AfPO about obofoundry.github.io

[pfabry]

Dear @Melek-C ,

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 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]

@Melek-C

As you are using ODK for developing your ontology you should do a release make prepare_release, because the released ontologies (afpo-full.owl, afpo-base.owl, etc.) in your repository are currently empty. The src/ontology/afpo-edit.owl file is for developers use only.
In addition, you should finalize the pre-registration checklist.
Thank you.

[Melek-C]

Dear @pfabry,

Here the relase: https://github.com/h3abionet/afpo/releases/tag/v2023-10-30

Thank you

[pfabry]

Dear @Melek-C,

Thank you for the update. Could you please also finalize the preregistration checklist ? To do this, you may wish to consult ontologies such as ENVO or the Gazetteer subset, which have classes and instances for geographic and geopolitical entities such as countries or regions.

[Melek-C]

Thank you @pfabry!
It should be ok with the preregistration checklist.
Please do not hesitate to conatct me in case of issues.
Best

[pfabry]

@Melek-C ,

Your ontology has been added to the NOR dahsboard and has passed the technical review. @lschriml has been assigned as reviewer. Thank you.

[lschriml]

Following the review SOP: http://obofoundry.org/docs/SOP.html#ROOM

I have identified a number of items to be worked on for this review process:

-- Not sure the reason, but the files (e.g., afpo.owl (1.1 M), afpo-full.owl, afpo.obo) is not loading easily in Protege, taking 10-20 minutes to load. And then Protege is freezing.
I checked that this was not a Protege issue, and my doid.owl file, which is 15x larger, loads in seconds.

1. Ontology Scope
   As stated in this ticket: AfPO is a tool which enables to annotate the African individuals, and brings together knowledge accumulated about existing populations with their genetic fingerprint in a standardized format. The AfPO can be employed to comprehensively classify African study participants in prospective research studies. It can also be used to classify study participants of past studies, by mapping participants using a language or ethnicity identifier or synonyms.
   Domain: is listed as Phenotype.
   I do not see how the content of this ontology
   The 'environment' or 'organisms' domain may be a better fit.

2. Terms with the new ontology prefix.
   --> All terms follow the correct OBO identifier scheme
   "http://purl.obolibrary.org/obo/AfPO_0000089

   • TODO -- Check to see if there are terms in other OBO Foundry ontologies that could be reused
     here. ENVO and GAZ were mentioned in a previous comment.

3. Correct use of imported terms
   - no imports included

4. Basic review of axiomatic patterns:
   -- The formatting of the axioms seems fine.

              The axioms are built to define 'Population_group' or 'Country of Origin' using AfPO relation terms
   

• TODO -- utilize the Relation Ontology, RO, terms to define axioms

5. Appropriate use of object properties
   Two upper level classes, Continent and Population.
   For each Class, I would expect to see, in addition to label, Annotations for ID, definition,
   obo_namespace

• TODO Definition formatting: should follow standard formatting. Beginning with the parent term.
  E.g., the definition for Eastern Africa (AfPO:0000188), which currently begins with:
  People living in: Birundi OR Cosmoros OR Djibouti OR
  The definition sentence structure should be grammatically correct.
  This definition could begin:
  A population which includes people living in Birundi, Cosmoros or Djibouti ...

  This ontology is using the **property "see Also"** for sources of the Class data/information. 
      http://www.w3.org/2000/01/rdf-schema#seeAlso
  
                   --> I would expect to see this kind of information under 'definition_source'
  

• TODO -- Consult IAO (Information Artifact Ontology) https://www.ebi.ac.uk/ols4/ontologies/iao
  There are many AfPO specific properties, e.g., AfPO:0000152, which is annotated
  with a PubMed URL.
  Instead of the AfPO property, the ontology could use hasDbXref
  e.g., AfPO:0000566 which looks to be used for synonyms

• TODO. - review duplications in property annotations:
  Class labels:
  In the afpo.owl file:
  for: http://purl.obolibrary.org/obo/AfPO_0000010
  I am seeing what looks like duplications of the label annotation:
  obo:AfPO_0000569Central Africa</obo:AfPO_0000569>
  rdfs:labelCentral Africa</rdfs:label>

        - [ ] TODO -- Please identify if both annotations are needed
  

6. Responsiveness to fixing changes.
   - as seen in this ticket, the AfPO developers are responsive in a timely fashion.

Regards,
Lynn Schriml

[Melek-C]

Dear @lschriml,

Thank you very much for your valuable comments, we will be back to you as soon as possible.

Best,
Melek

[Melek-C]

Dear @lschriml,
The Ontology Scope was changed to Organisms.
Were are going to work on the axiomatic patterns on in the next steps.
For the remaining comments "Issues" were post on the AfPO repository:

• h3abionet/afpo#16
• h3abionet/afpo#15

Best Regards