ontoneo-project / ontoneo

Obstetric and Neonatal Ontology

The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.

This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data in this medical specialties, in order to serve EHR interoperability of the associated data and information systems. Interoperability of EHR data in woman and child care is important to ensuring continuity of care during the prenatal and postnatal periods for both mother and child.

OntONeo is a collection of entities related to anatomy, embryology and medical specialties related to care of woman and child (gynecology, obstetric, pediatric, neonatology).

The current version of OntONeo is version 1.6 deployed on 04-29-2021.

The previous versions are located at releases folder according to the version deployed date.

There is a Google Group for discussing the project at http://groups.google.com/group/ontoneo-discuss. Click the "Apply for Membership" link to join.

ontoneo's Issues

'role in human social processes' (OMRSE:00000024) has been deprecated and replaced

In the future we plan on reaching out to developers of ontologies that import our classes to get their input prior to making such changes, but we have replaced this class with another one with the same label: 'role in human social processes' (OMRSE:00002072). The only change to the class was to the subClassOf axiom, which we changed from "inheres-in only human or organization" to "inhere-in only 'material entity'."

Include radiology tests

Possible problems with import statements

In ontoneo.owl (any probably elsewhere) these imports use uppercase "BFO" and "FMA":

    <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ontoneo/import/BFO_import.owl"/>
    <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ontoneo/import/FMA_import.owl"/>

https://github.com/ontoneo-project/Ontoneo/blob/master/ontoneo.owl#L24-L25

but the actual file names are consistently lowercase: https://github.com/ontoneo-project/Ontoneo/tree/master/import

The names in the imports should exactly match the file names, or the import might fail.

In general, it's best practise for the release version of your ontology to merge together all imports, so there are no owl:imports left to cause problems.

Register PURL Domains

Register the PURL domains at https://archive.org/services/purl/

'human parturition procedure': subclass does not categorically match axiom

'human parturition procedure' is the superclass of 'caesearean section' (implying that they are both processes), but 'human parturition procedure' is given the axiom:

realizes some (concretizes some
('caesarean section' or 'human parturition'))

which implies 'caesarean section' is a plan specification.

OBO Foundry: Normalise PURLs?

Hello! In our great OBO foundry ontology QC cleaning effort, we noticed that ONTONEO is using irregular PURLs.

There are, at least, two different IRI conventions in ONTONEO:
http://purl.obolibrary.org/obo/ontoneo/ONTONEO_1000002
http://purl.bioontology.org/OntONeo/ONTONEO_00000066

The one recognised by the OBO foundry would be:
http://purl.obolibrary.org/obo/ONTONEO_1000002

I know this is a long-shot, but would you be willing to normalise the ONTONEO IRIs in this way to make it easier to use with OBO Foundry tooling?

Submit Ontoneo to Obo-discuss

Submit Ontoneo registry to Obo-discuss list evaluation.

Registry at OBO Foundry

Registry at OBO Foundry

Create OSRD of iteration 1

Define the scope of the iteration and create the requirements specification document of the iteration 1.

Syntax error in ontoneo.owl

I tried to open the main ontoneo.owl file in Protege, but it failed due to a syntax error on this line:

<owl:versionIRI rdf:datatype="&xsd;string">v1.2</owl:versionInfo>

The start and end XML tags must match: owl:versionIRI.

bicornuate uterus as a subclassof mullerian duct malformation - is that correct?

hi!

I've noticed that some of the uterine congenital malformations (e.g. bicornuate uterus) are under mullerian duct malformation:

that looks a bit imprecise as far as I can tell; maybe they should be subClassOf congenital malformation?

cheers!

Ontology versionIRI should be an IRI

In the current ontoneo.owl file the versionIRI is 'v1.2'. It would be better for the value to be an IRI (URL) that points to this specific version of the file, and matches the PURL configuration. Most OBO ontologies use a date format such as: http://purl.obolibrary.org/obo/obi/2016-01-01/obi.owl

Set up project on github

Files:
readme.md
ontoneo.md
ontoneo.yml
PURL
etc

Include laboratory tests

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

Ontology uses rdf:comment instead of rdfs:comment

There are multiple occurrences in the OWL source file where rdf:comment is used instead of rdfs:comment, e.g., this line.

This caused an issue with our application (BioPortal), which hosts the ontology at this URL:

http://bioportal.bioontology.org/ontologies/ONTONEO

We were unable to load the ontology into our triplestore with errors like the following:

rdf:comment is an unknown RDF namespaced element

We modified all occurrences of rdf:comment to rdfs:comment and were able to load the ontology successfully, as detailed in this issue.

For the moment, we've disabled the functionality that looks for new versions of your ontology at the designated pull URL, pending modification of the rdf:comment tags.

BFO_0000051 erroneously labeled "part of"

@ontoneo-project @FernandaFarinelli

BFO_0000051 is erroneously labeled "part of" in Ontoneo.

BFO_0000050 is "part of"
BFO_0000051 is "has part"

This error seems to originate in Ontoneo/import/ro_import.owl

Import only selected subsets of other ontologies

The import directory contains a number of subsets from other ontologies, which is good practise. However the main ontoneo.owl file is importing the full versions of those ontologies, not the subsets.

One solution is to have a partial entry in your PURL configuration that will redirect a directory of files. Here is an example from DOID: https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/doid.yml In their OWL file they use those PURLs to redirect http://purl.obolibrary.org/obo/doid/imports/uberon_import.owl to their subsets in GitHub.

To make these imports work when doing local development, they use a catalog file that tells Protege to use the local versions. See the first several lines of this file: https://github.com/DiseaseOntology/HumanDiseaseOntology/blob/master/src/ontology/catalog-v001.xml

I wish this was easier, but it's the best way to get the behaviour that (I think) you want.