBO Operations Committee!

This was referenced Dec 12, 2023
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@nataled nataled closed this as completed Jan 9, 2024
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