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[bioontology-support] [BioPortal] Feedback from Christian Pich

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Oct 12 12:53:19 PDT 2021


Hi Christian,


On Oct 11, 2021, at 8:57 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Hi, I am getting an error when loading the obo file for the spatial ontology

In BioPortal, we’re hosting the OWL version of this ontology, not the OBO version. The Spatial Ontology entry is configured to retrieve the OWL source file from this GitHub URL:

https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.owl


because two terms (stanzas) are using a date-only syntax for the created_date for which the ontology parser are expecting a date/time stamp:

[Typedef]
id: BSPO:0000114
name: lateral to
def: "X lateral to y if x is further from the midsagittal plane than y." []
is_transitive: true
inverse_of: BSPO:0000115 ! medial to
created_by: Jennifer Girón
creation_date: 2021-04-21

[Typedef]
id: BSPO:0000115
name: medial to
name: X medial to y if x is closer to the midsagittal plane than y.
is_transitive: true
created_by: Jennifer Girón
creation_date: 2021-04-21

Is it possible to either remove those two lines or include a sull date and time-stamp like in GO.

Although we host and serve ontologies from BioPortal, we’re often not the ontology authors. If you’d like to request a change to the ontology content, I suggest reaching out to the ontology maintainers. Contact information for ontology maintainers is typically listed on the ontology summary page:

https://bioportal.bioontology.org/ontologies/BSPO

… in the Details pane. The homepage for this ontology is:

https://github.com/obophenotype/biological-spatial-ontology

According to their homepage, you can use their issue tracker to make requests related to content:

https://github.com/obophenotype/biological-spatial-ontology/issues

Kind regards,
Jennifer

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