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need to change parentage of numerous classes and references to BFO 1.1. classes from any Apollo-SV specific classes. Needs to be concurrent with updating GEO to BFO2 as well to avoid the "double BFO hierarchy" problem.

Element of XSD type 'Vaccine'

This type has 'softwareVersion' as an element, which would presumably preclude it from being the UAL for 'software identifier' which is defined as "An identifier that refers to all version [sic] of a specific software."

Existing class is 'liberal sick leave control strategy'.

Change to 'totalCaseCount'.

We MIREOT'd geographic location before we created and owned GEO. Now, GAZ is ambiguous and we are using GEO exclusively. So we need to change all references to 'geographic location' to 'geographical region' and eliminate MIREOT of GAZ.

Reflect change in XSD to its corresponding element name.

Right now each of these classes has an editor preferred term in place of their labels. Presumably, we'll just need to copy that over to the label, unless otherwise specified.

Must be careful not to miscategorize any classes that pertain to periods, and not durations.

No longer in XSD.

Previously was UAL for Apollo class 'temporal_interval' which has since been deleted. Double-checked XSD to make sure that it's referring only to time when referencing 'Interval' and it is.

Add 'sampleSize' as its UAL, once MIREOT'd.

This is more of a peer-peer project inquiry about how you are handling the relation between ontology datum fields and their use in non-ontology-driven apps. Now maybe APOLLO_SV is narrowly targeted at your Apollo app and therefore this is unnecessary; but since I was thinking of adopting some of your ontology terms ...

You have the AnnotationProperty APOLLO_SV_0000040, "Unique Apollo Label", UAL. "This annotation property gives the unique label of all Apollo_SV entities that are refered to in the schema. The UAL is the denotator for the Apollo_SV class in the schema. There can at all times only be ONE value of UAL for each class."

In GenEpiO I was planning on mapping terms to their database equivalents via the hasDbXref relation.

Just thinking that this is fairly multipurpose insofar as an ontology can use hasDbXref to map a field to any number of 3rd party database fields. Avoids having to introduce a relation for each of them. Thought that might be attractive?

Cleanup and get rid of all ro.owl#part_of style URIs and convert them to either RO_000000xxx ids or BFO_000000xxx ids, depending on the relation and what it means

Log normal distribution has two URIs, but the others listed have one.

Copy from elucidation.

Definition seems to be a bit circular, but because we're importing from GAZ we'll have to deprecate the class if we're going to make changes. At the very least, we should consider moving it since its definition elsewhere, as opposed to being a subclass of 'site'.

Information I've gathered on El Niño:

• Warm phase of the El Niño-Southern Oscillation (ENSO), which is a single "periodic variation in winds and sea surface temperatures over the tropical eastern Pacific Ocean, affecting much of the tropics and subtropics," according to Wikipedia.
• ENSO is almost certainly an individual process, based on what I've gathered from my preliminary research, that consists of three subprocesses: 1) La Niña, 2) El Niño, and 3) a neutral phase that marks the transitions between 1) and 2), in which sea temperatures, tropical precipitation, and wind patterns approach their long-term averages.
• In addition, my initial guess is that ENSO is an instance of 'environmental system process'

Class is 'maximum travel distance in km'

Probably should obsolete the former of the two.

The current definition for the term only incorporates mutualism, commensalism, and parasitism, while we're including all interspecies interactions under the term. Therefore, we should either remove the MIREOT of this term and create our own definition, or move certain terms, such as 'antagonism', so that they're subclasses of 'interspecies interaction between organisms'. Personally, I think we should go with the former of the two options since it requires the least amount of work without sacrificing any consistency with a large portion of the literature and without sacrificing the logical relations between classes. Moreover, I think that this option is preferable to the latter because it allows 'predation' and 'grazing' to be subclasses of 'symbiosis' (although not directly), which quite frankly seems like a rather obvious place for them.

Currently, we hasn't assigned a definition to 'non-parametric distribution'.

STATO's definition = Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution.

The 6 classes are listed below. Please note that, with the exception of 'clade name' and 'NCBI taxon identifier', all of them take 'NCBITaxonId' as their data type.

• clade name
• NCBI taxonomy identifier
• identifier for species of case
• identifier for species of diseased organism
• identifier of species of population
• species of treated organism

Not sure why we added 'unit of measure' in addition to MIREOT of 'measurement unit label' from Unit Ontology, but it merits further review and harmonization

Hi folks, I was perusing your ontology and attracted to a number of APOLLO_SV terms - population census etc - that I'd import into GenEpiO. One question though, I saw that you had a "count" term very similar to STATO's, and was wondering if this term was deliberate or an opportunity (MIEROT) for reuse.

Which raises another question - are there plans to make APOLLO_SV part of OBOFoundry / OntoFox (I just checked and couldn't see it there)?
Regards,

Damion

Two classes with the same label currently exist, both with different IRIs.

Add with comment, definition, and term editor(s).

Many currently say 'Matt Diller' or 'Matthew Diller'. Change all instances of the former to the latter, and add 'William R. Hogan' if missing.

Corresponding element name was changed in the XSD.

Replace each instance of its use with the object property that has correct URI.

Currently our definitions for 'symbiosis' and 'non-intimate agonism' are contradictory, while the label for the latter is less than ideal. The reason they're contradictory is that symbioses are interspecies interactions that are more or less intimate, whereas the latter is defined by a lack of or minimal intimacy. To correct this, I'd like to propose changing 'intimate agonism' to 'endosymbiotic agonism' and define it as, "An endosymbiosis that results in harm to some host organism, and benefit to some antagonist organism." We can then create a class for 'antagonist organism' that includes 'pathogen', 'parasite', 'predator', etc. as subclasses; and change the definitions for endosymbiotic parasitism/parasitoidism accordingly. Likewise, we can follow the same steps for 'intimate agonism', changing it to 'ectosymbiotic agonism', which will have 'grazing' and 'predation' as subclasses. This is consistent with the literature, as 'parasitism' and 'parasitoidism' are conceived of as being very similar to 'predation'.

I think we'll also want to specify that 'predation' is necessary for the completion of a biological function and is lethal (i.e., nutrient and energy acquisition), whereas 'parasitism' and 'parasitoidism' are typically non-lethal (parasitism) or are necessary for the completion of a stage in the life cycle (i.e., parasitoidism). I can create another issue for this though, since I think it may deserve its own discussion.

Currently has 'simulated population' as its UAL.

Class is 'voluntary household quarantine control strategy'.

Old class, old UAL format, and does not match anything in XSD.

Figure out what to do with these two classes, consider obsoleting them

Requested by Ginny: ability to index in MIDAS against travel recommendations. This is not a travel restriction or border control strategy, so we need a new class.

Ginny and I agreed via email on:

1. add travel-related infectious disease control strategy
2. add travel recommendation infectious disease control strategy
3. The latter is subtype of the former.
4. We can also move border control and travel restriction as subtypes to travel related.

Will need to discuss what to do with its child classes. Presumably will end up moving some of them over to the other 'material anatomical entity' class, and deprecating the rest. Note that the UBERON import is NOT the one that should be deprecated, but the other duplicate beginning with a big 'M'.

Current definition is: "A purely intentional entity that simulates an entity and its properties."

This definition is circular since 'simulate' is not defined in Apollo. Furthermore, it would be more accurate to say that it is the instantiation of some model over a specified time interval.

We should then create a class for 'model' that might be defined as, "A purely intentional entity that concretizes some class of particulars and is a theoretical composite of the qualities and dispositions that are unique to that class, but whose instance is brought about by the output of some material processing or algorithm and is subject to input from a finite number of specified information content entities."