jannahastings/mental-functioning-ontology

Ontology for all aspects of human mental functioning

mental-functioning-ontology's Issues

Edit ontology title of MFOMD

In the OWL file for MFOMD you have

        <dc:title>The Mental Disease Ontology was first described in the publication &apos;Foundations for a realist ontology of mental disease&apos; (Barry Smith and Werner Ceusters) which is available at http://www.jbiomedsem.com/content/1/1/10 . </dc:title>

Do you really want that to be the title of your ontology? OLS is respecting your dc:title tag, but it doesn't look great n the browser.

http://www.ebi.ac.uk/ols/beta/ontologies/mfomd

Do you think you could change it to something shorter?

Representation and 'is about'

The term representation is defined as "A dependent continuant which is about a portion of reality." Yet, the "is about" in the definition cannot be the same as the object property is about in IAO. For, the domain of that object property is information content entity.

While the meaning of representation is nonetheless fairly clear, perhaps it could be improved by using the phrase "is about" in a way that aligns with the object property is about.

For example, perhaps the definition could be revised to something like the following: "A specifically dependent continuant that concretizes an information content entity that is about a portion of reality."

Or perhaps, more simply, "A specifically dependent continuant that concretizes an information content entity."

Of course, that definition suggests that "concretization of an ICE" and "representation" are equivalent in meaning. Perhaps that is correct, though I'm not sure whether that is what MF intended to capture with representation.

Is this ontology still active?

@jannahastings - did you pass on ownership of this ontology?

Note that it has not been parseable by the OWLAPI, probably since google code shut down: OBOFoundry/OBOFoundry.github.io#410 (comment)

If it can't be repaired we'll have to tag it as obsolete

cc @phismith

Language

language has the following superclass restriction: inheres in at all times some has continuant part at all times some human being

We would like to use this class in OMRSE, but 'has continuant part at all times' some 'human being' does not seem to be a good characterization of populations that are bearers of languages. Through birth and death these populations can gain and lose members. We suggest using 'has part' or 'has member' instead.

Location of OWL files needs to be registered on OBO

OBOFoundry/OBOFoundry.github.io#216

Memory

Although MFO defines 'a memory' in terms of the disposition to remember, and defines the process of remembering, it does not simply define what a memory is. I suggest (tentatively) that a memory is a generically dependent continuant that depends of the brain to exist. The specifically dependent continuant (SDC) 'a memory' does not capture the fact that a memory is some kind of information-bearing entity, only the disposition to have memories and remember.

A generically dependent continuant (GDC), as Barry Smith writes in 'Building Ontologies with Basic Formal Ontology,' captures a few key aspects of memory: a GDC depends on some independent continuant (the brain), a GDC cannot migrate from one entity to another, and is concretized in some specifically dependent continuant ('a memory' which is already in MFO as the disposition to remember).

The disposition of memory (SDC) is realized in the process of remembering which remembers some memory (GDC). Another way of saying this is that a memory is a highly complex pattern that realizes some disposition to remember in the memory process.

I am not sure if a memory is an information content entity (ICE). An ICE inheres_in an information bearing entity,and I think that might not be a good spproach, but I think GDC is a step in the right direction.

I am happy to be wrong, and I just want to get a conversation started on this subject. Thank you!

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.

Revision of definition of "memory" (GO_0007613)

I am trying to consolidate relevant ontologies that model anything related to cognition and behaviour, such as Mammalian Phenotype, GO, MFOEM, Drosophila Phenotype and more.

Based on probably the same misunderstanding you faced when building the model for "memory" (GO_0007613), I created a ticket asking for a revision of the definition in GO itself (geneontology/go-ontology#14913), but they convinced me to come to you. For the sake of creating a consistent model of learning and memory across ontologies, would you consider to rework your definition (treating memory as a disposition, and therefore a BFO:continuant, rather than a process, as was the intention by the GO term?