Assignment 3

# Project 3

Your third project will require you to answer each of the 10 questions below.  You will be expected to open a pull request with your initial answers by the second class meeting, giving you one week to work on these problems. You and your peers will then have one week to work together to refine your respective initial answers, so they are ready for final submission. Once your pull requests have been reviewed and merged to the development branch, I will review them, then merge to the master branch. 

```
For any question involving the use of Protege, please be sure to import:
1. Basic Formal Ontology (https://raw.githubusercontent.com/BFO-ontology/BFO/v2019-08-26/bfo_classes_only.owl)
2. The Relations Ontology (https://raw.githubusercontent.com/oborel/obo-relations/master/ro.owl)
```

1. In BFO and RO identify at least one object property for each of a-e that _should have the listed property, but which does not_; argue for your case, using examples. Note: It will be easiest to view the object properties in BFO and RO using Protege. 
```
  (a)  Reflexive
      -Simultaneous_with. Any time is simultaneous with itself. It wouldn't make sense for there to be a time that occurs at a different time from itself.
      
  (b)  Transitive 
      -Causally_influences. If one entity causally influences one thing, and it causally influences another, then the original has causally influenced the last, albeit indirectly.
      
  (c)  Symmetric
      -Aligned_with. If a block A is placed in alignment with block B, then it's true that A is aligned with B and B is aligned with A. This works for political alignments. If one party is aligned with another, the reverse is also true. Otherwise, they weren't really in alignment.
      
  (d)  Functional 
      -Has_relative_magnitude. Relative to some entity, and object has a single, particular magnitude.
       
  (e)  Symmetric and Reflexive
      -Simultaneous_with. I've already explained why this should be reflexive. It's also symmetric, since if t1 is simultaneous with t2, then t2 is also simultaneous with t1.
      
```

2. In BFO and RO identify at least one object property for each of a-e that _should not have the listed property, but which does_; argue for your case, using examples. Note: It will be easiest to view the object properties in BFO and RO using Protege.
```
  (a)  Irreflexive
      -Has_role_in_modelling. Imagine a machine that is designed to model aspects of itself. It can be used to study itself, in virtue of its ability to reflect aspects of itself.
      
  (b)  Transitive 
      -Aligned_with. Imagine two lines of blocks that intersect at block B. Call one row 'Vertical' and the other 'Horizontal'. A is a block in Vertical, but not Horizontal. C is a block in Horizontal, but not Vertical. And B is in both Vertical and Horizontal. A is aligned with B, since they're in the same row, and B is aligned with C for the same reason, but A is not aligned with B.
      
  (c)  Asymmetric
      -Has_role_in_modelling. Imagine two machines that are designed to model aspects of eachother. They can be used to study eachother, in virtue of their ability to reflect aspects of eachother.
  
  (d)  Functional 
      -Phenotype_of. The color of an eye is a phenotype of the eye and of the person it belongs to. As a result, there is not exactly one entity it's in this relation to.
  
  (e)  Inverse Functional
      -Has_characteristic. A smile is a characteristic of a face, but also of a person. So characteristic_of is non-functional. So has_characteristic is not inverse functional.
      
```

3. Model the following natural language expressions using terms from BFO and RO; you are welcome to introduce new terms where needed:  
```
  (a) Sally has an arm Tuesday but does not have an arm Wednesday. 
  
  on the interpretation of her losing an arm, thereby having no arms on Wednesday:
  
  Sally is instance_of object
  Tuesday is an instance_of one-dimensional temporal region 
  Wednesday is an instance of one-dimensional temporal region 
  Arm is an instance of fiat object part
  “Sally participates in having at least one arm on Tuesday” is an instance of occurrent 
  “Sally participates in having no arms on Wednesday” is an instance of occurrent
  “Sally participates in having at least one arm on Tuesday precedes Sally participates in having no arms on Wednesday”
  
  on the interpretation of her not necessarily losing an arm, where this is merely saying there is at least one arm on Tuesday, and on Wednesday at least one arm is missing:
  
  Sally is instance_of object
  Tuesday is an instance_of one-dimensional temporal region 
  Wednesday is an instance of one-dimensional temporal region 
  Arm is an instance of fiat object part
  “Sally participates in having at least one arm on Tuesday” is an instance of occurrent 
  “Sally participates in lacking an arm on Wednesday” is an instance of occurrent
  “Sally participates in having at least one arm on Tuesday precedes Sally participates in lacking an arm on Wednesday”
  
  (b) Every liver has some cell as part at all times it exists.
  
  Liver has_part_at_all_times some Cell
  
  (c) John was a child, then an adult, then a senior. 
  
  John is an instance_of object
  childhood is an instance_of occurrent.
  adulthood is an instance_of occurrent.
  seniorhood is an instance_of occurrent.
  “John participates in childhood precedes John participates in adulthood which precedes John participates in seniorhood.”
  
  (d) Goofus and Gallant are married at each point in a three year span.
  
  Goofus is an instance_of object
  Gallant is an instance_of object
  Marriage is an instance_of occurent
  “Three years span 1” is an instance_of one-dimensional temporal region.
  t1 is an instance_of zero-dimensional temporal region
  If t1 is part_of the one-dimensional temporal region “three years span 1”, then Goofus participates in marriage at t1 and Galland participates in marriage at t1.

```

4. Using the language of First-Order Logic, represent the following natural language expressions; you are welcome to introduce new terms where needed: 
```
  (a) Sally has an arm Tuesday but does not have an arm Wednesday. 
  ∃x (Tx ∧ ∃y (Hsy∧Ay)) ∧ ∃x (Wx ∧ ~∃y(Hsy∧Ay))
  T: Tuesday
  H: has
  A: arm
  W: Wednesday
  s: Sally
  
  (b) Every liver has some cell as part at all times it exists.
  ∀t∀x∃y(Lx∧E(x,t)→Cy∧Pyx)
  L: liver
  C: cell
  P: part of
  E (x, t): exists at t
  
  
  (c) John was a child, then an adult, then a senior. 
 j = John
 E xy = is earlier than
 C (x, t) = being a child at t
 A (x, t) = being an adult at t
 S (x, t) = being a senior at t
 ∃t1∃t2∃t3 (C (j, t1) ∧ A (J, t2) ∧ S(J, t3) ∧ E (t1, t2) ∧ E (t2, t3))

  (d) Goofus and Gallant have been married for three years; for each day of that span, it is true to assert they are married.
 M(x, t) = being married at t
 Y(t) = belongs to 3 year span 1
 g1 = Goofus
 g2 = Gallant
 D(t) = t is a day
 ∀t(D(t) ∧ Y(t)→(M(g1,t) ∧ M(g2,t)))

  
```

5. Using BFO and RO, model the following scenario: the content of an rdf file is represented in two serializations - one in Turtle, one in XML - which are sent from one computer to two distinct computers on the same network.   

RDF File Content, Turtle Serialization and XML Serialization are all generically dependent continuants. RDF File Content has_model Turtle Serialization and XML Serialization. And Computer is carrier_of both the serializations.
Computer 1, 2, and 3 are all instance_of Computer. Computer 1 enables the process of Data Transmission, which ends_with another process, Data Reception, which has computers 2 and 3 as participants. 
Computers 1, 2, and 3 are all parts_of network I, which is instance_of Network, which is_a Object Aggregate.)
Turtle Serialization and XML Serialization is output_of Computer 1
Computer 2 and 3 has_input Turtle and XML Serialization.

6. Using Protege, place these in the BFO hierarchy where you think they fit best:
```
  (a) Bach's Well-Tempered Clavier
  -generically dependent continuent
  (b) Chair of the UB Philosophy Department
  -role
  (c) SARS-CoV-2
  -object
  (d) Mexico City
  -object aggregate
  (e) The trunk of a minivan
  -fiat object part
  (f) Occupation
  -role
  (g) Ocean
  -object aggregate
  (h) Lake
  -object aggregate
  
```

7. True or False; explain your answers:
```
  (a) An instance of Material Entity can have an instance of Immaterial Entity as part.
  True. The elucidation says that a material entity has some portion of matter as proper or improper continuant part. It doesn’t say all of its parts must be material. Ex. a person’s thoughts, even if immaterial, is a part of the material person. Material and immaterial entities are disjoint, but that does not prevent one from having a part that’s the other.  
  
  (b) An instance of Immaterial Entity can have an instance of Material Entity as part.
  False. I can’t think of any examples that would fit this.
  
  (c) An organization may have another organization as part.
  True. For example, a political committee can have a subcommittee as a part. 
  
  (d) An organization may have no members as part. 
  True. The debate club could lose all its members while still be being recognized by the school.
  
  (e) Any site is partially bounded by some instance of Material Entity.
  False, though I think BFO is trying to imply that it's true. Based on the description they give, a site could fail to be partially bounded by a material entity if it's a part of some immaterial entity. If they intend to allow parts to not be materially bounded, then they're in the strange position of saying sites can fail to be materially bounded only if the site is a part of something larger that is at least partially materially bounded. That just seems like a weird, unmotivated view to me
  
  (f) A book placed under the leg of a wobbly table has acquired a new function. 
  False. The elucidation excludes this by saying the potential disposition must be a product of its physical make-up that was either through evolution or intentional design. It wasn’t intentionally designed for this task, so this doesn’t count. But I personally don’t like saying that. I figure objects can acquire functions that weren’t intended.
  
  (g) A glass vase cushioned with packing material for all time, has the disposition to break. 
  True. Dispositions are in virtue of the bearer’s physical make-up, not its environment.
  
  (h) Spacetime is a class in BFO.
  False, it's a spatiotemporal region
  
  (i) The continuant fiat boundary class of BFO is closed, meaning, there are no subclasses beyond those identified presently in BFO. 
  False. We could construct any number of subclasses of zero-, one-, or two-dimensional continuant fiat boundaries, which would be subclasses of continuant fiat boundary.
```

8. Model the following scenario in BFO, introducing whatever terms are needed to do so: John runs for 3 hours, startin slowly, speeding up during the middle, then ending the run at a slower pace.  

– John (as an Object) participates_in John’s running (as a process), and John bears John’s speeds 1, 2, and 3, all of which are instances of dispositions.
–  John’s running includes 3 temporal parts: John’s beginning stage, John’s middle stage, and John’s final stage, each of which is a process. Besides, John’s beginning stage precedes John’s middle stage which precedes John’s final stage.
– A process realizes one’s disposition. So John’s beginning stage realizes John’s speed 1, John’s middle stage realizes John’s speed 2, and John’s final stage realizes John’s speed 3.
– Change in John’s speed: John's Speed is decreased_in_magnitude_relative_to John's Speed 2 (that is, speed 1＜speed 2), and John's Speed 2 is increased_in_magnitude_relative_to John's Speed 3 (that is, speed 2＞speed 3)
– John’s running occurs in this 3-hour, which is instance_of one-dimensional temporal region.)

9. The Pellet reasoner in Protege can be used in an incremental reasoning strategy. ELI5 when and why one should use Pellet for incremental reasoning. 

Imagine you are playing with some building blocks to build a tower. Every time you add a block to the tower, you don't need to start building the tower from the beginning. You just need to add the new block on top of the tower.
In the same way, when we use Pellet to reason about an ontology, we don't need to start reasoning from the beginning every time we add new information to the ontology. Instead, Pellet remembers what it has already figured out and uses that knowledge to figure out what the new information means. This is kind of like adding a new block to the tower without starting from the beginning. Thus, Pellet is especially important for large, complex ontologies where re-computing all the results every time new information is added would take a long time. 


10. Protege reasoners will not allow you to combine certain properties, e.g. reflexivity and transitivity. If you attempt to assert such pairs of the same object property, then run the reasoner, nothing will happen. If you combine such properties while a reasoner is running, then ask to synchronize the reasoner, an error will be thrown. Provide a table or series of tables illustrating which pairs of properties cannot be combined in Protege, either because nothing happens when the reasoenr is run or because an error is thrown when synchronizing a reasoner after making such changes. Review the github docs on [creating tables in markdown](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/organizing-information-with-tables).

|             | Functional| Inverse Fun | Transitive | Symmetric | Asymmetric | Reflexive | Irreflexive |
|-------------|-----------|-------------|------------|-----------|------------|-----------|-------------|
| Functional  | empty     | Yes         | No         | Yes       | Yes        | Yes       | Yes         |
| Inverse Fun | Yes       | empty       | No         | Yes       | Yes        | Yes       | Yes         |
| Transitive  | No        | No          | empty      | Yes       | No         | Yes       | No          |
| Symmetric   | Yes       | Yes         | Yes        | empty     | No         | Yes       | Yes         |
| Asymmetric  | Yes       | Yes         | No         | No        | empty      | No        | Yes         |
| Reflexive   | Yes       | Yes         | Yes        | Yes       | No         | empty     | No          |
| Irreflexive | Yes       | Yes         | No         | Yes       | Yes        | No        | empty       |